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crop breeding Chips and Genotyping Platforms： Progress, Challenges, and Perspectives

Molecular Plant 2017年第8期10卷 1047-1064页

作者： Awais Rasheed Yuanfeng Hao Xianchun Xia Awais Khan Yunbi Xu Rajeev K. Varshney Zh-onghu He Institute of crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) Beijing 100081 China International Maize and Wheat Improvement Center (CIMMY-F) c/o CAAS Beijing 100081 China Department of Plant Pathology and Plant-Microbe Biology Cornell University Geneva NY USA International crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 India

There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.

关键词： Single nucleotide polymorphisms （SNPs） Genotyping-by-sequencing （GBS） SNP arrays crop breeding Genotyping platforms

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Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future crop breeding

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Molecular Plant 2021年第1期14卷 77-94页

作者： Leiming Wu Linqian Han Qing Li Guoying Wang Hongwei Zhang Lin Li National Key Laboratory of crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China lnstitute of crop Science Chinese Academy of Agricultural SciencesBeijing 100081China

The functional genes underlying phenotypic variation and their interactions represent“genetic mysteries”.Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences.Due to advances in highthroughput multi-omics technologies,we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research.In this article,we provide a brief overview of current strategies to explore genetic mysteries.We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources.Next,we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries.We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning,which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits,and also provide a detailed procedure for systematic dissection of genetic mysteries,Finally,we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.

关键词： genetic mystery interactome big data machine learning crop breeding

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High-throughput phenotyping: Breaking through the bottleneck in future crop breeding

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The crop Journal 2021年第3期9卷 633-645页

作者： Peng Song Jinglu Wang Xinyu Guo Wanneng Yang Chunjiang Zhao National Key Laboratory of crop Genetic Improvement National Center of Plant Gene ResearchHuazhongAgricultural UniversityWuhan 430070HubeiChina Beijing KeyLab of Digital Plant Beijing Research Center for Information Technologyin AgricultureBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China

With the rapid development of genetic analysis techniques and crop population size,phenotyping has become the bottleneck restricting crop breeding.Breaking through this bottleneck will require phenomics,defined as the accurate,high-throughput acquisition and analysis of multi-dimensional phenotypes during crop growth at organism-wide levels,ranging from cells to organs,individual plants,plots,and fields.Here we offer an overview of crop phenomics research from technological and platform viewpoints at various scales,including microscopic,ground-based,and aerial phenotyping and phenotypic data analysis.We describe recent applications of high-throughput phenotyping platforms for abiotic/biotic stress and yield assessment.Finally,we discuss current challenges and offer perspectives on future phenomics research.

关键词： High-throughput phenotyping crop breeding crop phenomics Phenotyping platform Data analysis

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Teaching Reform and Research of crop breeding Experiment

Teaching Reform and Research of Crop Breeding Experiment

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作者： Long Jiang College of Agronomy Jilin Agricultural Science and Technology University

In order to improve the innovation ability and scientific research practice ability of agronomy students, and cultivate qualified applied and innovative talents. According to the characteristics of crop breeding experiment course, the author and his team fully draw on the experience of experimental teaching reform of this course in other agricultural colleges and universities. Comprehensive reform and course design of crop breeding experiment were carried out from the aspects of experimental outline, training plan, teaching conditions, teaching mode, teaching plan and so on, and good teaching results were obtained.

关键词： crop breeding experiment teaching reform

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Redesigning crop varieties to win the race between climate change and food security

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Molecular Plant 2023年第10期16卷 1590-1611页

作者： Kevin V.Pixley Jill E.Cairns Santiago Lopez-Ridaura Chris O.Ojiewo Maryam Abba Dawud Inoussa Drabo Taye Mindaye Baloua Nebie Godfrey Asea Biswanath Das Happy Daudi Haile Desmae Benoit Joseph Batieno Ousmane Boukar Clare T.M.Mukankusi Stanley T.Nkalubo Sarah J.Hearne Kanwarpal S.Dhugga Harish Gandhi Sieglinde Snapp Ernesto Adair Zepeda-Villarreal International Maize and Wheat Improvement Center(CIMMYT) TexcocoMexico International Maize and Wheat Improvement Center(CIMMYT) HarareZimbabwe International Maize and Wheat Improvement Center(CIMMYT) NairobiKenya Lake Chad Research Institute(LCRI) MaidiguriNigeria International Maize and Wheat Improvement Center(CIMMYT) DakarSenegal Ethiopian Institute of Agricultural Research(EIAR) Addis AbabaEthiopia National Agricultural Research Organization(NARO) KampalaUganda Tanzania Agricultural Research Institute(TARI) NaliendeleTanzania Institut de l'Environnement et de Recherches Agricoles(INERA) OuagadougouBurkina Faso International Institute of Tropicl Agriculture(IITA) KanoNigeria Alliance of Bioversity International and CIAT KampalaUganda

Climate change poses daunting challenges to agricultural production and food security.Rising temperatures,shifting weather patterns,and more frequent extreme events have already demonstrated their effects on local,regional,and global agricultural systems.crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance,productivity,and profitability under climate-changed environments.We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet,sorghum,maize,groundnut,cowpea,and common bean varieties,particularly in sub-Saharan Africa.We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops.Experts predict that most current breeding priorities will remain important,but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands.Importantly,the predicted future-essential traits include innovative breeding targets that must also be prioritized;for example,(1)optimized rhizosphere microbiome,with benefits for P,N,and water use efficiency,(2)optimized performance across or in specific cropping systems,(3)lower nighttime respiration,(4)improved stover quality,and(5)increased early vigor.We further discuss cutting-edge tools and approaches to discover,validate,and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision,accuracy,and speed.We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.

关键词： climate change food security crop breeding cropping systems expert survey sub-Saharan Africa

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Recent advances in understanding of the epigenetic regulation of plant regeneration

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aBIOTECH 2023年第1期4卷 31-46页

作者： Xuemei Liu Kehui Zhu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Ever since the concept of"plant cell totipotency"was first proposed in the early twentieth century,plant regeneration has been a major focus of study.Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture.Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration.The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation.Here,we summarize how various aspects of epigenetic regulation,including histone modifications and variants,chromatin accessibility dynamics,DNA methylation,and microRNAs,modulate plant regeneration.As the mechanisms of epigenetic regulation are conserved in many plants,research in this field has potential applications in boosting crop breeding,especially if coupled with emerging single-cell omics technologies.

关键词： Plant regeneration Epigenetic regulation Arabidopsis crop breeding

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Benefiting others and self: Production of vitamins in plants

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Journal of Integrative Plant Biology 2021年第1期63卷 210-227页

作者： Yufei Li Chenkun Yang Hasan Ahmad Mohamed Maher Chuanying Fang Jie Luo National Key Laboratory of crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China College of Tropical crops Hainan UniversityHaikou 570228China

Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.

关键词： crop breeding forward genetic plants vitamins

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Gene editing in plants:progress and challenges

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National Science Review 2019年第3期6卷 421-437页

作者： Yanfei Mao Jose Ramon Botella Yaoguang Liu Jian-Kang Zhu Shanghai Center for Plant Stress Biology CAS Center of Excellence in Molecular Plant Sciences Chinese Academy of Sciences School of Agriculture and Food Sciences University of Queensland State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Life Sciences South China Agricultural University Department of Horticulture and Landscape Architecture Purdue University

The clustered regularly interspaced short palindromic repeat(CRISPR)-associated protein 9(Cas9)genome editing system is a powerful tool for targeted gene modifications in a wide range of species,including plants. Over the last few years, this system has revolutionized the way scientists perform genetic studies and crop breeding, due to its simplicity, flexibility, consistency and high efficiency. Considerable progress has been made in optimizing CRISPR/Cas9 systems in plants, particularly for targeted gene mutagenesis. However, there are still a number of important challenges ahead, including methods for the efficient delivery of CRISPR and other editing tools to most plants, and more effective strategies for sequence knock-ins and replacements. We provide our viewpoint on the goals, potential concerns and future challenges for the development and application of plant genome editing tools.

关键词： CRISPR Cas9 genome editing base editing gene targeting crop breeding

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Creating a novel herbicide-tolerance OsALS allele using CRISPR/Cas9-mediated gene editing

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The crop Journal 2021年第2期9卷 305-312页

作者： Fangquan Wang Yang Xu Wenqi Li Zhihui Chen Jun Wang Fangjun Fan Yajun Tao Yanjie Jiang Qian-Hao Zhu Jie Yang Institute of Food crops Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjing 210014JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops Yangzhou UniversityYangzhou 225009JiangsuChina Provincial Key Laboratory of Agrobiology Jiangsu Academy of Agricultural SciencesNanjing 210014JiangsuChina CSIRO Agriculture and Food GPO Box 1700CanberraACT 2601Australia Institute of Life Science Jiangsu UniversityZhenjiang 212013JiangsuChina

Weeds and weedy rice plague commercial rice fields in many countries. Developingherbicide-tolerance rice is the most efficient strategy to control weed proliferation. CRISPR/Cas9-mediated gene editing, which generates small InDels and nucleotide substitutions atand around target sites using error-prone non-homologous end joining DNA repairing, hasbeen widely adopted for generation of novel crop germplasm with a wide range of geneticvariation in important agronomic traits. We created a novel herbicide-tolerance allele inrice by targeting the acetolactate synthase (OsALS) gene using CRISPR/Cas9-mediated geneediting. The novel allele (G628W) arose from a G-to-T transversion at position 1882 of OsALSand conferred a high level of herbicide tolerance. Transgene-free progeny carryinghomozygous G628W allele were identified and showed agronomic performance similar tothat of wild-type plants, suggesting that the G628W allele is a valuable resource fordeveloping elite rice varieties with strong herbicide tolerance. To promote use of the G628Wallele and to accelerate introgression and/or pyramiding of the G628W allele with other elitealleles, we developed a DNA marker for the G628W allele that accurately and robustlydistinguished homozygous from heterozygous segregants. Our result further demonstratesthe feasibility of CRISPR/Cas9-mediated gene editing in creating novel genetic variation forcrop breeding.

关键词： Rice CRISPR/Cas9 ALS Herbicide-tolerance crop breeding

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Progress in TILLING as a tool for functional genomics and improvement of crops

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Journal of Integrative Plant Biology 2014年第5期56卷 425-443页

作者： Liang Chen Liugen Hao Martin A. J. Parry Andrew L. Phillips Yin-Gang Hu State Key Laboratory of crop Stress Biology in Arid Areas and College of Agronomy Northwest A&F University Department of Plant Biology and crop Science Rothamsted Research Institute of Water Saving Agriculture in Arid Regions of China Northwest A&F University

Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes（TILLING）, which combines traditional chemical mutagenesis with high‐throughput genome‐wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or evenallohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small‐scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2（or M3） plants.

关键词： crop breeding functional genomics mutation detection TILLING

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