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Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 268-278 doi: 10.15302/J-FASE-2017164

摘要： Genomic selection is becoming increasingly important in animal and plant breeding, and is attracting greater attention for human disease risk prediction. This review covers the most commonly used statistical methods and some extensions of them, i.e., ridge regression and genomic best linear unbiased prediction, Bayesian alphabet, and least absolute shrinkage and selection operator. Then it discusses the measurement of the performance of genomic selection and factors affecting the prediction of performance. Among the measurements of prediction performance, the most important and commonly used measurement is prediction accuracy. In simulation studies where true breeding values are available, accuracy of genomic estimated breeding value can be calculated directly. In real or industrial data studies, either training-testing approach or -fold cross-validation is commonly employed to validate methods. Factors influencing the accuracy of genomic selection include linkage disequilibrium between markers and quantitative trait loci, genetic architecture of the trait, and size and composition of the training population. Genomic selection has been implemented in the breeding programs of dairy cattle, beef cattle, pigs and poultry. Genomic selection in other species has also been intensively researched, and is likely to be implemented in the near future.

关键词： genomic estimated breeding value     genomic selection     linkage disequilibrium     statistical methods    

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Genetic study and molecular breeding for high phosphorus use efficiency in maize

null

《农业科学与工程前沿（英文）》 2019年 第6卷 第4期   页码 366-379 doi: 10.15302/J-FASE-2019278

摘要：

Phosphorus is the second most important macronutrient after nitrogen and it has many vital functions in the life of plants. Most soils have a low available P content, which has become a key limiting factor for increasing crop production. Also, low P use efficiency (PUE) of crops in conjunction with excessive application of P fertilizers has resulted in serious environmental problems. Thus, dissecting the genetic architecture of crop PUE, mining related quantitative trait loci (QTL) and using molecular breeding methods to improve high PUE germplasm are of great significance and serve as an efficient approach for the development of sustainable agriculture. In this review, molecular and phenotypic characteristics of maize inbred lines with high PUE, related QTL and genes as well as low-P responses are summarized. Based on this, a breeding strategy applying genomic selection as the core, and integrating the existing genetic information and molecular breeding techniques is proposed for breeding high PUE maize inbred lines and hybrids.

关键词： maize     phosphorus use efficiency     quantitative trait loci     genetic study     molecular breeding     genomic selection    

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GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Horticultural crops are a major source of high value nutritious food, and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses, and to deliver novel, premium products to consumers. However, grower confidence in the performance of new germplasm, particularly across environmental variability, is important for commercial adoption and germplasm-environment matching to optimize production.

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Comments on this special issue on “Wheat Genetics and Breeding”

Zhonghu HE, Xu LLU

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 309-309 doi: 10.15302/J-FASE-2019264

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GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE

《农业科学与工程前沿（英文）》   页码 353-355 doi: 10.15302/J-FASE-2021387

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Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

《医学前沿（英文）》 doi: 10.1007/s11684-023-1008-8

摘要： Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer–promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.

关键词： 3D genome     cancer     TADs     loop     gene regulation    

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Highlights of special issue on “Wheat Genetics and Breeding”

Zhonghu HE, Zhendong ZHAO, Shunhe CHENG

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 207-209 doi: 10.15302/J-FASE-2019263

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Genomics and genetic breeding in aquatic animals: progress and prospects

Wenteng XU, Songlin CHEN

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 305-318 doi: 10.15302/J-FASE-2017154

摘要： Genomics focuses on dissection of genome structure and function to provide a molecular basis for understanding the genetic background. In a pivotal step, the expense of whole genome sequencing has been largely eliminated by the rapid updating of sequencing technology, leading to increasing numbers of decoded genomes of aquatic organisms, driving the aquaculture industry into the genomic era. Multiple aquatic areas have been influenced by these findings, such as accelerated generation shift in the seed industry and the process of breeding improved lines. In this article, we have summarized the latest domestic and international progress of aquatic animals in nine aspects, including WGS and fine mapping, construction of high density genetic/physical maps, trait-related marker/genes screening, as well as sex control, genome editing, and other molecular breeding technologies. Finally, the existing problems in this field have been discussed and five future counter measures have been proposed accordingly.

关键词： aquaculture     genomics     genetic breeding     progress    

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Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

《农业科学与工程前沿（英文）》 2014年 第1卷 第4期   页码 307-313 doi: 10.15302/J-FASE-2014039

摘要： Hair provides thermal regulation for mammals and protects the skin from wounds, bites and ultraviolet (UV) radiation, and is important in adaptation to volatile environments. Pigs in nature are divided into hairy and hairless, which provide a good model for deciphering the molecular mechanisms of hairlessness. We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data, with the aim to better understand the genetic basis for the hairless phenotype in pigs. A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population ( ) values. Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes (SSC) 1, 3, 7, 8, 10, 11 and 16, and the biological functions of two notable genes, and were revealed. When Mexican hairless pigs were contrasted with hairypigs, strong signatures were detected on SSC1 and SSC10, which harbor two functionally plausible genes, and . KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway, MAPK signaling pathway and the tight junction pathways. All of these pathways may be important in local adaptability of hairless pigs. The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time. and are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs, respectively. , , and as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs. These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.

关键词： hairlessness     pig     selective sweeping    

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Wheat research and breeding in the new era of a high-quality reference genome

Rudi APPELS

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 225-232 doi: 10.15302/J-FASE-2019265

摘要：

The publications of the International Wheat Genome Sequencing Consortium (IWGSC) released in August 2018 are reviewed and placed into the context of developments arising from the availability of the high-quality wheat genome assembly.

关键词： assembly technology     molecular markers     polyploidy     transcript networks     wheat genome    

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水产育种生物技术发展战略研究

陈松林,徐文腾,卢昇,胡炜,王德寿,胡晓丽,周茜,刘清华,赵紫霞,覃钦博,王师,刘洋,崔忠凯

《中国工程科学》 2023年 第25卷 第4期   页码 214-226 doi: 10.15302/J-SSCAE-2023.07.023

摘要： Evaluation of the 2b-RAD method for genomic selection in scallop breeding [J]‍.Prediction of total genetic value using genome-wide dense marker maps [J]‍.Evaluation of the 2b-RAD method for genomic selection in scallop breeding [J]‍.Predictive ability of genomic selection models for breeding value estimation on growth traits of PacificPrediction of genomic breeding values based on pre‑selected SNPs using ssGBLUP, WssGBLUP and BayesB for

关键词： 生物技术；水产育种技术；传统育种技术；分子育种技术；智能育种技术    

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

《医学前沿（英文）》   页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

null

《医学前沿（英文）》 2018年 第12卷 第3期   页码 280-288 doi: 10.1007/s11684-017-0580-1

摘要：

Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas. We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls (CNCs) and paired LUSCs of The Cancer Genome Atlas (TCGA) dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C:G→T:A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD (18.62%), MUC4 (8.79%), and RBMX (7.11%). CNC variations in CTAGE5 and USP17L7 were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the development of LUSC.

关键词： lung cancer     counterpart normal control     genomic variations    

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Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells

null

《医学前沿（英文）》 2015年 第9卷 第1期   页码 57-62 doi: 10.1007/s11684-015-0389-8

摘要：

The existence of cancer stem cells, stem-like cancer cells (SLCCs), or tumor-initiating cells is considered as the cause of tumor formation and recurrence, indicating the importance of studying novel therapy that targets SLCCs. The origin of SLCCs is controversial because of two competing hypotheses: SLCCs are either transformed from tissue adult stem cells or dedifferentiated from transformed progenitor cells. Our previous research demonstrates that SLCCs are inducible by increasing genomic instability in cancer cells. In this study, to block the emergence of SLCCs, aminoethyl isothiourea (AET), a compound that clears free radicals and is used to protect patients from radioactive exposure, was used as an agent that maintains genomic stability in combination with mitomycin C (MMC), a commonly used chemotherapeutic drug that damages DNA. Using a rabbit tumor model with VX2 hepatic carcinoma, we found that MMC alone increased lung metastases and disadvantaged survival outcome, but the combination of MMC and AET reversed this effect and even prolonged overall survival. Moreover, in a VX2 xenograft model by immunocompromised mice, MMC alone enriched tumor-initiating cells, but the administration of MMC in combination with AET eliminated tumor cells effectively. Furthermore, MMC alone enhanced genomic instability, but MMC combined with AET attenuated the extent of genomic instability in primary VX2 tumor tissue. Taken together, our data suggest that the genomic protector AET can inhibit the induction of SLCCs, and this combination treatment by AET and cytotoxic agents should be considered as a promising strategy for future clinical evaluation.

关键词： rabbit VX2 liver tumor     mitomycin C     AET     stem-like cancer cells     genomic instability    

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Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic

《医学前沿（英文）》 doi: 10.1007/s11684-023-1050-6

摘要： Pancreatic cancer, notorious for its late diagnosis and aggressive progression, poses a substantial challenge owing to scarce treatment alternatives. This review endeavors to furnish a holistic insight into pancreatic cancer, encompassing its epidemiology, genomic characterization, risk factors, diagnosis, therapeutic strategies, and treatment resistance mechanisms. We delve into identifying risk factors, including genetic predisposition and environmental exposures, and explore recent research advancements in precursor lesions and molecular subtypes of pancreatic cancer. Additionally, we highlight the development and application of multi-omics approaches in pancreatic cancer research and discuss the latest combinations of pancreatic cancer biomarkers and their efficacy. We also dissect the primary mechanisms underlying treatment resistance in this malignancy, illustrating the latest therapeutic options and advancements in the field. Conclusively, we accentuate the urgent demand for more extensive research to enhance the prognosis for pancreatic cancer patients.

关键词： pancreatic cancer     cancer screening     single cell     molecular alterations     precancerous lesion     therapy resistance    

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标题 作者 时间 类型 操作

Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

期刊论文

Genetic study and molecular breeding for high phosphorus use efficiency in maize

null

期刊论文

GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

期刊论文

Comments on this special issue on “Wheat Genetics and Breeding”

Zhonghu HE, Xu LLU

期刊论文

GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE

期刊论文

Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

期刊论文

Highlights of special issue on “Wheat Genetics and Breeding”

Zhonghu HE, Zhendong ZHAO, Shunhe CHENG

期刊论文

Genomics and genetic breeding in aquatic animals: progress and prospects

Wenteng XU, Songlin CHEN

期刊论文

Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

期刊论文

Wheat research and breeding in the new era of a high-quality reference genome

Rudi APPELS

期刊论文

水产育种生物技术发展战略研究

陈松林,徐文腾,卢昇,胡炜,王德寿,胡晓丽,周茜,刘清华,赵紫霞,覃钦博,王师,刘洋,崔忠凯

期刊论文

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

期刊论文

Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

null

期刊论文

Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells

null

期刊论文

Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic

期刊论文