《中国工程科学》 >> 2023年 第25卷 第4期 doi: 10.15302/J-SSCAE-2023.04.015
作物表型组大数据技术及装备发展研究
1. 北京市农林科学院信息技术研究中心,北京 100097;
2. 国家农业信息化工程技术研究中心,北京 100097;
3. 数字植物北京市重点实验室,北京 100097
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摘要
利用集成自动化平台装备和信息化技术手段,获取多尺度、多生境、多源异构的作物表型组大数据,将极大地促进作物功能基因组学、数字育种、智慧栽培的研究进程。本文分析了作物表型组大数据技术及装备的应用需求、产业发展形势,从物理、传输、数据、知识、应用5 个层面详细梳理了相应研发现状;从作物表型组大数据高通量获取、作物表型组大数据智能解析技术两方面着手,剖析了我国相关技术、装备、产业应用方面的问题和态势。研究建议,从底层芯片层面突破作物表型传感器关键技术,在可控开源的基础上形成自主化的表型解析技术体系,加强作物表型组大数据技术及装备标准体系建设,提出基因 – 表型 – 环境多维大数据驱动的数字育种和智慧栽培创新模式,建设作物表型组大数据技术及装备人才队伍和协作网络。
参考文献
[ 1 ]
赵春江 . 植物表型组学大数据及其研究进展 [J]. 农业大数据学报 , 2019 , 1 2 : 5 ‒ 18 .
Zhao C J . Big data of plant phenomics and its research progress [J]. Journal of Agricultural Big Data , 2019 , 1 2 : 5 ‒ 18 .
[ 2 ] Ninomiya S, Baret F, Cheng Z M. Plant phenomics: Emerging transdisciplinary science [J]. Plant Phenomics, 2019, 2019: 2765120.
[ 3 ] Araus J L, E Cairns J. Field high-throughput phenotyping: The new crop breeding frontier [J]. Trends in Plant Science, 2014, 19(1): 52‒61.
[ 4 ]
周济 , Tardieu F , Pridmore T , 等 . 植物表型组学: 发展、现状与挑战 [J]. 南京农业大学学报 , 2018 , 41 4 : 580 ‒ 588 .
Zhou J , Tardieu F , Pridmore T , al e t . Plant phenomics: History, present status and challenges [J]. Journal of Nanjing Agricultural University , 2018 , 41 4 : 580 ‒ 588 .
[ 5 ] Zhao C, Zhang Y, Du J, al et. Crop phenomics: Current status and perspectives [J]. Frontiers in Plant Science, 2019, 10: 714.
[ 6 ] Yang W N, Feng H, Zhang X H, al et. Crop phenomics and high-throughput phenotyping: Past decades, current challenges, and future perspectives [J]. Molecular Plant, 2020, 13(2): 187‒214.
[ 7 ] Jin X, Zarco-Tejada P, Schmidhalter U, al et. High-throughput estimation of crop traits: A review of ground and aerial phenotyping platforms [J]. IEEE Geoscience and Remote Sensing Magazine, 2020, 9(1): 200‒231.
[ 8 ] Pieruschka R, Schurr U. Plant phenotyping: Past, present, and future [J]. Plant Phenomics, 2019, 2019: 7507131.
[ 9 ]
胡伟娟 , 傅向东 , 陈凡 , 等 . 新一代植物表型组学的发展之路 [J]. 植物学报 , 2019 , 54 5 : 558 ‒ 568 .
Hu W J , Fu X D , Chen F , al e t . A path to next generation of plant phenomics [J]. Chinese Bulletin of Botany , 2019 , 54 5 : 558 ‒ 568 .
[10] Tao H, Xu S, Tian Y, al et. Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives [J]. Plant Communications, 2022, 3(6): 100344.
[11] Watson A, Ghosh S, Williams M J, al et. Speed breeding is a powerful tool to accelerate crop research and breeding [J]. Nature Plants, 2018, 4(1): 23‒29.
[12] Watt M, Fiorani F, Usadel B, al et. Phenotyping: New windows into the plant for breeders [J]. Annual Review of Plant Biology, 2020, 71: 689‒712.
[13]
王晓鸣 , 邱丽娟 , 景蕊莲 , 等 . 作物种质资源表型性状鉴定评价: 现状与趋势 [J]. 植物遗传资源学报 , 2022 , 23 1 : 12 ‒ 20 .
Wang X M , Qiu L J , Jing R L , al e t . Evaluation on phenotypic traits of crop germplasm: Status and development [J]. Journal of Plant Genetic Resources , 2022 , 23 1 : 12 ‒ 20 .
[14]
全国人民代表大会常务委员会专题调研组 . 关于加强种质资源保护和育种创新情况的调研报告 [ROL]. 2021-10-21 [ 2023-04-15 ]. http:www.npc.gov.cnnpcc30834202110b05ec4244ddb4fabb3eb560c5452258d.shtml .
Standing Committee of the National People´s Congress Special Research Group . Research report on strengthening the conservation of germplasm resources and breeding innovation [ROL]. 2021-10-21 [ 2023-04-15 ]. http:www.npc.gov.cnnpcc30834202110b05ec4244ddb4fabb3eb560c5452258d.shtml .
链接1
[15] Song P, Wang J L, Guo X Y, al et. High-throughput phenotyping: Breaking through the bottleneck in future crop breeding [J]. Crop Journal, 2021, 9(3): 633‒645.
[16]
万建民 . 作物分子设计育种 [J]. 作物学报 , 2006 3 : 455 ‒ 462 .
Wan J M . Perspectives of molecular design breeding in crops [J]. Acta Agronomica Sinica , 2006 3 : 455 ‒ 462 .
[17]
朱艳 , 汤亮 , 刘蕾蕾 , 等 . 作物生长模型CropGrow研究进展 [J]. 中国农业科学 , 2020 , 53 16 : 3235 ‒ 3256 .
Zhu Y , Tang L , Liu L L , al e t . Research progress on the crop growth model CropGrow [J]. Scientia Agricultura Sinica , 2020 , 53 16 : 3235 ‒ 3256 .
[18]
曹卫星 , 朱艳 , 田永超 , 等 . 作物精确栽培技术的构建与实现 [J]. 中国农业科学 , 2011 , 44 19 : 3955 ‒ 3969 .
Cao W X , Zhu Y , Tian Y C , al e t . Development and implementation of crop precision cultivation technology [J]. Scientia Agriculture Sinica , 2011 , 44 19 : 3955 ‒ 3969 .
[19] Coherent Market Insights. Plant phenotyping market [EB/OL]. (2021-08-01)[2023-04-15]. https://www.coherentmarketinsights.com/market-insight/plant-phenotyping-market-4584. 链接1
[20] Gojon A, Nussaume L, Luu D T, al et. Approaches and determinants to sustainably improve crop production [J]. Food and Energy Security, 2023, 12(1): e369.
[21] Araus J L, Kefauver S C, Zaman-Allah M, al et. Translating high-throughput phenotyping into genetic gain [J]. Trends in Plant Science, 2018, 23(5): 451‒466.
[22] Singh A, Ganapathysubramanian B, Singh A K, al et. Machine learning for high-throughput stress phenotyping in plants [J]. Trends in Plant Science, 2016, 21(2): 110‒124.
[23] Fan J C, Li Y L, Yu S, al et. Application of Internet of Things to agriculture‒The LQ-FieldPheno platform: A high-throughput platform for obtaining crop phenotypes in field [J]. Research, 2023, 6(2): 0059.
[24]
郑庆华 , 刘欢 , 龚铁梁 , 等 . 大数据知识工程发展现状及展望 [J]. 中国工程科学 , 2023 , 25 2 : 208 ‒ 220 .
Zheng Q H , Liu H , Gong T L , al e t . Development and prospect of big data knowledge engineering [J]. Strategic Study of CAE , 2023 , 25 2 : 208 ‒ 220 .
[25] Sun D, Robbins K, Morales N, al et. Advances in optical phenotyping of cereal crops [J]. Trends in Plant Science, 2021, 27(2): 191‒208.
[26] Jin S C, Sun X L, Wu F F, al et. Lidar sheds new light on plant phenomics for plant breeding and management: Recent advances and future prospects [J]. ISPRS Journal of Photogrammetry and Remote Sensing, 2021, 171: 202‒223.
[27]
张慧春 , 李杨先 , 周宏平 , 等 . 植物表型平台与图像分析技术研究进展与展望 [J]. 农业机械学报 , 2019 , 51 3 : 1 ‒ 22 .
Zhang H C , Li Y X , Zhou H P , al e t . Research progress and prospect in plant phenotypingplatform and image analysis technology [J]. Transactions of the Chinese Society for Agricultural Machinery , 2019 , 51 3 : 1 ‒ 22 .
[28] Yang W N, Guo Z L, Huang C L, al et. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice [J]. Nature Communications, 2014, 5: 5087.
[29] Du J J, Fan J C A, Wang C A Y, al et. Greenhouse-based vegetable high-throughput phenotyping platform and trait evaluation for large-scale lettuces [J]. Computers and Electronics in Agriculture, 2021, 186: 106193.
[30] Wu S, Wen W, Wang Y, al et. MVS-Pheno: A portable and low-cost phenotyping platform for maize shoots using multiview stereo 3D reconstruction [J]. Plant Phenomics, 2020, 2020: 1848437.
[31]
杜建军 , 郭新宇 , 王传宇 , 等 . 基于全景图像的玉米果穗流水线考种方法及系统 [J]. 农业工程学报 , 2018 , 34 13 : 195 ‒ 202 .
Du J J , Guo X Y , Wang C Y , al e t . Assembly line variety test method and system for corn ears based on panoramic surface image [J]. Transactions of the Chinese Society of Agricultural Engineering , 2018 , 34 13 : 195 ‒ 202 .
[32]
施巍松 , 孙辉 , 曹杰 , 等 . 边缘计算: 万物互联时代新型计算模型 [J]. 计算机研究与发展 , 2017 , 54 5 : 907 ‒ 924 .
Shi W S , Sun H , Cao J , al e t . Edge computing—An emerging computing model for the Internet of everything era [J]. Journal of Computer Research and Development , 2017 , 54 5 : 907 ‒ 924 .
[33] Wu S, Wen W L, Gou W B, al et. A miniaturized phenotyping platform for individual plants using multi-view stereo 3D reconstruction [J]. Frontiers in Plant Science, 2022, 13: 897746.
[34] Ma Z, Du R, Xie J, al et. Phenotyping of silique morphology in oilseed rape using skeletonization with hierarchical segmentation [J]. Plant Phenomics, 2023, 5: 0027.
[35] Li Y, Wen W, Miao T, al et. Automatic organ-level point cloud segmentation of maize shoots by integrating high-throughput data acquisition and deep learning [J]. Computers and Electronics in Agriculture, 2022, 193: 106702.
[36] Du J J, Li B, Lu X J, al et. Quantitative phenotyping and evaluation for lettuce leaves of multiple semantic components [J]. Plant Methods, 2022, 18(1): 54.
[37] Zavafer A, Bates H, Mancilla C, al et. Phenomics: Conceptualization and importance for plant physiology [J]. Trends in Plant Science, 2023: 2439.
[38] Jin S, Su Y, Zhang Y, al et. Exploring seasonal and circadian Rhythms in structural traits of field maize from LiDAR time series [J]. Plant Phenomics, 2021, 2021: 9895241.
[39] Jiang Y, Li C Y. Convolutional neural networks for image-based high-throughput plant phenotyping: A review [J]. Plant Phenomics, 2020, 2020: 4152816.
[40]
王璟璐 , 张颖 , 潘晓迪 , 等 . 作物表型组数据库研究进展及展望 [J]. 中国农业信息 , 2018 , 30 5 : 13 ‒ 23 .
Wang J L , Zhang Y , Pan X D , al e t . Research progress and prospect on crop phenomics database [J]. China Agricultural Informatics , 2018 , 30 5 : 13 ‒ 23 .
[41] Neveu P, Tireau A, Hilgert N, al et. Dealing with multi-source and multi-scale information in plant phenomics: The ontology-driven Phenotyping Hybrid Information System [J]. New Phytologist, 2019, 221(1): 588‒601.
[42] Zhang Y, Wang J, Du J, al et. Dissecting the phenotypic components and genetic architecture of maize stem vascular bundles using high-throughput phenotypic analysis [J]. Plant Biotechnology Journal, 2020, 19(1): 35‒50.
[43] Reynolds D, Ball J, Bauer A, al et. CropSight: A scalable and open-source information management system for distributed plant phenotyping and IoT-based crop management [J]. GigaScience, 2019, 8(3): 11.
[44] Gui S T, Yang L F, Li J B, al et. ZEAMAP, a comprehensive database adapted to the maize multi-omics era [J]. Iscience, 2020, 23(6): 31.
[45] Mcguire A L, Gabriel S, Tishkoff S A, al et. The road ahead in genetics and genomics [J]. Nature Reviews Genetics, 2020, 21(10): 581‒596.
[46] Guo Z L, Li B, Du J J, al et. LettuceGDB: The community database for lettuce genetics and omics [J]. Plant Communications, 2023, 4(1): 100425.
[47] Cabrera-Bosquet L, Fournier C, Brichet N, al et. High-throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform [J]. New Phytologist, 2016, 212(1): 269‒281.
[48] Wen W, Gu S, Xiao B, al et. In situ evaluation of stalk lodging resistance for different maize (Zea mays L.) cultivars using a mobile wind machine [J]. Plant Methods, 2019, 15(1): 96.
[49] Ferguson J N, Fernandes S B, Monier B, al et. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions [J]. Plant Physiology, 2021, 187(3): 1481‒1500.
[50] Wu X, Feng H, Wu D, al et. Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance [J]. Genome Biology, 2021, 22(1): 185.
[51] Wang W, Guo W, Le L, al et. Integration of high-throughput phenotyping, GWAS, and predictive models reveals the genetic architecture of plant height in maize [J]. Molecular Plant, 2023, 16: 1‒20.
[52] Le L, Guo W J, Du D Y, al et. A spatiotemporal transcriptomic network dynamically modulates stalk development in maize [J]. Plant Biotechnology Journal, 2022, 20(12): 2313‒2331.
[53] Ren W, Zhao L F, Liang J X, al et. Genome-wide dissection of changes in maize root system architecture during modern breeding [J]. Nature Plants, 2022, 8(12): 1408.
[54]
张颖 , 廖生进 , 王璟璐 , 等 . 信息技术与智能装备助力智能设计育种 [J]. 吉林农业大学学报 , 2021 , 43 2 : 119 ‒ 129 .
Zhang Y , Liao S J , Wang J L , al e t . Information technology and intelligent equipment facilitating smart breeding [J]. Journal of Jilin Agricultural University , 2021 , 43 2 : 119 ‒ 129 .
[55] Xu Y, Zhang X, Li H, al et. Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction [J]. Molecular Plant, 2022, 15(11): 1664‒1695.
[56] Ninomiya S. High-throughput field crop phenotyping: Current status and challenges [J]. Breeding Science, 2022, 72(1): 3‒18.
[57]
顾生浩 , 温维亮 , 卢宪菊 , 等 . 作物智慧栽培学——信息 ‒ 农艺 ‒ 农机深度融合的新农科 [J]. 农学学报 , 2023 , 13 2 : 67 ‒ 76 .
Gu S H , Wen W L , Lu X J , al e t . Smart crop cultivation: A new agricultural science toward deep integration of information, agronomy and machinery [J]. Journal of Agriculture , 2023 , 13 2 : 67 ‒ 76 .
[58] Li Y, Wen W, Fan J, al et. Multi-source data fusion improves time-series phenotype accuracy in maize under a field high-throughput phenotyping platform [J]. Plant Phenomics, 2023, 5: 0043.