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Back to wild relatives for future breeding through super-pangenome

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Molecular Plant 2023年第9期16卷 1363-1365页

作者： Ali Raza Abhishek Bohra Vanika Garg rajeev k.varshney College of Agriculture Fujian Agriculture and Forestry UniversityFuzhou 350002China WA State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWA 6150Australia

Crop wild relatives(CWRs)deliver untapped genetic diversity,as they contain valuable breeding traits absent in the cultivated pool,e.g.,traits imparting climate *** genetic material from CWRs to breeding programs can advance effective traits and broaden the genetic base of cultivated crops(Bohra et al.,2022).The availability of genetic diversity in crop breeding programs is important for accelerating crop production while safeguarding food safety and agricultural *** domestication and artificial selection have paved the way for crop cultivars tailored to evolving human requirements and modern cultivation ***,domestication and breeding have significantly reduced genetic diversity in modern crops(khan et al.,2020;Bohra et al.,2022).Owing to the extensive genetic and phenotypic variability,CWRs serve as valuable genetic reservoirs for crop improvement(Bohra et al.,2022;Li et al.,2023).The use of CWRs in breeding programs is not that straightforward,as linkage drags often remain difficult to overcome.

关键词： breeding crops cultivated

Trehalose:A sugar molecule involved in temperature stress management in plants

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The Crop Journal 2024年第1期12卷 1-16页

作者： Ali Raza Savita Bhardwaj Md Atikur Rahman Pedro García-Caparrós Madiha Habib Faisal Saeed Sidra Charagh Christine H.Foyer kadambot H.M.Siddique rajeev k.varshney College of Agriculture Fujian Agriculture and Forestry University(FAFU)Fuzhou 350002FujianChina Department of Botany School of Bioengineering and BiosciencesLovely Professional UniversityPhagwara 144411India Department of Botany MCM DAV CollegeKangraHimachal Pradesh 176001India Grassland and Forage Division National Institute of Animal ScienceRural Development AdministrationCheonan 31000Republic of Korea Agronomy Department of Superior School Engineering University of AlmeríaAlmeríaSpain National Institute for Genomics and Advanced Biotechnology National Agricultural Research CentrePark Rd.Islamabad 45500Pakistan Agriculture Health and Environment DepartmentNatural Resources InstituteFaculty of Engineering&ScienceUniversity of GreenwichKent ME44TBUK State key Laboratory of Rice Biology China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhouZhejiangChina School of Biosciences College of Life and Environmental SciencesUniversity of BirminghamEdgbaston B152TTUK The UWA Institute of Agriculture The University of Western AustraliaCrawleyPerth 6009Australia WA State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWA 6150Australia

Trehalose(Tre)is a non-reducing disaccharide found in many species,including bacteria,fungi,invertebrates,yeast,and even plants,where it acts as an osmoprotectant,energy source,or protein/membrane *** relatively small amounts in plants,Tre concentrations increase following exposure to abiotic ***-6-phosphate,a precursor of Tre,has regulatory functions in sugar metabolism,crop production,and stress *** the various abiotic stresses,temperature extremes(heat or cold stress)are anticipated to impact crop production worldwide due to ongoing climate *** small amounts of Tre can mitigate negative physiological,metabolic,and molecular responses triggered by temperature *** also interacts with other sugars,osmoprotectants,amino acids,and phytohormones to regulate metabolic reprogramming that underpins temperature stress *** plants expressing Tre-synthesis genes accumulate Tre and show improved stress ***-wide studies of Tre-encoding genes suggest roles in plant growth,development,and stress *** review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism,crosstalk,and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant *** consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture.

关键词： Abiotic stress Gene expression Genetic engineering Osmolyte Trehalose-6-phosphate

Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction

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Molecular Plant 2022年第11期15卷 1664-1695页

作者： Yunbi Xu Xingping Zhang Huihui Li Hongjian Zheng Jianan Zhang Michael S.Olsen rajeev k.varshney Boddupalli M.Prasanna Qian Qian Institute of Crop Sciences CIMMYT-ChinaChinese Academy of Agricultural SciencesBeijing 100081China CIMMYT-China Tropical Maize Research Center School of Food Science and EngineeringFoshan UniversityFoshanGuangdong 528231China Peking University Institute of Advanced Agricultural Sciences WeifangShandong 261325China CIMMYT-China Specialty Maize Research Center Shanghai Academy of Agricultural SciencesShanghai 201400China MolBreeding Biotechnology Co. Ltd.ShijiazhuangHebei 050035China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanyaHainan 572024China CIMMYT(International Maize and Wheat Improvement Center) ICRAF CampusUnited Nations AvenueNairobiKenya State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochAustralia

The first paradigm of plant breeding involves direct selection-based phenotypic observation,followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and,more recently,by incorporation of molecular marker ***,plant performance or phenotype(P)is determined by the combined effects of genotype(G),envirotype(E),and genotype by environment interaction(GEI).Phenotypes can be predicted more precisely by training a model using data collected from multiple sources,including spatiotemporal omics(genomics,phenomics,and enviromics across time and space).Integration of 3D information profiles(G-P-E),each with multidimensionality,provides predictive breeding with both tremendous opportunities and great ***,we first review innovative technologies for predictive *** then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy,particularly envirotypic data,which have largely been neglected in data collection and are nearly untouched in model *** propose a smart breeding scheme,integrated genomic-enviromic prediction(iGEP),as an extension of genomic prediction,using integrated multiomics information,big data technology,and artificial intelligence(mainly focused on machine and deep learning).We discuss how to implement iGEP,including spatiotemporal models,environmental indices,factorial and spatiotemporal structure of plant breeding data,and cross-species prediction.A strategy is then proposed for prediction-based crop redesign at both the macro(individual,population,and species)and micro(gene,metabolism,and network)***,we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding *** call for coordinated efforts in smart breeding through iGEP,institutional partnerships,and innovative technological support.

关键词： smart breeding genomic selection integrated genomic-enviromic selection spatiotemporal omics crop design machine and deep learning big data artificial intelligence

Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China,India and the US using simple sequence repeat markers

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Journal of Integrative Plant Biology 2016年第5期58卷 452-465页

作者： Hui Wang Pawan khera Bingyan.Huang Mei Yuan Ramesh katam Weijian Zhuang karen Harris-Shultz kim M.Moore Albert k.Culbreath Xinyou Zhang rajeev k.varshney Lianhui Xie Baozhu Guo Fujian Agricultural and Forestry University College of Plant ProtectionFuzhou 350002China Department of Plant Pathology University of GeorgiaTiftonGA 31794USA USDA-ARS Crop Protection and Management Research UnitTiftonGA 31794USA Shandong Peanut Research Institute qingdao 266100China International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Patancheru 502324India Henan Academy of Agricultural Sciences Cash Crops Research InstituteZhengzhou 450002China Department of Biological Sciences Florida A&M UniversityTallahasseeFL 32307USA Fujian Agricultural and Forestry University College of Crop ScienceFuzhou 350002China USDA-ARS Crop Genetics and Breeding Research UnitTiftonGA 31794USA AgResearch Consultants Shingler Little River RoadSumnerGA 31789USA

Cultivated peanut is grown worldwide as rich- source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat （SSR） markers and to assess the genetic diversity and popuJation structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content （PIC） were 0.480 and o.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, o.489 and 0.47 with an average PIC of 0.323, 0.43 and o.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations （P1, P2）, which was consistent with the dendro- gram based on genetic distance （G1, G2） and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

关键词： Arachis hypogaea breeding genetic diversity populationstructure simple sequence repeat

Resistance to Aspergillus flavus in maize and peanut:Molecular biology, breeding, environmental stress,and future perspectives

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The Crop Journal 2015年第3期3卷 229-237页

作者： Jake C.Fountain Pawan khera Liming Yang Spurthi N.Nayak Brian T.Scully Robert D.Lee Zhi-Yuan Chen Robert C.kemerait rajeev k.varshney Baozhu Guo Department of Plant Pathology University of Georgia Tifton GA USA International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad Telangana India USDA-ARS Crop Protection and Management Research Unit Tifton GA USA Huaiyin Normal University School of Life Sciences USDA-ARS US Horticultural Laboratory Fort Pierce FL USA Department of Crop and Soil Sciences University of Georgia Tifton GA USA Department of Plant Pathology and Crop Physiology Louisiana State University Baton Rouge LA USA

The colonization of maize(Zea mays L.) and peanut(Arachis hypogaea L.) by the fungal pathogen Aspergillus flavus results in the contamination of kernels with carcinogenic mycotoxins known as aflatoxins leading to economic losses and potential health threats to humans. The regulation of aflatoxin biosynthesis in various Aspergillus spp. has been extensively studied, and has been shown to be related to oxidative stress responses. Given that environmental stresses such as drought and heat stress result in the accumulation of reactive oxygen species(ROS) within host plant tissues, host-derived ROS may play an important role in cross-kingdom communication between host plants and A. flavus. Recent technological advances in plant breeding have provided the tools necessary to study and apply knowledge derived from metabolomic, proteomic, and transcriptomic studies in the context of productive breeding populations. Here, we review the current understanding of the potential roles of environmental stress, ROS, and aflatoxin in the interaction between *** and its host plants, and the current status in molecular breeding and marker discovery for resistance to A. flavus colonization and aflatoxin contamination in maize and peanut. We will also propose future directions and a working model for continuing research efforts linking environmental stress tolerance and aflatoxin contamination resistance in maize and peanut.

关键词： Host resistance Molecular breeding Aflatoxin contamination Reactive oxygen species ROS

Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut(Arachis hypogaea L.)

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The Crop Journal 2014年第Z1期2卷 110-119页

作者： Varsha kumari M.V.C.Gowda Vinod Tasiwal Manish k.Pandey Ramesh S.Bhat Nalini Mallikarjuna Hari D.Upadhyaya rajeev k.varshney Department of Genetics and Plant Breeding University of Agricultural Sciences Dharwad International Crops Research Institute for the Semi-Arid Tropics Department of Plant Pathology University of Agricultural Sciences Dharwad Department of Biotechnology University of Agricultural Sciences Dharwad CGIAR Generation Challenge Programme c/o CIMMYT

Groundnut(Arachis hypogaea L.)is widely grown and consumed around the world and is considered to have originated from a single hybridization event between two wild *** utilization of wild germplasm in breeding programs has been restricted by reproductive barriers between wild and cultivated species and technical difficulties in making large numbers of *** to overcome these hurdles have resulted in the development of synthetic amphidiploids,namely ISATGR 278-18(Arachis duranesis×Arachis batizocoi)and ISATGR 5B(Arachis magna×***),which possess several desirable traits,including resistance to foliar diseases that generally cause huge yield losses annually in groundnut growing areas of Asia,America,and *** an objective to improve foliar disease resistance,the primary gene pool was diversified by introgressing foliar disease resistance in five cultivated genotypes(ICGV 91114,ICGS 76,ICGV 91278,JL 24,and DH 86)from synthetic amphidiploids using a backcross breeding *** introgression lines with resistance to two foliar diseases(rust and late leaf spot)were identified with levels of resistance equal to the *** backcross derived lines have shown a wide range of variation for several morphological and agronomic *** lines,after further evaluation and selection,can serve as donors in future breeding programs aimed atdeveloping improved cultivars with desirable agronomic traits,high resilience to biotic/abiotic stresses and a broadened genetic base.

关键词： Groundnut Peanut Wild species Wide crosses Interspecific hybridization

Fast integration and accumulation of beneficial breeding alleles through an AB–NAMIC strategy in wheat

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Plant Communications 2023年第3期4卷 66-79页

作者： Chengzhi Jiao Chenyang Hao Tian Li Abhishek Bohra Lanfen Wang Jian Hou Hongxia Liu Hong Liu Jing Zhao Yamei Wang Yunchuan Liu Zhiwei Wang Xin Jing Xiue Wang rajeev k.varshney Junjie Fu Xueyong Zhang The National key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics InstituteNanjing Agricultural UniversityNanjingJiangsu 210095China Centre for Crop&Food Innovation WA State Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityPerthWA 6150Australia Smartgenomics Technology Institute Tianjin 301700China

Wheat(Triticum aestivum)is among the most important staple crops for safeguarding the food security of the growing world *** bridge the gap between genebank diversity and breeding programs,we developed an advanced backcross-nested association mapping plus inter-crossed population(AB-NAMIC)by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core *** backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC *** performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660k SNP ***-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in ***,genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B(TraesCS7B03G1216700),which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield *** commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat *** information on genome-wide association studymapping,candidate genes,and their haplotypes for breeding traits are available through *** research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.

关键词： wheat genebank AB-NAMIC genome-wide association studies GWAS beneficial alleles genomics-assisted breeding WheatGAB

Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing

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The Crop Journal 2020年第1期8卷 1-15页

作者： Yaduru Shasidhar Murali T.Variath Manish k.Vishwakarma Surendra S.Manohar Sunil S.Gangurde Manda Sriswathi Hari kishan Sudini keshavji L.Dobariya Sandip k.Bera Thankappan Radhakrishnan Manish k.Pandey Pasupuleti Janila rajeev k.varshney International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) HyderabadIndia Department of Genetics Osmania UniversityHyderabadIndia Junagadh Agricultural University JunagadhIndia ICAR-Directorate of Groundnut Research JunagadhIndia

Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut *** oleic acid has emerged as a key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to ***-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked *** used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were *** parent genome analysis using the 58 k Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third backcross *** of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome *** ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.

关键词： Foliar disease resistance High oleic acid Late leaf spot Marker-assisted backcrossing SNP array Background genome recovery

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

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Molecular Plant 2019年第7期12卷 920-934页

作者： Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li Manish k.Pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson rajeev k.varshney Xuanqiang Liang South China Peanut Sub-center of National Center of Oilseed Crops Improvement Guangdong Key Laboratory for Crops Genetic Improvement Crops Research Institute Guangdong Academy of Agricultural Sciences (GAAS) Guangzhou China Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources College of Forestry Fujian Agriculture and Forestry University Fuzhou 350002 China Plant Genome Mapping Laboratory University of Georgia Athens USA National Foxtail Millet Improvement Center Minor Cereal Crops Laboratory of Hebei Province Institute of Millet Crops Hebei Academy of Agriculture and Forestry Sciences Shijiazhuang China MolBreeding Biotechnology Co. Ltd. Shijiazhuang China School of Life Sciences and Center for Genomics and Computational Biology North China University of Science and Technology Tangshan China Center of Excellence in Genomics & Systems Biology International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad India Shenzhen key Laboratory for Orchid Conservation and Utilization National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen Shenzhen China Shandong Peanut Research Institute Shandong Academy of Agricultural Sciences Qingdao China UWA Institute of Agriculture The University of Western Australia Crawley Australia key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry University Fuzhou 350002 China

Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

关键词： cultivated peanut denovo sequencing comparative genomics genome evolution oil metabolism