《1 Engineering research fronts》

1 Engineering research fronts

《1.1 Trends in Top 11 engineering research fronts》

1.1 Trends in Top 11 engineering research fronts

The Top 11 engineering research fronts in the agriculture field can be classified into three groups: ① research on the molecular biological mechanism on animal and plant production, including “immunosuppression and escape mechanisms of important animal pathogens”, “mechanism of efficient soil carbon sequestration and regulation”, “molecular biological mechanisms of wood formation”, and “interaction network mechanism of breeding environment-livestock and poultry-gut microorganism-nutrient metabolism”; ② molecular breeding as usual, including “polyploid breeding of aquatic animals” and “polygenic breeding of livestock and poultry”; ③ research on improving the production of animal and plant products and green production, including “organ development and quality regulation of horticultural crops”, “green cultivation techniques for crops”, “discovery of resistosome of plant”, “de novo domestication and germplasm utilization of wild crops”, and “response of food security to climate change”. The number of core papers of these research fronts ranges from 7 to 143 with an average of 59, close to 2020 and 2021. The citations per paper ranged from 5.06 to 178.69 with an average of 59.58. Most core papers were published in 2018 and 2019 whereas the core papers of “immunosuppression and escape mechanisms of important animal pathogens” and “de novo domestication and germplasm utilization of wild crops” were mostly published in recent years and showed an increasing trend (Tables 1.1.1 and 1.1.2).

(1)  De novo domestication and germplasm utilization of wild crops

Crop domestication, the process of adapting wild plants into cultivated crops, has played an essential role in the origin of farming civilization and promoted the continuous development of human civilization and the rapid evolution of society. Specifically, domestication is the process of screening beneficial agronomic traits from wild germplasm as the starting material through long-term artificial selection throughout history. The target trait, such as less grain shattering, reduced branching, compact growth, reduced awn, larger seeds, and suitable hand-harvesting. In the view of genetics, domestication is a process of aggregating and retaining ideal genetic variations in the genome. However, this process mostly took a long historical time and the selection

《Table 1.1.1》

Table 1.1.1 Top 11 engineering research fronts in agriculture

No. Engineering research front Core papers Citations Citations per paper Mean year
1 De novo domestication and germplasm utilization of wild crops 74 2 345 31.69 2019.4
2 Immunosuppression and escape mechanisms of important 45 7 556 167.91 2020.2
3 Mechanism of efficient soil carbon sequestration and regulation 83 14 831 178.69 2018.9
4 Organ development and quality regulation of horticultural crops 61 588 9.64 2018.9
5  Polyploid breeding of aquatic animals 18 91 5.06 2019.2
6 Green cultivation techniques for crops 98 4 868 49.67 2017.6
7 Polygenic breeding of livestock and poultry 50 569 11.38 2019.2
8 Response of food security to climate change 143 11 032 77.15 2017.8
9 Molecular biological mechanisms of wood formation 7 167 23.86 2017.7
10 Discovery of resistosome of plant 34 800 23.53 2020.2
11 Interaction network mechanism of environment-livestock gut microorganism-nutrient metabolism 37 2 842 76.81 2017.3

《Table 1.1.2》

Table 1.1.2 Annual number of core papers published for the Top 11 engineering research fronts in agriculture

No. Engineering research front 2016 2017 2018 2019 2020 2021
1 De novo domestication and germplasm utilization of wild crops 4 10 6 12 13 29
2 Immunosuppression and escape mechanisms of important 0 0 4 5 15 21
3 Mechanism of efficient soil carbon sequestration and regulation 9 11 7 25 15 16
4 Organ development and quality regulation of horticultural crops 4 10 14 9 7 17
5  Polyploid breeding of aquatic animals 2 2 1 3 5 5
6 Green cultivation techniques for crops 29 17 26 21 5 0
7 Polygenic breeding of livestock and poultry 0 7 11 12 6 14
8 Response of food security to climate change 32 32 34 25 16 4
9 Molecular biological mechanisms of wood formation 2 2 1 0 2 0
10 Discovery of resistosome of plant 0 1 0 6 11 16
11 Interaction network mechanism of environment-livestock gut microorganism-nutrient metabolism 15 6 9 4 3 0

of the targeted traits was random and mindless. Moreover, screening for superior traits also significantly reduced the genetic diversity of the domesticated population. Compared to modern cultivars, wild relatives often have advantages in particular traits, such as greater stress resistance, broader environmental adaptability, and relatively higher biomass. Nowadays, with the development of biotechnology, especially gene editing, de novo domestication is starting to be proposed as a promising strategy for crop breeding. That strategy starts from the selection of wild or semi-wild plant species with particularly outstanding traits, then the rapid introduction of the required domestication traits through modern breeding technology, and eventually novel crop species may be achieved in a short time term. This new crop, which repurposes the good wild germplasm that has been lost in the traditional crop domestication or breeding, is of great significance for sustainable agricultural development under the current global trend of environmental change.

(2)  Immunosuppression and escape mechanisms of important animal pathogens

China is the world’s largest consumer of livestock and poultry and animal-derived food. In recent years, the level of intensive and large-scale animal husbandry has continuously improved. However, infectious diseases, especially some major animal diseases, have always restricted the healthy development of animal husbandry and threaten social public health security. How to effectively prevent and control these important animal pathogens has always been a focus and research hotspot in the fields of veterinary medicine, medicine and biosafety. One of the main reasons that hinders the prevention and control of epidemic diseases is that these important animal pathogens have developed various strategies to escape and suppress host immunity in the long-term evolution. The body’s defense against pathogenic infection mainly relies on host innate and adaptive immune responses. Some important pathogens can evade host surveillance and inhibit key antiviral innate immune responses, resulting in pathogens effectively breaking through the body’s immune barriers and establishing productive infections; meanwhile, pathogens can escape host-elicited adaptive responses by generating new variants or strains through mechanisms such as mutation or recombination, which escape neutralizing antibodies or T-cell immunity in the host, thereby preventing them from being cleared by the body and establishing a productive infection. Elaborating the key mechanisms by which pathogens inhibit and evade the body’s immunity is the premise for effective prevention and control of important animal pathogens, and it is also a challenging and hot topic in veterinary medicine. The relevant research results will surely provide important guidance and technical support for the prevention and control of major animal diseases.

(3)   Mechanism of efficient soil carbon sequestration and regulation

Soil is the largest carbon pool in the terrestrial ecosystem. The global soil organic carbon is 1 500–2 000 Pg, equivalent to 2–3 times of the carbon in the atmosphere. Agricultural soil carbon sequestration was found to account for 25% of the potential for natural climate solutions. Therefore, promoting agricultural soil carbon sequestration is of great significance for ensuring food security, mitigating climate change and promoting agricultural green development. The core of efficient soil carbon sequestration and regulation is to understand the key processes of turnover and stability of soil organic matter, and to establish a regulatory strategy for efficient carbon sequestration and slowing down its mineralization and decomposition. Soil is an open and complex system in which multiple substances coexist, multiple processes occur simultaneously, and multiple factors influence together. At present, the mechanism of efficient soil carbon sequestration is still unclear. Therefore, in-depth research on carbon sequestration and regulation mechanism needs to be strengthened in the future. For example, accurately distinguishing carbon sources of different organic components, exploring the microbial action mechanism of plant residues to soil organic matter, accelerating research on organic matter stability based on multi-factor coordinated regulation, exploring soil carbon balance mechanism and plant residue input thresholds, etc. Innovate new carbon- based materials with high efficiency of carbon sequestration and nutrient use, improve soil carbon sequestration efficiency, integrate and innovate key technologies for soil carbon sequestration, land conservation and productivity improvement, and promote the application of large-scale agricultural soil carbon sequestration are becoming the frontier in applied research direction in this field.

(4)  Organ development and quality regulation of horticultural crops

The products of horticultural crops, such as vegetables, fruit trees, flowers, are diverse, including roots and modified roots, stems and modified stems, leaves and leafy heads, flowers and bolting, fruits and seeds, etc., which are the basis for the production of horticultural crops. The quality of horticultural products includes nutritional quality (such as content of carbohydrates, lipids, proteins, vitamins, minerals, trace elements and other nutrients), sensory quality (including product appearance, texture, palatability, etc., such as size, shape, color, gloss, juice, hardness, defects, freshness, etc.), hygienic quality (including surface cleanliness of fruits and vegetables, heavy metal content in fruit and vegetable tissues, pesticide residues and other restricted substances such as nitrite content, etc.), commercial processing quality (such as easy to clean, etc.), and other complex characters. With the rapid development of the horticultural industry and the increasing crop yields, close attention has been paid to the changes in product quality traits, the content of healthy ingredients, and the quality and safety of horticultural products. In recent years, my country has carried out some researches on the formation and regulation mechanism of horticultural crops in terms of fruit shape, color, nutritional quality, flavor and bitterness. Mining and analysis of related genes for substance metabolism and their regulatory networks, the molecular mechanism and regulatory network of important agronomic traits such as yield and quality are provided for the further research in theory, but most of the metabolites that determine the organ development and product quality of horticultural crops are still unclear. Therefore, in the future, study the gene expression cascade regulation mechanism and regulatory network analysis should be carried out in terms of transporters, transcriptional regulators, epigenetic modifiers and non-coding RNAs, so as to explore the organ development of horticultural crops, which will provide a scientific basis for the improvement of quality and efficiency of the horticultural industry.

(5) Polyploid breeding of aquatic animals

Polyploid organisms are organisms with three or more complete sets of chromosomes. In plants and animals, polyploidy is widespread. In the long-term evolutionary process, polyploidy is one of the important driving forces for speciation. With the in-depth study of genome and phylogeny, the results of multiple studies support that most species have undergone polyploidy events during their evolution. Once polyploidy occurs, its stability depends on rapid genome recombination and changes in gene expression regulation. The formation of fertile polyploidy not only promotes the exchange of genetic material between species and enriches species diversity, but also lays the foundation for polyploid breeding. Aquatic animal polyploids can be obtained by distant hybridization, physical induction, and chemical induction. Among them, distant hybridization can obtain large-scale polyploid fertile lineages. At present, based on the polyploid breeding technology of aquatic animals, several new germplasms of aquatic animals such as fish, shrimps, crabs, and shellfish have been obtained, and systematic research has been carried out. The study of polyploid breeding of aquatic animals not only has important theoretical significance, but also has important application value.

(6) Green cultivation techniques for crops

Green cultivation is an applied science that studies the mechanisms of crop growth and its relationship with the environmental factors, and to achieves high-yield, high- quality, high-efficiency, ecological safety. The grain yields of rice, wheat and maize per area in China are significantly higher than the world average, and the total grain yield increased continuously for many years, which has made great contributions to ensuring the food security of our country. However, there are still many prominent problems need to be solved in China’s crops production, such as inefficient and extensive cultivation practices, imperfect mechanized cultivation techniques, low-integration of engineering technologies, high inputs of water, fertilizer and pesticides, and insufficient integration of green and low- carbon agriculture, intelligence and agricultural machinery. Green cultivation of crops has become a crucial and difficult problem to be solved. The key scientific problems are: ① mechanisms and technologies of synchronizing high- quality, high- yield, high- efficiency, and green crop production; ② synergistic rules of high-quality and high-yield (super-high-yield), and high-efficiency of field crops production and the replicable cultivation mode; ③ green cultivation techniques that is healthy, stress tolerant, carbon sequestered, green house emission reduced, and energy saving for field crops; ④ key technologies of integration of agricultural machinery and intelligent agriculture for field crops; ⑤ the mode and technologies of unmanned green cultivation in the whole process of crops production. Through the innovation of crop cultivation and the cross-integration with frontier science such as physiology, environmental ecology, informatics and mechanical engineering, a new theory of high-quality, high-yield, green and efficient cultivation technology of crops with Chinese characteristics is created, and a unmanned cultivation technology system for agricultural machinery and intelligent agriculture integration for large-scale green production can be established, so as to realize the synergy promotion of yield and quality, production efficiency and production benefit of field crops, to increase comprehensive crop production capacity by 10%–30%, to effectively promote the green high-yielding cultivation level and the modernization of field crop production.

(7)  Polygenic breeding of livestock and poultry

Polygenic breeding of livestock and poultry is one of the main methods of molecular breeding of livestock and poultry, which refers to the aggregation of the excellent genes of excellent individuals scattered in different varieties or lines into the genome of the same individual, so as to obtain new varieties (lines) with specific characteristics. At present, there are two main ways to achieve polygene aggregation. First, on the basis of determining the molecular markers related to the excellent characteristics, the individuals with multiple excellent genes were selected by hybridization, backcrossing and marker-assisted selection. The molecular markers closely linked to the target quantitative trait genes obtained by molecular marker-assisted selection have strong reliability and are not affected by allele dominant-recessive relationships and the environment. The application in animal breeding accelerates the genetic progress and shortens the breeding cycle. However, the aggregated genes in the progeny of individuals selected by this method may resegregate, resulting in the instability of target trait. In recent years, with the continuous development of transgenic technology and gene editing technology, the realization of multi-gene aggregation through gene modification technology has become the research frontier of multi-gene aggregation breeding of livestock and poultry. However, there are still multiple technical difficulties in realizing multiple gene editing simultaneously in animal genomes. On the one hand, the functional genes related to important traits of livestock and poultry have not been completely analyzed, and the targets of genome manipulation are still unclear. On the other hand, the number of simultaneous gene editing in animal genomes is limited, and it is difficult to edit dozens or hundreds of sites at the same time. China has abundant genetic resources of livestock and poultry. Various phenotypes and genotype databases are constantly enriched, and important functional genes and regulatory sequences related to various traits are continuously excavated. At the same time, with the continuous improvement of the efficiency, accuracy and safety of stem cell breeding technology and gene editing technology, using the characteristics of long-term subculture of stem cells in vitro, multiple gene editing operations can be performed, which is expected to solve the technical difficulties of gene editing aggregation breeding.

(8)  Response of food security to climate change

Global climate change refers to a statistically significant change in the average state of the climate on a global scale or a climate change that lasts for a long period of time. The response of food production to climate change is highly sensitive, and global climate change, characterized by climate warming, and has brought serious impacts on global food security. With global warming, the rise of surface temperature will increase the respiration consumption of crops, affect the progress of photosynthesis and the growth and development of crops. Globally, 18% of the inter-annual variability in maize yields is the result of climate variability, while soybean and wheat are less at risk of simultaneous crop failure, with climate variability accounting for 7% and 6% of their global yield variability, respectively. Research has showed that by 2050, global warming may reduce world food production by 18%. At present, climate change has posed a major threat to the basic survival of human beings and social and economic stability. Elucidating the driving mechanism of climate change and the law of its impact on crop production has become a hot and difficult issue to be solved urgently. And the core scientific issues mainly include: ① identification of the core driving factors of climate change; ② the response mechanism of water flux and productivity of farmland ecosystem to global change; ③ the change mechanism of crop damage under the action of climate change and human activities. With the development of artificial intelligence and big data technology, the core driving factors of climate change can be identified from the global scale, and the law of global crop yield changes can be analyzed from multiple dimensions such as nature, economy, and policy. Also scientific decision-making basis and guarantee will be provided for building a global community with a shared future for mankind.

(9) Molecular biological mechanisms of wood formation

Formation of wood (secondary xylem) is a sequential developmental process that starts from the vascular cambium proliferation, cell expansion and differentiation, secondary cell wall (SCW) deposition and programmed cell death (PCD) to form wood tissue. The main research interests include: ① synthesis mechanism of main components of secondary cell wall; ② regulation of auxin, cytokinin, short peptide and transcription factors on vascular cambium cell genesis, proliferation and xylem cell differentiation; ③ mechanisms of cambium stem cell maintenance, differentiation and co-regulation of xylem development and environmental adaptation; ④ regulation of protein post-translational modification and epigenetic modification in cambium activity and wood development; ⑤ molecular mechanism of tension wood formation; ⑥ QTL mapping of growth and wood quality traits; ⑦ genome-wide association analysis of important important wood properties.

Its development trends mainly include: ① More attention is paid to the application of advanced research methods, technologies and analytical instruments, such as spatio- temporal transcriptome, spatial metabolome, single-molecule imaging, and atomic force microscopy. ② Establish a fine multi-level transcriptional regulation network and feedback regulation mechanisms at different levels. ③ Excavation and identification of important wood quality and properties, and the analysis of hierarchical regulation mechanism. ④ Collect and analyze wood quality information by using new sensor technology. ⑤ Crystal structure analysis of key regulatory proteins and identification of protein interaction surface sites. ⑥ Gene editing technology to create new forest varieties with excellent wood properties. ⑦ Carry out tree molecular design breeding to cultivate new varieties trees with fast growing, high quality and high yield.

(10) Discovery of resistosome of plant

Phytopathogens secrete diverse effectors to interfere with plant immune response. In the resistance plants, there are a set of NB-LRR (nucleotide-binding site, leucine-rich repeat) proteins (R proteins) to directly or indirectly perceive these effectors and to initiate immune response. Based on the “gene for gene” hypothesis proposed by Harold Flor in 1956, hundreds of effectors from various pathogens have been cloned over the years. Correspondingly, many NB-LRR proteins have been cloned, and many of them have been discovered to perceive the cognate effectors. Following these discoveries, several hypothesizes have been proposed to explain how the NB-LRR-mediated immunity is initiated in plants, for example the “guard hypothesis” and “bait hypothesis”. In these hypotheses, the NB-LRR activation has been proposed to hydrolyze ATP in the NB domain, leading to the overall allosteric conformational change and the dimerization of N-terminus coil-coil (CC) domain and Toll/IL-1 receptor (TIR) domain that is known to induce hypersensitive response (HR). However, due to lack of resolved protein structures, none of the hypothesis has been experimentally proved, and the NB-LRR-mediated immune activation remains elusive. Until 2019, two Chinese groups resolved the crystal structure of a CC-NB-LRR ZAR1 immune complex for the first time. This immune complex is a wheel-like pentamer, and is activated by exchanging ADP with ATP upon binding the effector AvrAC from Xanthomonas campestris pv. campestris. The activated immune complex forms a funnel with five N-terminal helices of the ZAR1 proteins to target the plasma membrane to create a selective calcium channel. The activation of the resistosome triggers apoplastic calcium influx through this channel and induces the accumulation of reactive oxygen species in cytosol, which eventually results in HR-associated cell death, thereby restricting pathogen further infection. Because the ZAR1 immune complex activation resembles the inflammasomes in animal immune system, the complex is then named as plant resistosome. This is a landmark event in plant science, which answers the question for how the NB- LRR-mediated immunity is initiated in the last 30 years since this type of proteins is discovered. Following this discovery, the tetramer immune complex was characterized for TIR-NB- LRR-mediated immunity by a German group and an American group. These groundbreaking discoveries substantially push the move towards fully elucidating the plant disease resistance.

(11)  Interaction network mechanism of environment-livestock gut microorganism-nutrient metabolism

The environmental pollution problem of animal husbandry has seriously compressed the development space of animal husbandry, and the new production ecosystem is still in the exploratory stage. According to the investigation of the former State Environmental Protection Administration, the amount of livestock and poultry feces produced in China is about 1.9 billion tons, 2.4 times that of industrial solid waste. The annual discharge of chemical oxygen demand (COD) from animal husbandry in China is more than 12 million tons, accounting for 95.8% of the total agricultural discharge and 41.9% of the total National COD discharge, exceeding industrial pollution. In view of the problems of cost efficiency and environmental pollution, it is necessary to focus on solving major technical bottlenecks such as improving feed quality, improving feed nutritional value and utilization efficiency, reducing processing costs, precision feed preparation and environment- friendly feed production, and realizing automation and intelligent equipment research and development of precision feeding. Develop new in vitro pre digestion technology for efficient utilization of feed nutrients; To study the mechanism of high-efficient utilization and transformation of livestock and poultry feed nutrition, and to develop microbial cell factories according to different feed raw materials by using microbial culturing omics technology, microbial transformation engineering technology, protein engineering technology and synthetic biology technology, and create in vitro pre digestion additives with high-efficient utilization of feed, anti-nutritional factors and toxin elimination; Based on the process route of bacterial enzyme collaborative fermentation, the key process parameters, safety evaluation and quality control system were established with the aim of acid soluble protein content, anti- nutritional components and toxin degradation rate. Effectively improve the utilization rate of feed nutrients, reduce the addition of feed protein, reduce the anti-nutritional factors and toxic components of feed, promote the digestion and absorption of feed, and effectively reduce environmental pollution.

《1.2 Interpretation for three key engineering research fronts》

1.2 Interpretation for three key engineering research fronts

1.2.1 De novo domestication of crops and exploitation and utilization of wild germplasm resources

(1)   The significance of de novo domestication of crops and exploitation and utilization of wild germplasm resources

Crop domestication, the process of adapting wild plants into cultivated crops, has played an essential role in the origin of farming civilization and promoted the continuous development of human civilization and the rapid evolution of society. Specifically, domestication is the process of screening beneficial agronomic traits from wild germplasm as the starting material through long-term artificial selection throughout history. The target trait, such as less grain shattering, reduced branching, compact growth, reduced awn, larger seeds, and suitable hand-harvesting. In the view of genetics, domestication is a process of aggregating and retaining ideal genetic variations in the genome. However, this process mostly took a long historical time and the selection of the targeted traits was random and mindless. Moreover, screening for superior traits also significantly reduced the genetic diversity of the domesticated population. Compared to modern cultivars, wild relatives often have advantages in particular traits, such as greater stress resistance, broader environmental adaptability, and relatively higher biomass. Nowadays, with the development of biotechnology, especially gene editing, de novo domestication is starting to be proposed as a promising strategy for crop breeding. That strategy starts from the selection of wild or semi-wild plant species with particularly outstanding traits, then the rapid introduction of the required domestication traits through modern breeding technology, and eventually novel crop species may be achieved in a short time term. This new crop, which repurposes the good wild germplasm that has been lost in the traditional crop domestication or breeding, is of great significance for sustainable agricultural development under the current global trend of environmental change.

The domesticated crops from wild species enable the adaption to a variety of climatic and soil conditions, as well as the expansion of early cultivation into larger areas. The subsequent crop breeding spawned higher food production, which has been the major contributor to population growth and human civilization. Domestication, similar to the breeding process, aims to select the best combination of genotype and phenotype. Many crops have certain common patterns of trait changes through domestication, including compact growth habits, increased spike size, more seeds, loss of grain shattering, reduced dormancy, changes in flowering time response, changes in seed pigmentation, etcetera. New genotypes arise from new mutations, while different genotypes rely on recombination to achieve the aggregation of different superior traits into a single plant. However, both genotypic mutations and recombination are random processes that cannot be accurately predicted or modulated by our ancestor breeders. In addition, the frequency of genomic spontaneous mutations is extremely low, and the immigration of interspecific fragments during domestication or breeding may also inhibit recombination, leading to fixation of deleterious alleles in these regions and resulting in linkage drag and failure to aggregate superior alleles. A classic example is the introduction of root-knot nematode resistance in tomatoes (controlled by the Mi-1 gene) and yellow leaf curl virus resistance (controlled by the Ty-1 gene), and both genes are located within a suppressed recombination region on chromosome 6, and the simultaneous combining of these two resistance traits requires extensive, long-term genetic screening. On the other hand, domestication and the early stage of breeding focused on crop yield improvement, and a large number of ideal variations for other traits were less under selection and thus have been lost, resulting in a “domestication bottleneck”. Meanwhile, the selection of a gene region controlling a specific target trait results in a significant reduction of genetic diversity within that selected region and also its adjacent regions, resulting in “selective eradication”. The above scenarios result in the relatively narrow genetic diversity in our current breeding population, leading to the lack of breakthrough crop varieties with a synergistic improvement of yield, resistance and nutritional quality.

(2) Current study on de novo domestication

Without any underlying biological mechanisms understood, domestication and early stage of breeding were basically done empirically at that time. The recent study of domestication population genetics, especially the rise of the emerging pan- genome sequencing, thoroughly furthers our understanding of the genetic mechanism for crop domestication. Different crops have undergone long-term domestication processes for hundreds or even thousands of years, nevertheless, analysis of more than 200 crops for a set of domestication traits showed that 84% of the crops had only two to five major traits as the main domestication traits. Results of domestication genetics analysis, as exemplified by maize, confirmed that crop domestication is often controlled by a few key genes. Through the in-depth understanding of the genetic basis of crop domestication, combined with the rapidly developing genome editing technology, the era for de novo domestication of wild crop relatives or semi-domesticated crops is emerging. In 2008, Research groups from China and Brazil simultaneously reported the de novo domestication of wild tomatoes, which maintained the excellent salinity tolerance and disease resistance from wild tomatoes but also achieved new tomato crop showing excellent plant architecture, synergistically improved yield and quality. Shortly after that, scientists in the USA also successfully re-domesticated the semi-domesticated Physalis pruinosa, illustrating rapid improvements in yield and overall agronomic traits. A team of Chinese scientists reported the de novo domestication of allotetraploid wild rice in 2021, shedding a fresh insight into a novel breeding strategy for the new generation of rice crops with high yields and strong environmental adaptability.

(3) Future research trends and innovation directions.

To further explore wild germplasm resources and expand the application of de novo domestication, the technical potential of crop de novo domestication needs to be further enhanced in the following directions: ① deepening the analysis of the genetic mechanism of domestication of major crops, mining the interspecifically conserved or species-specific genes responsible for key domestication traits, providing the genetic and genomic basis for de novo domestication; ② collection and genotypic identification of wild germplasm resources, screening wild species or semi-domesticated species with superior agronomic traits, providing germplasm basis for de novo domestication; ③ establishment and continuous optimization of efficient genetic transformation system in wild species, breaking the speed-limiting steps that wild species are normally difficult to transform, providing technical prerequisites for de novo domestication; ④ establishment and continuous optimization of efficient gene editing system in wild species, achieving precisely modulated gene knockout, single-base editing, prime editing, expression activation or repression editing in wild species; ⑤ high-throughput phenotype identification on domestication traits, achieving precise and efficient screening of superior traits in large-scale transformation experiments.

In the study of “de novo domestication of crops and development and utilization of wild germplasm resources”, the top three countries in terms of the publication of core papers (Table 1.2.1) are China (51.35%), the USA (37.84%), and Germany (13.51%). The citation frequency of these core papers in this research field is distributed from 12.00 to 127.00, of which the citation frequency of Israel and Saudi Arabia exceeds 100. In terms of the distribution of research institutions (Table 1.2.2), Chinese Academy of Sciences (CAS), Chinese Academy of Agricultural Sciences (CAAS), and Huazhong Agricultural University (HZAU) have produced many core papers and cited many times. In terms of cooperation networks among countries (Figure 1.2.1), research cooperation

《Table 1.2.1》

Table 1.2.1 Countries with the greatest output of core papers on “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

No. Country Core papers Percentage of core papers/% Citations Citations per paper Mean year
1 China 38 51.35 1 189 31.29 2019.8
2 USA 28 37.84 1 486 53.07 2019.2
3 Germany 10 13.51 633 63.3 2019.5
4 Australia 9 12.16 844 93.78 2019
5 UK 7 9.46 456 65.14 2019.1
6 France 6 8.11 197 32.83 2018.8
7 Japan 6 8.11 72 12 2020.3
8 Brazil 5 6.76 332 66.4 2019.2
9 Israel 3 4.05 381 127 2019
10 Saudi 3 4.05 309 103 2020.3

《Table 1.2.2》

Table 1.2.2 Institutions with the greatest output of core papers on “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

No. Institution Core papers Percentage of core papers/% Citations Citations per paper Mean year
1  Chinese Academy of Sciences 13 17.57 779 59.92 2019.8
2  Chinese Academy of Agricultural Sciences 8 10.81 197 24.62 2020.8
3  Huazhong Agricultural University 7 9.46 181 25.86 2020
4  U.S. Department of Agriculture-Agricultural Research Service 4 5.41 359 89.75 2019
5  Zhejiang University 4 5.41 336 84 2019.8
6  University of Minnesota System 4 5.41 329 82.25 2018.2
7 University of Sao Paulo 4 5.41 326 81.5 2019.2
8  Federal University of Vicosa 3 4.05 300 100 2020
9  University of Arizona 3 4.05 198 66 2019.7
10 University of Toulouse 3 4.05 143 47.67 2019.7

among countries is more common, and cooperation among China, the USA and Germany is relatively closer. The output is mainly in the cooperation network among agencies (Figure 1.2.2), and there are certain cooperation relations among these agencies. The main output countries of the cited core papers are China, the USA, and Australia, with China accounting for more than 1/3 and the USA accounting for more than 20% (Table 1.2.3). In terms of the main output institutions of the cited core papers (Table 1.2.4), CAAS, CAS, and the Agricultural Research Service of U.S. Department of Agriculture (USDA ARS) ranked among the top three in the number of citing papers. Figure 1.2.3 shows the roadmap of the engineering research front of “de novo domestication of crops and exploitation and utilization of wild germplasm resources”.

1.2.2   Immunosuppression and escape mechanisms of important animal pathogens

China is a major breeding country and a major consumer of animal-sourced food in the world. Live pigs in China reach an annual output of approximately 700 million heads and account for 50% of the world’s total, and China has approximately 14 billion poultry per year. The output of meat and poultry in China ranks first in the world, and the total output value of national animal husbandry exceeds 3.2 trillion. National animal husbandry accounts for nearly 30% of the total agricultural output value and drives the output value of upstream and downstream related industries up to more than 3 trillion RMB. However, the production level of animal husbandry in China is far below the world average level, and the main bottleneck restricting its development is the

《Figure 1.2.1》

Figure 1.2.1 Cooperation network among major countries in the engineering research front of “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

《Figure 1.2.2》

Figure 1.2.2 Cooperation network among major institutions in the engineering research front of “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

《Figure 1.2.3》

Figure 1.2.3 Roadmap of the engineering research front of “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

《Table 1.2.3》

Table 1.2.3 Counturies with the greatest output of citing papers on “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

No. Country Citing papers Percentage of citing papers/% Mean year
1 China 863 35.81 2020.4
2 USA 499 20.71 2020.2
3 Australia 164 6.8 2020.2
4 India 160 6.64 2020.2
5 Germany 159 6.6 2020.3
6 UK 142 5.89 2020.1
7 France 119 4.94 2020
8 Italy 92 3.82 2020.3
9 Japan 81 3.36 2020.1
10 Spain 66 2.74 2020.2

《Table 1.2.4》

Table 1.2.4 Institutions with the greatest output of citing papers on “de novo domestication of crops and exploitation and utilization of wild germplasm resources”

No. Institution Citing papers Percentage of citing papers/% Mean year
1  Chinese Academy of Agricultural Sciences 207 23.44 2020.5
2  Chinese Academy of Sciences 129 14.61 2020.3
3  U.S. Department of AgricultureAgricultural Research Service 91 10.31 2020.2
4  Huazhong Agricultural University 83 9.4 2020.6
5  Nanjing Agricultural University 68 7.7 2020.4
6  Zhengzhou University 67 7.59 2020.7
7  China Agricultural University 55 6.23 2020.6
8  Zhejiang University 55 6.23 2020.7
9  University of Western Australia 45 5.1 2020.2
10  The University of Queensland 43 4.87 2019.9

problem of infectious diseases. The continuous occurrence of animal diseases has caused huge economic losses to our country’s animal husbandry and seriously affected the output and quality of animal products. For example, in African swine fever (ASF) and peste-des-petits-ruminants, ASF caused devastating damage in 2019, with the number of live pigs falling by 60%, and in some places, it even exceeded 70%. The price of pork soared from 22–24 CNY to more than 60 CNY per kilogram. In addition, the epidemics of zoonotic diseases such as brucellosis, tuberculosis, plague, influenza, rabies, and Ebola pose serious threats to public health security. For example, COVID-19 has caused more than 6 million deaths to date. How to effectively prevent and control the occurrence and prevalence of animal diseases has always been a focus and research hotspot in the fields of veterinary medicine, medicine and biosafety.

However, the key reason for the failure in the prevention and control of animal diseases and zoonotic diseases is the immunosuppression and immune escape of pathogens. The body’s defense against pathogenic infections relies primarily on the body’s immune system. Immune evasion can lead to pathogens being able to effectively break through the body’s immune barrier or vaccine-induced immune responses to establish a productive infection. Immunosuppression can promote pathogenic infection or the establishment of persistent infection. For example, influenza viruses and coronaviruses have the ability to establish infection through a variety of strategies during long-term evolution to escape host immunity and the protection of existing vaccines by constantly producing new mutants. Therefore, revealing the mechanism by which pathogens inhibit the body’s immune function and evade host immunity is the premise of effective prevention and control of these important animal pathogens, and it is also a hotspot and challenge in the current scientific research field.

The host immune system, including innate and acquired immunity, is a key force against pathogenic infection. The host initially induces an innate immune response after surveilling pathogen infection through pattern recognition receptors (PRRs). The innate immune response is the first line of host defense against pathogen infection, and many pathogens have acquired the ability to evade or actively suppress host innate immunity during long-term coevolution with their hosts. Pattern recognition receptors (PRRs) are key components of anti-infection immunity that detect conserved molecular features of viral pathogens and initiate innate immune responses. Therefore, many pathogens have the capacity of immune evasion or suppression, and their molecular mechanisms include: ① sequestering or modifying viral RNA or DNA nucleic acid ligands from the recognition and activation of intracellular PRRs. For example, the nonstructural protein 1 (NS1) of influenza virus and the E3 protein of vaccinia virus prevent viruses from being recognized by the RNA sensor RIG-I by binding to viral dsRNA; ② destabilize or degrade PRRs by manipulating the posttranslational modification of PRR protein. For example, papain-like protease (PLP) of coronavirus and lead protease (Lpro) of foot-and-mouth disease virus (FMDV) can cleave or degrade RLR and MAVS, key proteins in innate immunity, to escape the innate immune response. In addition, many viruses suppress the innate immune response by targeting some of the key downstream molecules shared by the innate immune response, such as TBK1, IRF3, IRF7, and NF-κB, or by blocking IFNα/β receptor signaling.

In addition to the ability to escape or suppress innate immune responses, some important pathogens escape or suppress acquired immune responses through various mechanisms during long-term evolution. After the pathogen breaks through the body’s innate immune barrier to establish infection, the host suppresses and eliminates the pathogen primarily through adaptive immunity. The body’s adaptive immune system mainly functions through antibody-mediated (especially neutralizing antibodies) humoral immunity and cytotoxic T-cell-mediated (CTL) cellular immunity. However, pathogens can evade neutralizing antibodies and CTLs by generating new mutant strains through genetic mutation and recombination. Viral genomes, especially RNA viruses, constantly and continually mutate to adapt to host systems under immune selection pressure. For example, influenza viruses and coronaviruses can evade the recognition of T cells and virus-neutralizing antibodies through antigenic drift, weakening the body’s acquired immune protection, and some of these mutant strains can even also acquire stronger transmission ability or virulence than the original strain. For example, the transmission ability of the current COVID-19 Omicron variant has increased significantly compared with the original Wuhan strain, the Omicron BA.4/5 R0 has increased from 3.3 to 18.6 of the original Wuhan strain, and the protection of the existing vaccine is greatly decreased due to the spike protein mutation. This is also one of the main reasons for the repeated COVID-19 epidemic.

In addition to passively evading the body’s immunity, some important pathogens can actively attack the host’s immune system through a variety of mechanisms to suppress the host’s immune response and promote infection. Many pathogens themselves infect important immune organs of the body. For example, porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus can infect the thymus and bone marrow, which are important immune organs responsible for the development of T cells and B cells, respectively, resulting in damage to immune organ function and the suppression of the body’s adaptive immunity, thereby establishing persistent infection. In addition, PRRSV and porcine pseudorabies virus can inhibit the induction of adaptive immune responses by interfering with antigen processing and presentation.

The long-term interaction between pathogens and hosts is similar to an endless evolutionary arms race. If humans want to win this arms race, they must know themselves and their enemies, continue to enhance research and invest in related fields, break through traditional models, and develop innovative ideas from the perspective of pathogens and hosts. ① The immune systems of various species are very different. It is necessary to continue to strengthen the basic research on animal and poultry immune systems to reveal some important molecules and signaling pathways that play critical roles in inducing immune responses in the body, as well as the molecular mechanisms of immune protection after infection with important pathogens. ② Construct gene deletion strains by gene editing technology to further identify the key pathogenic genes mediating immune escape or immune suppression and then develop attenuated vaccine strains on this basis. ③ Development of broad-spectrum vaccines.

The development of broad-spectrum vaccines through new technologies is the most effective and economical way to effectively prevent and control the current highly variable important pathogens. Although viruses evolve faster than their hosts, important proteins of viruses are restricted by many functions that affect viral replication, and there are some conserved sites in the pathogen. A large number of studies have confirmed the existence of broad-spectrum neutralizing antibodies and T-cell epitopes in easily mutated viruses. Broad-spectrum neutralizing antibodies and CD8+ T-cell recognition epitopes are identified by using single- cell sequencing technology and high-throughput screening technology, and broad-spectrum mRNA or DNA vaccines containing conserved antigen genes are designed and synthesized through bioinformatics and nucleic acid synthesis technology. These studies can provide important guidance for the development of broad-spectrum vaccines in the future.

Considering the distribution of papers by country, it can be seen that the main contributors of core papers on the “Immune suppression and escape mechanisms of important animal pathogens” were the USA (51%), the UK (31%), and China (18%) (Table 1.2.5). The citations per paper in this field ranged from 240 to 3 616 across the top ten countries, and the citations per paper of the 10 countries all exceeded 100, the citations per paper of the UK exceeded 200, the citations per paper of Thailand and Denmark exceeded 300. The distribution of papers by research institution shows that the number of core papers and the citations were the

《Table 1.2.5》

Table 1.2.5 Countries with the greatest output of core papers on “immunosuppression and escape mechanisms of important animal pathogens”

No. Country Core papers Percentage of core papers/% Citations Citations per paper Mean year
1 USA 23 51.11 3 063 133.17 2020
2 UK 14 31.11 3 616 258.29 2020.4
3 China 8 17.78 1 156 144.5 2019.9
4 Switzerland 4 8.89 554 138.5 2021
5 Netherlands 4 8.89 510 127.5 2019.5
6 South Africa 3 6.67 438 146 2021
7 Thailand 2 4.44 774 387 2020.5
8 Denmark 2 4.44 681 340.5 2021
9 India 2 4.44 300 150 2021
10 Singapore 2 4.44 240 120 2020.5

highest for University of Oxford, University of Southampton, and University of Cambridge (Table 1.2.6). The collaboration networks among the major countries were common, with the UK and USA sharing the closest collaborative relationship (Figure 1.2.4). From the collaboration network among major institutions (Figure 1.2.5), it can be seen that collaborative relationships existed among all institutions.

The main contributors of core paper citations were USA and China (Table 1.2.7), the number of citing papers in the USA accounts for more than one third, China accounts for more than 10%, and the average citations year of core papers was also relatively recent, which is indicative of the strong developmental momentum of research in this field. From the list of the major core paper citation-contributing institutions (Table 1.2.8), it can be seen that Chinese Academy of Sciences, University of Harvard and University of Oxford were far ahead of all other institutions, and Chinese Academy of Sciences ranked first. Figure 1.2.6 shows the roadmap of the engineering research front of “immunosuppression and escape mechanisms of important animal pathogens”.

1.2.3   Mechanism of efficient soil carbon sequestration and regulation

(1)  The significance of efficient soil carbon sequestration and regulation

Soil organic matter is the core of soil health, maintains soil fertility and crop productivity, and also highly connected to the ecosystem function and the sustainability. In addition, soil is the largest carbon pool in the terrestrial ecosystem.

《Table 1.2.6》

Table1.2.6 Institutions with the greatest output of core papers on “immunosuppression and escape mechanisms of important animal pathogens”

No. Institution Core papers Percentage of core papers/% Citations Citations per paper Mean year
1  University of Oxford 8 17.78 2202 275.25 2020.5
2  University of Southampton 5 11.11 1493 298.6 2020.2
3  University of Cambridge 4 8.89 1183 295.75 2020.2
4  University of Texas Austin 3 6.67 879 293 2020.3
5  Harvard University 3 6.67 570 190 2021
6  University of Edinburgh 2 4.44 1101 550.5 2021
7  University of Glasgow 2 4.44 775 387.5 2021
8  Wellcome Sanger Institute 2 4.44 739 369.5 2021
9  Imperial College London 2 4.44 681 340.5 2021
10  University of Copenhagen 2 4.44 681 340.5 2021

《Figure 1.2.4》

Figure 1.2.4 Collaboration network among major countries in the engineering research front of “immunosuppression and escape mechanisms of important animal pathogens”

《Figure 1.2.5》

Figure 1.2.5 Collaboration network among major institutions in the engineering research front of “immunosuppression and escape mechanisms of important animal pathogens”

《Table 1.2.7》

Table 1.2.7 Countries with the greatest output of citing papers on “immunosuppression and escape mechanisms of important animal pathogens”

No. Country Citing papers Percentage of citing papers/% Mean year
1 USA 1 835 31.7 2020.7
2 China 1 050 18.14 2020.7
3 UK 555 9.59 2020.7
4 India 419 7.24 2020.7
5 Germany 404 6.98 2020.8
6 Italy 354 6.12 2020.7
7 France 283 4.89 2020.7
8 Brazil 263 4.54 2020.8
9 Australia 235 4.06 2020.7
10 Canada 218 3.77 2020.7

《Table 1.2.8》

Table 1.2.8 Institutions with the greatest output of citing papers on “immunosuppression and escape mechanisms of important animal pathogens”

No. Institution Citing papers Percentage of citing papers/% Mean year
1 Chinese Academy of Sciences 263 22.87 2020.8
2 Harvard University 147 12.78 2020.8
3 University of Oxford 146 12.7 2020.7
4 University of Washington 100 8.7 2020.7
5 University of Cambridge 77 6.7 2020.8
6 University of Hong Kong 73 6.35 2020.6
7 Fudan University 73 6.35 2020.7
8 Imperial College London 70 6.09 2020.8
9 University of Sao Paulo 68 5.91 2020.8
10 Icahn School of Medicine at Mount Sinai 68 5.91 2020.7

《Figure 1.2.6》

Figure 1.2.6 Roadmap of the engineering research front of “immunosuppression and escape mechanisms of important animal pathogens”

The global soil organic carbon is 1 500–2 000 Pg, equivalent to 2–3 times of the carbon in the atmosphere. Agricultural soil carbon sequestration was found to account for 25% of the potential for natural climate solutions. Therefore, promoting agricultural soil carbon sequestration is of great significance for ensuring food security, mitigating climate change and promoting agricultural green development. The core of efficient soil carbon sequestration and regulation is to understand the key processes of turnover and stability of soil organic matter, and to establish a regulatory strategy for efficient carbon sequestration and slowing down its mineralization and decomposition.

(2)  Research status of efficient soil carbon sequestration and regulation

The formation and stabilization of soil organic matter is relatively complex. At present, the formation, occurrence form and stabilization mechanism of soil organic matter are still poorly understood and divergent. The humus defined by the classical humification theory is complex and highly ambiguous, and the current methods are not enough to establish a clear “white box” model for it. Based on the current study in soil organic matter and protection mechanisms in plant residue decomposition, the formation and stability of organic matter is explained as the organic matter continuum model, i.e., the transformation of plant residues into soil organic matter is a step-by-step microbial decomposition process from large plant biopolymers to small molecular compounds, so the existence of soil organic matter is a continuous process from large plant fragments to gradually decomposed into small molecular compounds.

In this model, the volume of exogenous organic materials decreases continuously during the process of microorganism utilization, the thermodynamic gradient gradually decreases, and the polar components, soluble components and ionized components increase accordingly. Moreover, as the molecular complexity gradually decreases, organic compounds are more likely to bind to the mineral surface or enter the interior of the agglomerates to increase their stability. However, there are also studies showed that although soil microorganisms can completely or partially decompose humus, new humus will be produced at the same time to renew organic matter. In a word, both the traditional humification theory and the organic matter continuum model admit that the animal and plant fragments will be broken up by physicochemical action after input into the soil, and then degraded into relatively smaller components by extracellular enzymes, etc. sequestered in the soil.

The process of organic matter formation and stabilization is closely related to the interaction with surrounded soil matrix. Soil aggregates are the main place for the occurrence of soil organic matter, which protect the organic matter through the physical coating, to prevent the decomposition of microorganisms. Therefore, aggregate protective capacity is the physical basis for realization of soil carbon sequestration potential. The chemical protection effect of soil on organic matter mainly refers to the interaction between soil inorganic molecules and organic molecules, which makes organic matter difficult to be utilized by microorganisms. Previous studies have focused on the decomposition of organic carbon by microorganisms. However, more and more studies have found that microorganisms contribute available soil carbon sources to soil organic matter in the form of metabolites through assimilation, which account for more than 50% of organic carbon in agricultural soils. In addition, it indirectly affects soil organic matter stability through the turnover of aggregates. Therefore, current research believes that the stability of organic matter is the result of the interaction and interdependence of the physical protection of aggregates, the binding of soil minerals, and the metabolic process of microorganisms.

Reasonable management could regulate soil carbon sequestration by affecting the balance between carbon input and output. The input of exogenous carbon is an important source of soil organic matter formation. The metabolic activities of soil microorganisms can convert plant residues into soil organic matter. For example, compared with chemical fertilizers, long-term application of organic fertilizers can significantly increase soil carbon sequestration rates, while improving both organic carbon content and quality. Insufficient supply of organic materials and frequent soil turnover in traditional farming lead to the destruction of soil aggregate structure and the accelerated loss of organic carbon, which limits the growth and metabolism of microorganisms, as well as the accumulation of soil organic matter. In addition, diversified planting and crop rotation changed the quantity and quality of crop residues, significantly affect the structure and activity of soil microbial community, and thus increase the content of soil organic matter.

(3)  Future research directions and innovations

Soil is an open and complex system in which multiple substances coexist, multiple processes occur simultaneously, and multiple factors influence together. At present, the mechanism of efficient soil carbon sequestration is still unclear, and it is difficult to improve soil organic matter. Therefore, in-depth research on carbon sequestration and regulation mechanism needs to be strengthened in the future. For example, accurately distinguishing carbon sources of different organic components, exploring the microbial action mechanism of plant residues to soil organic matter, accelerating research on organic matter stability based on multi-factor coordinated regulation, exploring soil carbon balance mechanism and plant residue input thresholds, etc. Innovate new carbon- based materials with high efficiency of carbon sequestration and nutrient use, improve soil carbon sequestration efficiency, integrate and innovate key technologies for soil carbon sequestration, land conservation and productivity improvement, and promote the application of large-scale agricultural soil carbon sequestration are becoming the frontier in applied research direction in this field (Figure 1.2.7).

In the front of “efficient soil carbon sequestration and regulation mechanism”, the top three countries with the most published core papers are China, the USA, and Germany (Table 1.2.9). The citations per paper of core papers in this front ranges from 94.80 to 297.75. Except for Saudi Arabia, the citation frequency of papers from other countries exceeds 100. In terms of the distribution of research institutions (Table 1.2.10), Lanzhou University, ETH Zurich, University of Sussex, and Tsinghua University produced more core papers and more citations. Countries with the greatest output of citing papers are China, the USA, and Australia (Table 1.2.11). In terms of the main institutions producing citing core papers (Table 1.2.12), University of Chinese Academy of Sciences, Hunan University, and Tsinghua University ranked the top three in terms of the number of citing papers. The cooperation among countries is more common and complex (Figure 1.2.8) where China, the USA, Germany, and the UK cooperate more closely. In terms of the cooperation network among major institutions (Figure 1.2.9), there are certain cooperation relationships

《Figure 1.2.7》

Figure 1.2.7 Roadmap of the engineering research front of “mechanism of efficient soil carbon sequestration and regulation”

《Table 1.2.9》

Table 1.2.9 Countries with the greatest output of core papers on “mechanism of efficient soil carbon sequestration and regulation”

No. Country Core papers Percentage of core papers/% Citations Citations per paper Mean year
1 China 51 61.45 9 480 185.88 2019.1
2 USA 32 38.55 5 545 173.28 2018.5
3 Germany 15 18.07 2 954 196.93 2018.3
4 UK 13 15.66 2 702 207.85 2018.5
5 Australia 10 12.05 1 821 182.1 2018.5
6 South Korea 9 10.84 1 267 140.78 2018.6
7 Austrian 5 6.02 1 061 212.2 2018
8 Saudi Arabia 5 6.02 474 94.8 2019.6
9 Switzerland 4 4.82 1 191 297.75 2018.5
10 France 4 4.82 1 098 274.5 2019.5

《Table 1.2.10》

Table 1.2.10 Institutions with the greatest output of core papers on “mechanism of efficient soil carbon sequestration and regulation”

No. Institution Core papers Percentage of core papers/% Citations Citations per paper Mean year
1 Hunan University 5 6.02 782 156.4 2018
2 Korea University 4 4.82 605 151.25 2018.5
3 Chinese Academy of Sciences 4 4.82 480 120 2019.5
4 King Saud University 4 4.82 257 64.25 2019.5
5 Lanzhou University 3 3.61 1 227 409 2018.3
6 ETH Zurich 3 3.61 1 079 359.67 2018.3
7 University of Sussex 3 3.61 971 323.67 2019
8 Tsinghua University 3 3.61 852 284 2018.7
9 University of Massachusetts 3 3.61 784 261.33 2016.7
10 Monash University 3 3.61 763 254.33 2019.7

《Table 1.2.11》

Table 1.2.11 Countries with the greatest output of citing papers on “mechanism of efficient soil carbon sequestration and regulation”

No. Country Citing papers Percentage of citing papers/% Mean year
1 China 1 492 43.9 2019.3
2 USA 522 15.36 2019.1
3 Australia 240 7.06 2019.3
4 UK 236 6.94 2019.4
5 Germany 225 6.62 2019.1
6 South Korea 148 4.35 2019.4
7 Canada 123 3.62 2019.4
8 India 116 3.41 2019.8
9 Spain 115 3.38 2019.1
10 Netherlands 96 2.82 2019.3

《Table 1.2.12》

Table 1.2.12 Institutions with the greatest output of citing papers on “mechanism of efficient soil carbon sequestration and regulation”

No. Institution Citing papers Percentage of citing papers/% Mean year
1 University of Chinese Academy of Sciences 246 26.59 2019
2 Hunan University 160 17.3 2019
3 Tsinghua University 123 13.3 2019.3
4 Korea University 62 6.7 2019.5
5 The Hong Kong Polytechnic University 58 6.27 2019.5
6 Lanzhou University 48 5.19 2017.9
7 ETH Zurich 47 5.08 2018.9
8 Sejong University, Korea 47 5.08 2019.4
9 Zhejiang University 47 5.08 2019.1
10 Harbin Institute of Technology 44 4.76 2019.2

《Figure 1.2.8》

Figure 1.2.8 Collaboration network among major countries in the engineering research front of “mechanism of efficient soil carbon

《Figure 1.2.9》

Figure 1.2.9 Collaboration network among major institutions in the engineering research front of “mechanism of efficient soil carbon sequestration and regulation”

between different institutions in the same country and among institutions in different countries. For example, Lanzhou University and Chinese Academy of Sciences, Tsinghua University and Korea University, ETH Zurich, University of Sussex, and Monash University have close cooperations.

《2 Engineering development fronts》

2 Engineering development fronts

《2.1 Trends in Top 11 engineering development fronts》

2.1 Trends in Top 11 engineering development fronts

The Top 11 engineering research fronts in the agricultural field mainly involve biological breeding, smart agriculture, green agriculture, and other directions (Table 2.1.1). Among them, the research fronts related to biological breeding include animal precision gene editing and breeding technology, advanced seed production technology, genome- wide selection in forest tree breeding, and RNAi-based pest control technology. The research fronts related to intelligent agriculture include agricultural autonomous robot, unmanned intelligent cultivation technology for crops, aquaculture technology of ecological intelligent pond. The research fronts related to green agriculture include catalytic degradation processes for organic pollutants, feed antibiotic substitution technology and products. At the same time, the monitoring and early warning for emerging and reemerging animal infectious diseases are also the hot research objects of scientific researchers. The average number of citations of the advanced seed production technology in the Top 11 research front is as high as 67.69, which indicates that the advanced seed production technology has received extensive attention from scientific researchers in recent years.

The disclosures of core patents involved in various research fronts from 2016 to 2020 are shown in Table 2.1.2. Among them, the number of core patents related to animal precision gene editing and breeding technology is the largest, with 829 in 2021, far higher than other research fronts. The core patents of the genome-wide selection in forest tree breeding are the least, only appeared in 2017 and 2021.

(1) Monitoring and early warning for emerging and reemerging animal infectious diseases

“Emerging and reemerging animal infectious diseases” is defined as a new infection resulting from the evolution or change of an existing pathogen resulting in a change of host range, vector, pathogenicity, or strain; or the occurrence of a previously unrecognized infection or disease. And the re- emerging disease is considered as an already existing disease that either shifts its geographical region or expands its host range or significantly increases its prevalence as altered drug resistance or weakened control measures. In recent years, more than 30 new emerged animal diseases, such as African swine fever, peste des petits ruminants, and bovine lumpy skin disease have been introduced into our country. In particular, African swine fever has swept across the whole country and severely damaged the pork industry. At the same time, many infectious diseases including African horse fever,

《Table 2.1.1》

Table 2.1.1 Top 11 engineering development fronts in agriculture

No. Engineering research front Core papers Citations Citations per paper Mean year
1 Monitoring and early warning for emerging and reemerging animal infectious diseases 454 1 186 2.61 2018.7
2 Animal precise gene editing and breeding technology 4 546 10 294 2.26 2018.2
3  Advanced seed production technology 88 5 957 67.69 2016.7
4 Application of gene editing technology in horticultural crops 50 121 2.42 2019.3
5  Genome-wide selection in forest tree breeding 2 7 3.5 2019
6 RNAi-based pest control technology 94 913 9.71 2018.4
7  Agricultural autonomous robot 259 861 3.32 2019.3
8  Catalytic degradation processes for organic pollutants 1 000 2 039 2.04 2018.4
9  Feed antibiotic substitution technology and products 108 140 1.3 2018.4
10 Unmanned intelligent cultivation technology for crops 261 720 2.76 2018.9
11 Aquaculture technology of ecological intelligent pond 103 182 1.77 2019.04

《Table 2.1.2》

Table 2.1.2 Annual number of core patents published for the Top 11 engineering development fronts in agriculture

No. Engineering research front 2016 2017 2018 2019 2020 2021
1  Monitoring and early warning for emerging and reemerging 78 62 62 76 68 108
2 Animal precise gene editing and breeding technology 433 654 697 814 685 829
3  Advanced seed production technology 4 9 10 14 9 15
4 Application of gene editing technology in horticultural crops 1 4 11 9 13 12
5 Genome-wide selection in forest tree breeding 0 1 0 0 0 1
6 RNAi-based pest control technology 10 20 19 22 12 11
7 Agricultural autonomous robot 9 28 48 43 56 63
8 Catalytic degradation processes for organic pollutants 68 142 240 191 211 95
9 Feed antibiotic substitution technology and products 16 10 13 11 22 24
10 Unmanned intelligent cultivation technology for crops 22 28 36 47 48 72
11 Aquaculture technology of ecological intelligent pond 3 16 25 8 13 35

animal infectious diseases

Bovine Spongiform Encephalopathy (mad cow disease), etc. are often outbreak and spread in countries and regions along the “Belt and Road”, increasing the risk of cross-border introduction. These economically important animal diseases do not only seriously threaten the safety of meat production, economic safety, and ecological safety, but some of them are also zoonosis. The International Food and Agriculture Organization (FAO) has stated that “the strong international and national animal health control systems are key to preventing animal disease, ensuring food safety and nutrition, and protecting farmers’ interests”. Therefore, monitoring and early warning of emerging and reemerging animal infectious diseases are crucial to safeguarding national biosecurity and preventing and controlling disease outbreaks and epidemics. The core technical requirements of this field mainly include: ① innovation and integration for rapid, accurate, convenient, high-throughput, and differential diagnosis detection technology; ② clarifying the basic characteristics of disease etiology, transmission rules, distribution characteristics, molecular evolution pathway, and co-evolution with the host, disease occurrence and spread models based on pathogen molecular ecology, and prediction indicators of proposing corresponding disease outbreak; ③ establish and improve the information databases of emerging and reemerging animal infectious diseases, early warning, and reporting systems, and improve the accurate assessment of incidence probability and potential hazard. These relevant technological breakthroughs will provide technical support and solutions for the prevention and control of emerging and reemerging animal infectious diseases and early warning of biosecurity.

(2)  Animal precision gene editing and breeding technology

Animal breeding technology has experienced a leap-forward development from the initial phenotypic value breeding technology to the modern genome editing breeding technology. The traditional method of hybrid improvement method is costly, time-consuming and complicated, and defective genes may also be introduced due to gene linkage, while gene editing technology can precisely modify the target gene, through modifying key functional genes and regulatory sequences related to important animal traits, new animal breeds (lines) with characteristic phenotypes can be obtained in one generation, thereby improving the efficiency of animal breeding. Since its introduction, gene editing technology has developed and updated three generations: Zinc-finger nucleases (ZFNs) , transcription activator-like effector nucleases (TALENs) and Clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9). Gene editing technology has achieved a major breakthrough in technology from the random targeting and inactivation of the target gene to the accurate replacement of a single base of the gene. In recent years, gene editing technology has become an important method of animal breeding, and has been fully developed and applied in the field of animal breeding. A batch of new materials and new lines with high-yield, high-quality, high-reproduction and disease-resistant breeding have been precisely created through gene editing technology, such as gene edited swines for resistance to porcine reproductive and respiratory syndrome, gene edited beef cattle with myostatin knockout, and tuberculosis-resistant dairy cows. With the continuous progress of multi-omics sequencing technology, various phenotype and genotype databases are constantly enriched, important functional genes and regulatory sequences related to various traits are continuously mined, and the efficiency, accuracy and safety of gene editing technology are constantly improving. Animal precision gene editing and breeding technology will gradually develop in the direction of engineering and large-scale, and will be widely used in the field of animal breeding in the future, providing important technical support for the cultivation of new animal species.

(3) Advanced seed production technology

The utilization of hybrid vigor in maize, rice and other crop breeding since the middle of the last century was one of the major revolutions in the history of agricultural production. The production of hybrid seeds can be achieved by using male sterile lines or by emasculation of the maternal parent. However, male sterility may be highly affected by environmental factors, and incomplete emasculation is almost inevitable. Consequently, the self-pollination of the maternal parent lines, which would generate a much lower yield than the hybrids, could be adulterated in the hybrids seeds and this has long been the priority issue to be addressed in seed production. Additionally, traditional sterile seed production technology relies on time-consuming introgression for multiple generations and suitable restorer lines. On the other hand, emasculation requires intense labor and experienced skills. Therefore the establishment of a new generation of intelligent seed production technology for hybrids can significantly reduce seed production costs, but also increase the purity and quality of the hybrid seeds as well as the potential yield. Recently, a set of high throughput and high-precision technologies of hybrid seed have been initially established, combining the usage of nuclear sterile lines and selective markers including seed size, transgenic fluorescence, and the pigment of seed coat or seedling. This emerging breakthrough opens more improvement and optimized rooms for integrating multiple sterility genes and different selecting markers, which could be a very promising direction for hybrid seed production technology in China.

(4)  Application of gene editing technology in horticultural crops

Gene editing is a technology that changes the original gene sequence by knocking out several base pairs or a DNA sequence. The three main tool enzymes used are ZFNs, TALENs, and CRISPR-Cas9. Among them, due to the advantages of high editing efficiency, simple operation, and low cost, CRISPR-Cas9 gene editing has become a hot tool for gene editing in recent years and has been widely used in plants. Gene editing technology has been able to achieve precise replacement of a single base of a gene, while it can implement random targeting and inactivation of target genes in the startup phase. A major breakthrough has been achieved in the technology and it has made important contributions to gene function research and crop trait improvement. In 2021, a gamma-aminobutyric acid-rich tomato modified with CRISPR technology has been marketed in Japan. Gene editing technology has been widely used in crops and model plants. Compared with traditional hybrid breeding, gene editing technology has great advantages in crop genetic improvement. Gene editing system has been established in tomato and other horticultural crops. However, many other horticultural crops do not yet have a good gene editing system. It is necessary to establish an efficient gene editing system in different horticultural crops so as to promote the gene editing technology in practice.

(5) Genome-wide selection in forest tree breeding

Genome-wide selection (GS) in forest tree breeding belongs to the discipline of forestry science and is an emerging frontier technology of forest tree breeding. Most of the important traits of forest trees are complex quantitative traits and high genetic heterozygosity. Conventional breeding techniques are difficult to efficiently and rapidly cultivate improved tree varieties. Molecular marker-assisted selection (MAS) is difficult to capture minor-effective loci, and the resolution of genetic mapping is low. The results of MAS are difficult to verify each other and cannot effectively promote the process of forest tree genetic improvement. GS refers to a breeding method that uses high-density genome-wide marker genetic markers to predict complex quantitative traits, which can greatly improve the capture efficiency of polygenic traits compared to MAS. The main technical procedures include: ① establishing a training population, phenotyping and genotyping of all individuals, estimating the effect value of SNPs by a suitable statistical model, and establishing a GS prediction model between phenotype and genotype; ② based on the individual genotype data in the candidate population, calculating the genome estimated breeding value (GEBV) of each individual using the GS prediction model; ③ screening and selecting individuals at the seedling stage according to the GEBV ranking, inclusion of the phenotypic and genotypic data of selective individuals in the training population to continuously update and optimize the GS model, enhancing the prediction accuracy and efficacy; ④ promoting the integration of forest tree GS with emerging technologies such as early flowering, somatic embryogenesis, gene editing and other technologies, and truly realizing the use of genomic information to guide breeding practices. Genome-wide selection in forest tree breeding is a forest tree breeding strategy with great potential, which can carry out the selection of excellent genotypes at the seedling or even seed stage of forest trees, enhance genetic gain, speed up the breeding process, and promote precise and efficient forest tree breeding.

(6)  RNAi-based pest control technology

RNA interference (RNAi) is a great discovery and has won the Nobel Prize in Physiology or Medicine in 2006. RNAi technology has shown great application prospects in many fields, such as medicine and agriculture. By 2022, nearly 20 new RNAi-based pharmaceutical products have entered the clinical research stage. In the field of agriculture, RNAi could be used to silence key genes in the growth, development or important processes of pests, block the normal growth and reproduction, cause death of pests, thereby reducing the damages from pests. RNAi-based pest control technology is called “the third revolution in the pesticide history”. It is an environment-friendly pest management method because of the high target specificity, non-toxicity, and non-residue. In 2017, the U.S. Environmental Protection Agency (EPA) registered the first commercial planting for RNAi-biased genetically modified maize (MON87411, Bayer). This product has obtained the Agricultural GMOs Safety Certificate (2020) from the Ministry of Agriculture and Rural Affairs in China. In addition, a variety of RNAi-based biopesticides have been submitted to EPA such as BioDirect (Bayer), Ledprona GS2 (GreenLight Biosciences), etc. RNAi-based pest control technology has been studied early from last century but the commercial application process is somehow slow, lacking the relevant technical standards, laws and regulations. Besides, several key core issues need to be solved urgently for the commercial R&D process: ① identify the target genes; ② develop industrial synthesis methods for dsRNA; ③ screen the delivery or sustained-release carriers. China need to solve the above problems as soon as possible so as to promote the commercialization of RNAi-based pest control technology in China, make China highest-ranking in the research on RNAi technology, and seize the international pest control marketplace in the future.

(7)  Agricultural autonomous robot

Agricultural autonomous robot is an intelligent agricultural machinery equipment with perception, decision-making, control and execution functions. As the major branch of robotics, Agricultural Autonomous Robot is a cross- integration field of agricultural machinery, artificial intelligence, robot technology and information engineering, and has become an important trend of modern agriculture development. Currently, the agricultural comprehensive mechanization rate in china has exceeded 70%. Agricultural mechanization liberates labor force, improves labor productivity and resource utilization, and promotes farmers’ income. However, with the acceleration of urbanization process, a large number of rural labors entering cities. Rural areas faced the problem of seasonal and structural shortage of farm labor. Thus, Agricultural autonomous robot will be an important support to solve the problem of “who will farm land and how to farm”. In view of the unstructured and complex agricultural scenes, agricultural autonomous operating robots focus on breaking through the following key theories and technologies: ① the accurate sensing mechanism and sensing technology of information for operating robots, operating environments and operating objects; ② the scene cognition method based on multi-source perception of heterogeneous information, and the autonomous decision- making, planning and control technology based on job flow and machine learning; ③ design and accurate and efficient operation technology of operating device, terminal actuator and manipulator integrated with advanced agronomics; ④ chassis structure design and line control technology in all terrain, multi-occlusion and dynamic agricultural scenes, and map construction, autonomous planning and obstacle avoidance navigation technology based on multi-sensor fusion; ⑤ key technologies of robot group real- time communication, group autonomous cooperation and man-machine integration. Agricultural autonomous robot represents the most advanced agricultural productivity, which can completely liberate agricultural labor force, greatly improve agricultural productivity, resource utilization and output rate, and realize agricultural intelligent production.

(8) Catalytic degradation processes for organic pollutants

Organic pollutants are a group of compounds with diverse composition and structure, which have environmental mobility, bioaccumulation and ecotoxicity. The occurrence of organic pollutants has become an emerging concern in the field of agricultural environment, which affects the quality of farmland soil, and brings challenges to urban and rural domestic wastewater treatment as well as resource utilization of agricultural organic waste. The development of cost-effective and efficient catalytic degradation processes for organic pollutants is a hotspot in scientific research and application frontier. At present, popular catalytic degradation processes for organic pollutants mainly include photocatalytic degradation, persulfate-based heterogeneous catalytic degradation, catalytic ozonation, and electrocatalytic degradation. Although catalytic degradation processes could achieve high removal efficiency for organic pollutants, the interference of coexisting substances limits specific removal of target organic pollutants in practical applications. In addition, the generation of a series of intermediate products during the catalytic degradation of organic pollutants not only affect the catalytic degradation efficiency, but also may pose a threat to the ecosystem. Therefore, improving the mineralization efficiency of organic pollutants, revealing their catalytic degradation pathways and mechanisms, and developing energy-saving and efficient catalytic degradation new technology and related equipment are the key and difficult points that need to be broken through in technical applications.

(9) Feed antibiotic substitution technology and products

The massive and long-term use of antibiotics has not only caused serious ecological environment pollution, but also made some pathogenic microorganisms produce drug resistance, resulting in the emergence of “super bacteria”, which endangers the health of human beings and animals. China has officially banned the use of feed antibiotics since July 1, 2020. From the perspective of the history of “prohibition and resistance” in Europe, after the comprehensive “prohibition and resistance” of feed, the livestock and poultry incidence rate and mortality will increase, and the breeding cost will increase. Developing high-efficiency, environmental friendly, and non-toxic feed antibiotic substitutes to improve the autoimmune disease resistance of livestock and poultry is conducive to promoting the healthy development of China’s aquaculture industry. The alternatives of feed antibiotics that have been studied more include Acidifiers, antimicrobial peptides and plant essential oils. Probiotics, prebiotics, antimicrobial peptides, plant extracts, Chinese herbal medicines, and enzyme preparations have been proved to have good effects on regulating the intestinal micro ecology of livestock and poultry and improving the intestinal health, and have broad prospects in the development of non- antibiotic breeding. Synthetic biology plays an important role in the creation of these products. At present, the third generation biotechnology with synthetic biology as the core has entered a new stage of rapid technological change and vigorous industrial development. The organization for economic cooperation and development (OECD) predicts that by 2030, 35% of chemicals and other industrial products will come from biological manufacturing, which has laid the core position of biological manufacturing industry as a global strategic emerging industry. Under the guidance of synthetic biology, the development of agricultural biological manufacturing technology based on microorganisms, the design of efficient synthetic routes and artificial organisms for feed bioactive molecules, the breakthrough of the limitations of natural biological synthesis, the reshaping of biological feed production mode, the creation of new feed resources and feed additives and the realization of industrialization can effectively solve the problems of shortage of feed raw materials, excessive addition of antibiotics and safety of animal husbandry products in China, It will produce extensive social and economic benefits.

(10) Unmanned intelligent cultivation technology for crops

With the rapid development of modern science and technology as well as the upgrading transformation of agricultural management mode, the unmanned and intelligent crop production will become the main research area of crop production in the future. Countries around the world once relied on investment in economy and science and technology have shifted to investments in the unmanned intelligent crop production. The crop unmanned intelligent cultivation aims at the green, high-quality, high- yield and efficient production of crops, which integrates the modern crop cultivation technologies and new generation of information technologies such as satellite navigation, internet of things, big data, artificial intelligence and so on. In the crop unmanned intelligent cultivation, intelligent machines (equipment) could accurately monitor and diagnose crop growth, and exactly and variably apply of water, fertilizer and drugs, and resulted in the unmanned cultivation and steady growth of crops in whole crop growth. Thus, the unmanned and intelligent crop cultivation will be a major innovation in the crop production with the features of precision, intelligence, automation, high efficiency, safety, reliability and versatility et al. The crop unmanned intelligent cultivation, which is a system engineering technology with deep integration of multi-disciplinary such as crop cultivation, mechanical engineering and information science, focusing on the following core scientific problems: ① the effective approaches and mechanisms of crop unmanned intelligent cultivation that can realize of green, high-quality, high-yield and efficient cooperative production; ② the development and screening of the products suitable for unmanned intelligent cultivation system such as seeds, fertilizers and pesticides; ③ the manufacturing and selection of agricultural machines which can integrated with information technologies and applied to unmanned intelligent cultivation; ④ the research and application of the green, high-quality, high-yield and efficient integrated “cultivation-machinery-information” cultivation technologies. For example, in a rice-wheat rotation system, the green, high-quality, high-yield and efficient synergetic cultivation technologies were integrated with the simplest unmanned intelligency in the whole processes of crop production. The unmanned and intelligent rate of rice- wheat rotation reaches more than 85%, the annual average yield of rice-wheat has stabilized to more than 1 300 kg/667 m2, and the unmanned and intelligent crop cultivation technology achieves large-scale promotion and application, it will promote the unmanned intelligent cultivation in rice- wheat rotation to reach leading level internationally.

(11)  Aquaculture technology of ecological intelligent pond

At present, the aquaculture area in China is about 7 036 thousand hectares, of which freshwater aquaculture accounts for 5 041 thousand hectares (71.6%). In the freshwater aquaculture area, pond aquaculture is the main type of freshwater aquaculture (accounting for 74%). Pond aquaculture occupies a pivotal position and is the basis for stabilizing the supply of aquatic products. The healthy and sustainable development of pond aquaculture involves national food security and urgently requires continuous and steady development. The key problems faced by pond culture include lack of high-quality fry, old ponds for aquaculture and backward supporting technologies. In response to these problems, domestic and foreign researchers have provided high-quality fry for aquaculture, improved the intelligence and precise control technology for water quality, developed efficient purification equipment and emission reduction systems, established full-process information aquaculture management and control system based on the Internet of Things (IoT) to evaluate the intelligence and precise control level for pond aquaculture. The establishment of the ecological, intelligent and industrialized modern pond aquaculture model has promoted the healthy and sustainable development of modern pond aquaculture.

《2.2 Interpretations for three key engineering development fronts》

2.2 Interpretations for three key engineering development fronts

2.2.1 Animal precision gene editing and breeding technology

Animal breeding technology has experienced a leap-forward development from the initial phenotypic value breeding technology to the modern genome editing breeding technology. The traditional method of hybrid improvement method is costly, time-consuming and complicated, and defective genes may also be introduced due to gene linkage, while gene editing technology can precisely modify the target gene, through modifying key functional genes and regulatory sequences related to important animal traits, new animal breeds (lines) with characteristic phenotypes can be obtained in one generation, thereby improving the efficiency of animal breeding. Since its introduction, gene editing technology has developed and updated three generations: zinc-finger nucleases (ZFNs) , transcription activator-like effector nucleases (TALENs) and Clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9). Gene editing technology has achieved a major breakthrough in technology from the random targeting and inactivation of the target gene to the accurate replacement of a single base of the gene. In recent years, gene editing technology has become an important method of animal breeding, and has been fully developed and applied in the field of animal breeding. A batch of new materials and new lines with high-yield, high-quality, high-reproduction and disease-resistant breeding have been precisely created through gene editing technology, such as gene edited swines for resistance to porcine reproductive and respiratory syndrome, gene edited beef cattle with myostatin knockout, and tuberculosis-resistant dairy cows. With the continuous progress of multi-omics sequencing technology, various phenotype and genotype databases are constantly enriched, important functional genes and regulatory sequences related to various traits are continuously mined, and the efficiency, accuracy and safety of gene editing technology are constantly improving. Animal precision gene editing and breeding technology will gradually develop in the direction of engineering and large-scale, and will be widely used in the field of animal breeding in the future, providing important technical support for the cultivation of new animal species.

Animal Precision gene editing and breeding technology refers to a method that uses CRISPR-Cas9 and other genome editing tools to precisely modify the functional genes and regulatory sequences related to important animal traits, and directionally breed new animal breeds (lines) with specific phenotypes. Since its introduction, gene editing technology has developed and updated three generations: ZFNs, TALENs, and CRISPR-Cas9. From the first introduction of mutations in the target gene by shearing and breaking, to now, the precise replacement of a single base of the gene, as well as the precise insertion or replacement of large fragments, can be realized, which has achieved a major breakthrough in technology. With the continuous progress of multi-omics sequencing technology, various phenotype and genotype databases are constantly enriched, important functional genes and regulatory sequences related to various traits are continuously mined, and the efficiency, accuracy and safety of gene editing technology are constantly improving. Animal precision gene editing and breeding technology will gradually develop in the direction of engineering and large-scale, and will be widely used in the field of animal breeding in the future, providing important technical support for the cultivation of new animal species.

Gene editing technology has become an important method of animal breeding, and has been fully developed and applied in the field of animal breeding. A batch of new materials and new lines with high-yield, high-quality, high-reproduction and disease-resistant breeding have been precisely created through gene editing technology, such as gene edited swines for resistance to porcine reproductive and respiratory syndrome, gene edited beef cattle with myostatin knockout, and tuberculosis-resistant dairy cows. The improvement of livestock meat yield and quality, fluff yield and quality and other production traits is crucial to the efficient and sustainable development of animal husbandry. The precise modification of key genes through gene editing technology has become an effective tool for improving important economic traits of livestock. Using gene editing technology to mutate BMP15 and GDF9 genes has significantly improved the reproductive efficiency of cattle and sheep, and created breeding materials for high-breeding animals. By precisely modifying the key gene MSTN, which regulates muscle production, the gene-edited swines, beef cattle and sheep obtained showed a double-muscle phenotype, and the meat production rate was significantly improved. The exogenous Fat1 gene was successfully inserted into the swine genome by gene editing technology, which significantly increased the content of n-3 polyunsaturated fatty acids in pork and improved the flavor of pork. Precise mutation of the FGF5 gene improves wool quality in Alpine Merino sheep. New breeding materials for specific pathogen resistance can be developed through precise modification of the receptor gene of pathogen entry into cells or precise insertion of resistance gene into the safety locus of animal genome. Swines with resistance to African swine fever were generated using ZFNs. CSFV-resistant pigs were obtained by gene editing technology. CRISPR-Cas9 knockout of the CD163 receptor to produce PRRS-resistant swines. Aiming at the pathogens that cause diseases such as porcine pseudorabies, porcine reproductive and respiratory syndrome, and multisystem wasting syndrome of weaned piglets, the CRISPR-Cas9 system was used to modify a number of key genes in the host, and the corresponding disease-resistant pig breeds were bred. By precisely integrating the Ipr1 and NRAMP1 genes, a tuberculosis-resistant dairy cow was created. The chicken subtype B leukemia-resistant chicken cell line was established by editing the chicken subtype B tumor virus gene (TVB) using CRISPR-Cas9 technology. The above studies show that animal precision gene editing and breeding technology has important application value in the field of new animal breed breeding.

Gene editing technology solves the problem of long animal breeding cycle, accelerates the breeding process and reduces breeding costs. The precise gene editing technology based on CRISPR-Cas9 and other systems can be applied to the gene editing in various organisms and cells, and the targeted modification is more accurate, the action time is shorter, and the operation is simpler. The modified genes can also achieve germline inheritance, showing great potential and advantages in the field of animal production. However, the current gene editing technology is still in the initial stage of research and application, and key issues need to be solved, such as its high off-target efficiency and the need for further improvement of editing efficiency .In the future development, the continuously improved and mature gene editing technology in practice will surely become a powerful auxiliary tool in the field of animal husbandry research and production, and ultimately promote the high-quality development of animal husbandry.

The countries and institutions with the greatest output of core patents on “animal precision gene editing breeding technology” are shown in Tables 2.2.1 and 2.2.2, respectively. China has the most core patents, with 3 860 patents, accounting for 84.91%; the second is the USA, with 187 patents, accounting for 4.11%; the third is South Korea, with 168 patents, accounting for 3.7%. The percentage of citations of China is 56.63%, far exceeding the second- ranked USA, but the citations per patent is only 1.51, far behind France, Canada, and the USA. In terms of cooperation between countries in this front, there is cooperation between the USA, the UK, the Netherlands, Canada, and Australia; there is no cooperation among

《Table 2.2.1》

Table 2.2.1 Countries with the greatest output of core patents on “animal precision gene editing breeding technology”

No. Country Published patents Percentage of published patents/% Citations Percentage of citations/% Citations
per patent
1 China 3 860 84.91 5 830 56.63 1.51
2 USA 187 4.11 2 854 27.72 15.26
3 South Korea 168 3.7 155 1.51 0.92
4 Russia 88 1.94 55 0.53 0.62
5 Japan 69 1.52 190 1.85 2.75
6 France 20 0.44 664 6.45 33.2
7 UK 20 0.44 480 4.66 24
8 Australia 18 0.4 98 0.95 5.44
9 Canada 13 0.29 382 3.71 29.38
10 Netherlands 12 0.26 52 0.51 4.33

《Table 2.2.2》

Table 2.2.2 Institutions with the greatest output of core patents on “animal precision gene editing breeding technology”

No. Institution Published patents Percentage of published patents/% Citations Percentage of citations/% Citations
per patent
1 Chinese Academy of Agricultural Sciences 237 5.21 336 3.26 1.42
2  China Agricultural University 146 3.21 448 4.35 3.07
3  Northwest A&F University 124 2.73 197 1.91 1.59
4  South China Agricultural University 123 2.71 222 2.16 1.8
5 Yangzhou University 96 2.11 114 1.11 1.19
6 Huazhong Agricultural University 51 1.12 98 0.95 1.92
7  Shandong Agricultural University 45 0.99 72 0.7 1.6
8  Sichuan Agricultural University 43 0.95 94 0.91 2.19
9  Guizhou University 36 0.79 37 0.36 1.03
10  Nanjing Agricultural University 33 0.73 54 0.52 1.64

other countries (Figure 2.2.1). The institution that produced the most core patent was the Chinese Academy of Agricultural Sciences, with a total of 237 patents, followed by China Agricultural University, and Northwest Agriculture and Forestry University. The top three institutions in terms of citation ratio are China Agricultural University (4.35%), Chinese Academy of Agricultural Sciences (3.26%), and South China Agricultural University (2.16%). The institution with the highest citations on average is China Agricultural University with 3. 07 times. There is no cooperation between the different institutions. Figure 2.2.2 shows the roadmap of this front.

2.2.2 Application of gene editing technology in horticultural crops

The gene editing technology of horticultural crops changes the original gene sequence by knocking out a few base pairs or a DNA sequence. It has been developed and updated for three generations since its inception: ZFNs editing technology, TALENs editing technology and CRISPR-Cas9 editing technology. Among them, the CRISPR-Cas9 editing system has become the current horticultural crop due to its high editing efficiency, simple operation and low cost. Gene editing technology now can achieve precise replacement of a single base of a gene, as well as precise insertion or replacement of large fragments. A major breakthrough has been achieved in genome analysis of important horticultural crops such as tomato, watermelon, cucumber, Chinese cabbage, citrus, apple, kiwi, Chinese rose, and Chinese lotus. Some important achievements have been made in gene mining of important traits such as development, stress resistance, yield and quality. With the continuous improvement of the efficiency, accuracy and safety of gene editing technology, the gene editing technology of horticultural crops will gradually develop towards engineering and scale, and will be widely used in the field of horticultural crop production in the future.

《Figure 2.2.1》

Figure 2.2.1 Cooperation network among major countries in the engineering development front of “animal precision gene editing breeding technology”

《Figure 2.2.2》

Figure 2.2.2 Roadmap of the engineering development front of “animal precision gene editing breeding technology”

Gene editing technology has become an important method for the study of important gene functions of horticultural crops, and has been greatly developed and applied in the field of horticultural crop research. The CRISPR-Cas9 system was first applied in tomato in 2014, researchers successfully knocked out the Argonaute7 gene to produce a wiry phenotype in tomato leaves. With the development of CRISPR-Cas9 technology, it has been applied in more and more horticultural crops, including cucumbers, strawberries, bananas, grapes, apples, watermelons and kiwifruit, in the study of plant growth and development, product quality, biotic and abiotic stresses, and crop domestication. For example, using CRISPR-Cas9 technology to knock out ARF8 (Auxin Response Factor 8) in strawberry produces plants with faster growth of seedlings; tomato SlCLV3 promoter mutation results in more locules and larger fruit; tomato yellow leaf curl virus resistance more stronger than wild-type tomato; it has become possible to accelerate the domestication process of various wild plants by using the known agronomic traits of the model plants. In addition, the availability and purpose of gene editing, regenerated genetic material without exogenous DNA and the opening of regulatory regulations for genetically improved crops are promoting the research and application of gene editing in horticultural crops.

Horticultural crop gene editing technology not only plays a great role in promoting scientific research, but also in commercial applications. In 2021, a tomato enriched γ-aminobutyric acid, five times more than ordinary tomatoes, with CRISPR technology has been for sale in Japan, which is a very important milestone for CRISPR technology to be used in horticultural crop breeding. However, most horticultural crops have not yet established a successful CRISPR gene editing system, the transformation rate is low, or gene editing plants cannot be obtained. Therefore, it is still a challenge to break through the CRISPR gene editing system of different horticultural crops.

The countries and institutions with the greatest output of core patents on “application of gene editing technology in horticultural crops” are shown in Tables 2.2.3 and 2.2.4, respectively. In terms of quantity, the number is generally low. China has the most disclosed core patents, with 38 patents, accounting for 76.00%; the second is South Korea, with 4 patents, accounting for 8.00%; the third is Japan, with 3 patents, accounting for 6.00%. China patents were cited 117 times, accounting for 96.69%, far exceeding the second- ranked South Korea. There is no cooperation between countries. The institution with the most core patent output is Jiangsu Academy of Agricultural Sciences, with a total of 6. Beijing Academy of Agricultural and Forestry Sciences and Institute of Horticulture Corp Xinjiang Academy of Agricultural Sciences ranked second and third respectively. The top three institutions in terms of citation ratio are Jiangsu Academy of Agricultural Sciences (29.75%), Zhejiang Academy of Agricultural Sciences (19.01%), and Institute of Horticulture Corp Xinjiang Academy of Agricultural Sciences (14.05%). The institution with the highest average number of citations is Shanghai Institutes for Biological Sciences, CAS, whose citations per patent is 14. There is no cooperation between the different agencies. Figure 2.2.3 Shows the roadmap of this front.

《Table 2.2.3》

Table 2.2.3 Countries with the greatest output of core patents on “application of gene editing technology in horticultural crops”

No. Country Published patents Percentage of published patents/% Citations Percentage of citations/% Citations
per patent
1 China 38 76 117 96.69 3.08
2 South Korea 4 8 0 0 0
3 Japan 3 6 1 0.83 0.33
4 Germany 1 2 2 1.65 2
5 USA 1 2 1 0.83 1
6 Switzerland 1 2 0 0 0
7 Netherlands 1 2 0 0 0
8 Russia 1 2 0 0 0

《Table 2.2.4》

Table 2.2.4 Institutions with the greatest output of core patents on “application of gene editing technology in horticultural crops”

No. Institution Published patents Percentage of published patents/% Citations Percentage of citations/% Citations
per patent
1  Jiangsu Academy of Agricultural Sciences 6 12 36 29.75 6
2  Beijing Academy of Agricultural and Forestry Sciences 4 8 2 1.65 0.5
3  Institute of Horticulture Corp Xinjiang Academy of Agricultural Sciences 3 6 17 14.05 5.67
4 Zhejiang Academy of Agricultural Sciences 2 4 23 19.01 11.5
5  Northwest A&F University 2 4 6 4.96 3
6  Zhejiang University 2 4 2 1.65 1
7  Chinese Academy of Agricultural Sciences 2 4 1 0.83 0.5
8  Nanjing Agricultural University 2 4 0 0 0
9  Shanghai Institutes for Biological Sciences, CAS 1 2 14 11.57 14
10  South China Agricultural University 1 2 6 4.96 6

《Figure 2.2.3》

Figure 2.2.3 Roadmap of the engineering development front of “application of gene editing technology in horticultural crops”

2.2.3 Genome-wide selection in forest tree breeding

Most of the important traits of forest trees are complex quantitative traits and high genetic heterozygosity. Conventional breeding techniques are difficult to efficiently and rapidly cultivate improved tree varieties. Molecular marker-assisted selection cannot capture micro-effective loci, the resolution of genetic mapping is low, and the results of quantitative trait genetic mapping cannot be mutually verified, resulting in slow progress in forest tree breeding, and the growth and production efficiency of artificial forests are far from meeting economic and ecological needs. In view of the shortcomings of phenotypic selection and MAS breeding strategies, Meuwissen et al. proposed genome selection (GS), also known as genome-wide selection. GS is a genome-wide marker-assisted selection method, which mainly uses the high-density genetic marker information covering the whole genome to estimate the individual GEBV, and selects excellent genotypes based on GEBV ranking. GS is an early selection technology established by combining the research results of functional genomics and single nucleotide polymorphism (SNP) chip technology. Based on the genotype of tree seeds or seedlings, it can predict the forest tree phenotypic traits, identify and screen individuals with excellent genes accurately. In order to the final establishment of an intelligent-design- breeding-system for forest trees with GS as technical core, we should: investigate the realization path of GS technology in tree parent selection, hybrid combination prediction and early breeding of excellent progeny; accurately select new forest trees with polygenes and excellent phenotypes, and scientifically control the breeding process; promote the cross- integration of multi-technology and disciplines including tree GS, gene editing, quantitative trait locus (QTL), genome wide association study (GWAS) and phenomics, accelerate the mining of key genes for complex tree traits.

The advantages of GS mainly include the following aspects. ① Breeding speed is faster. Compared with phenotypic selection, early individual selection based on GEBV can effectively reduce the generation interval. ② The intensity of selection is greater. The cost of high-throughput genotyping is lower than that of phenotyping, and more candidates can be evaluated based on genotypes. Increasing the size of the breeding population is particularly important for plant breeding with large progeny populations. ③ The prediction accuracy is higher. Molecular marker-based GEBV is more accurate than EBV estimation based solely on phenotype and pedigree, and can greatly improve the capture efficiency of minor-effective loci, thereby improving the accuracy and genetic standard deviation of complex quantitative trait prediction. ④ It is more conducive to maintaining genetic diversity. By effectively integrating the genetic populations of different hybridized combinations and breeding programs, conducting genetic evaluation and selection in large-scale population is conducive to the preservation of abundant genetic resources. ⑤ It saves time and labor costs. The asexual propagation and progeny test can be directly performed on preselected individuals instead of all individuals. Overall, GS is a tree breeding strategy with great potential and can significantly improve the genetic improvement accuracy of target traits and reduce operating costs. GS is especially suitable for tree species with long breeding cycle, complex genetic target traits, and difficult phenotype measurement with high cost.

GS is a key technology and research hotspot in animal and crop genetics and breeding, and important progress has been made in the genetic improvement of some animals and plants. However, forest tree GS breeding is relatively backward and is still in its infancy. Since 2010, nearly 80 studies in the field of forest GS have been published, most of which focus on eucalyptus, spruce, loblolly pine, Douglas fir and other timber species. The scope of these studies involves GS prediction models that are mainly built for traits such as tree growth, wood properties, and resistance to pests and diseases, and its influencing factors exploration, including the size and composition of the training population, the heritability of traits, the density and number of markers, and the comparison and optimization of model algorithm. The application examples of GS breeding in forest trees and across multiple generations are rarely reported. The reasons for the lag of forest trees GS breeding include: the genetic resources collection of most tree species and the evaluation of germplasm are not in-depth, and there is a lack of established test plantation for rapidly establishing large- scale training populations; weak genetic research foundation, backward high-throughput phenotyping technology, and lack of standardized low-cost genotyping technology; lack of genotype × age/environment interaction model and analysis tools for tree characteristics. The low quality of tree reference genome and molecular markers that can reduce the prediction accuracy of the GS model.

In order to overcome the difficulties and promote the development of forest tree GS breeding, we should carry out research in the following directions. ① Establish a unified genotype and phenotype acquisition platforms.

Collect genotype data in a high-throughput, low-cost, and standardized manner by using high-density SNP chips and other technologies. Obtain non-destructive, large- scale, multidimensional phenotype data by using high-throughput phenotype determination platform. ② Optimize and develop forest tree GS model algorithm. According to the characteristics of forest trees, combine with multi- omics, -environment and -year data, develop genotype × environment/age interaction models by using machine learning and deep learning to realize the optimization and improvement of GS algorithm, and continuously expand and update the training population, to improve the universality and long-term efficacy of the GS model of forest trees in unknown climate environment. ③ Integrate and analyze the large-scale data of thousands samples spanning multiple populations, obtain stable and reliable molecular markers by integrating GS and meta-QTL, and develop SNP chip products for specific trait breeding. ④ Use programming languages, such as C++, Julia, and R to develop analysis tools for the characteristics of forest trees (perennial, outcrossing, and large sample size). It is necessary to develop analysis software that can quickly process massive molecular marker data (>100 k) for the low analysis speed of the most commonly used R software. ⑤ Carry out tree pan-genome research and establish high-quality reference genomes for conifers and polyploid species which difficult to obtain high-quality genomes to improve the GS model prediction accuracy. In addition, the demand of population sample and cost for forest tree GS is large and high, the collaboration and sharing of data and population materials between research institutions and breeding companies is important, to ensure long-term stable investment and research.

The front of “genome-wide selection in forest tree breeding” includes two core patents (Tables 2.2.5 and 2.2.6), which have been cited seven times, all of which are Chinese patents and both from South China Agricultural University. The inventor is a forest tree genetics and breeding research team led by LIN Yuanzhen. The patent “a method based on genome selection of traits is forest breeding for multiple traits polymerization”, combining GS technology and multi-trait polymeric breeding technology, establishes a new method system of multi- trait polymeric breeding of forest trees, realizes multi-trait oriented and precise breeding, and significantly shortens the breeding cycle of forest trees. The patent “forest genome selection method based on individual genetic competition and environment space analysis and application” fully considering the differences in genetic material and planting environment background. The method markedly improves the accuracy of the forest tree GS by constructing the genomic relationship matrix by using SNP markers, fitting individual genetic competition effect by the US structure, and fitting environment space effect by AR1 structure. Figure 2.2.4 Shows the roadmap of this front.

《Table 2.2.5》

Table 2.2.5 Countries with the greatest output of core patents in the engineering development front on “genome-wide selection in forest tree breeding”

No. Country Published patents Percentage of published patents/% Citations Percentage of citations/% Citations
per patent
1 China 2 100 7 100 3.5

《Table 2.2.6》

Table 2.2.6 Institutions with the greatest output of core patents in the engineering development front on “genome-wide selection in forest tree breeding”

No. Institution Published patents Percentage of published patents/% Citations Percentage of citations/% Citations
per patent
1  South China Agricultural University 2 100 7 100 3.5

《Figure 2.2.4》

Figure 2.2.4 Roadmap of the engineering development front of “genome-wide selection in forest tree breeding”

 

 

Participants of the Field Group

Leader

ZHANG Fusuo

Experts

CAO Guangqiao, CHEN Yuanquan, DAI Jingrui, HAN Dandan, HAN Jianyong, HAN Jun, HAO Zhihui, KANG Shaozhong,

LI Defa, LI Daoliang, LI Hu, LIU Shaojun, LIU Pinghuang, LI Tianlai, LIU Xiaona, LUO Xiwen, DONG Chaobin, PU Juan,

QI Mingfang, SHEN Jianbo, SHEN Jianzhong, WANG Guirong, WANG Hongliang, WANG Junjun, WEI Haiyan, WU Kongming,

WU Pute, WU Zhenlong, ZHANG Fusuo, ZHANG Hongcheng, ZHANG Shougong, ZHANG Xiaolan, ZHANG Yong,

ZHAO Chunjiang, ZANG Ying, ZHOU Lei, ZHOU Yi, ZHU Qichao, ZHU Wangsheng, ZHU Zuofeng

Research Group

CHU Xiaoyi, GAO Xiangrong, LI Hongjun, LI Yunzhou, LIU Dejun, LIU Jun, SHI Lijuan, SUN Huijun, TANG Chenchen,

WANG Guirong, YAO Yinkun, ZHANG Jinning, ZHAO Jie, ZHOU Liying

Report Writers

DONG Chaobin, GAO Hui, HAN Dandan, Han Jianyong, HU Lian, JIN Chengqian, LI Shaofeng, LI Si, LIU Jun,

LIU Xiaona, LUO Xiwen, QIAN Yongqiang, QIAN Zhenjie, QUAN Fusheng, SUN Kangtai, Sun Shikun, TIAN Jing,

WANG Junhui, WANG Junjun, WU Zhenlong, XING Zhipeng, YANG Qing, ZHAO Chunjiang, ZHANG Yong,

ZHANG Miaomiao, ZHOU Huanbin, ZHOU Yi, ZHU Qichao