Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut  

作　　者：Josh Clevenger Ye Chu Carolina Chavarro Gaurav Agarwal David J. Bertioli Soraya C.M. LeaI-Bertioli Manish K. Pandey Justin Vaughn Brian Abernathy Noelle A. Barkley Ran Hovav Mark Burow Spurthi N. Nayak Annapurna Chitikineni Thomas G. Isleib C. Corley Holbrook Scott A. Jackson Rajeev K. Varshney Peggy Ozias-Akins 

机构地区：[1]Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA [2]Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA [3]International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India [4]University of Brasilia, Institute of Biological Sciences, Campus Darcy Ribeiro, 70910-900 Brasilia, DF, Brazil [5]Embrapa Genetic Resources and Biotechnology, 70770-917 Brasflia, DF, Brazil eUSDA-ARS PGRCU, Griffin, GA 30223, USA [6]Agricultural Research Organization, Plant Sciences Institute, 7528809 Rishon LeZion, Israel [7]Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409-2122, USA [8]Department of Crop and Soil Sciences, North Carolina State University, Box 7629, Raleigh, NC 28695-7629, USA [9]USDA-ARS, Tifton, GA 31793. USA

出　　处：《Molecular Plant》2017年第2期309-322,共14页分子植物（英文版）

摘　　要：Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facil- itate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide poiymorphisms （SNPs） were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide key insights on the inclusion of new genetic diversity in culti- vated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facil- itate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide poiymorphisms （SNPs） were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide key insights on the inclusion of new genetic diversity in culti- vated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.

关 键 词：single nucleotide polymorphism GROUNDNUT Arachis hypogaea 

分 类 号：S511.03[农业科学—作物学] Q524.3[生物学—生物化学]