title: Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut.
abstract: 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 facilitate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (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 regions 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 positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated 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.
authors.affiliation: Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Clevenger
authors.affiliation: Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Chu
authors.affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA.
authors.forename: Carolina
authors.initials: C
authors.lastname: Chavarro
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Agarwal
authors.affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA; University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, 70910-900 Brasília, DF, Brazil.
authors.forename: David J
authors.initials: DJ
authors.lastname: Bertioli
authors.affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA; Embrapa Genetic Resources and Biotechnology, 70770-917 Brasília, DF, Brazil.
authors.forename: Soraya C M
authors.initials: SCM
authors.lastname: Leal-Bertioli
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
authors.forename: Manish K
authors.initials: MK
authors.lastname: Pandey
authors.affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Vaughn
authors.affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.affiliation: USDA-ARS PGRCU, Griffin, GA 30223, USA.
authors.forename: Noelle A
authors.initials: NA
authors.lastname: Barkley
authors.affiliation: Agricultural Research Organization, Plant Sciences Institute, 7528809 Rishon LeZion, Israel.
authors.forename: Ran
authors.initials: R
authors.lastname: Hovav
authors.affiliation: Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409-2122, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Burow
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
authors.forename: Spurthi N
authors.initials: SN
authors.lastname: Nayak
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
authors.forename: Annapurna
authors.initials: A
authors.lastname: Chitikineni
authors.affiliation: Department of Crop and Soil Sciences, North Carolina State University, Box 7629, Raleigh, NC 28695-7629, USA.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Isleib
authors.affiliation: USDA-ARS, Tifton, GA 31793, USA.
authors.forename: C Corley
authors.initials: CC
authors.lastname: Holbrook
authors.affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA. Electronic address: pozias@uga.edu.
authors.forename: Peggy
authors.initials: P
authors.lastname: Ozias-Akins
mesh_terms: D010367:Arachis / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012641:Selection, Genetic; D058670:Tetrasomy
chemical_list: D005819:Genetic Markers
keywords: Arachis hypogaea; groundnut; single nucleotide polymorphism