The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

查看全文 作　　者：Xin [1]Wang;Kan [1]Bao;Umesh [2]K.Reddy;Yang [1]Bai;Sue [3]A.Hammar;Chen [1]Jiao;Todd [4]C.Wehner;Axel O.Ramírez-[5]Madera;Yiqun [5,6]Weng;Rebecca [3]Grumet;Zhangjun [1,7]Fei

机构地区：[1]Boyce Thompson Institute,Cornell University,Ithaca,NY,14853,USA;[2]Gus R.Douglass Institute and Department of Biology,West Virginia State University,Institute,Virginia,WV,25112,USA;[3]Department of Horticulture,Michigan State University,East Lansing,MI,48824,USA;[4]Horticultural Science Department,North Carolina State University,Raleigh,NC,27695,USA;[5]Horticulture Department,University of Wisconsin,Madison,WI,53706,USA;[6]USDA-ARS Vegetable Crops Research Unit,Madison,WI,53706,USA;[7]USDA-ARS Robert W.Holley Center for Agriculture and Health,Ithaca,NY,14853,USA

出　　处：《Horticulture Research》索引2018年第5卷第1期,共13页

基　　金：This research was supported by grants from USDA National Institute of Food and Agriculture Specialty Crop Research Initiative(2015-51181-24285). 摘　　要：Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement.Optimal collection,preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection.Here we use the high-throughput genotyping-by-sequencing(GBS)technology to characterize the United States National Plant Germplasm System(NPGS)collection of cucumber(Cucumis sativus L.).The GBS data,derived from 1234 cucumber accessions,provided more than 23 K high-quality single-nucleotide polymorphisms(SNPs)that are well distributed at high density in the genome(~1 SNP/10.6 kb).The SNP markers were used to characterize genetic diversity,population structure,phylogenetic relationships,linkage disequilibrium,and population differentiation of the NPGS cucumber collection.These results,providing detailed genetic analysis of the U.S.cucumber collection,complement NPGS descriptive information regarding geographic origin and phenotypic characterization.We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies(GWAS).Finally,we developed a molecularly informed,publicly accessible core collection of 395 accessions that represents at least 96%of the genetic variation present in the NPGS.Collectively,the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection,and will provide a valuable resource for genetic analyses,gene discovery,crop improvement,and germplasm preservation. 关键词：SUSTAINED COLLECTION structure

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The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

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