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ARS Home » Southeast Area » Tifton, Georgia » Crop Genetics and Breeding Research » Research » Publications at this Location » Publication #347629
Title: Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut

Author
item CLEVENGER, J - University Of Georgia
item CHU, Y - University Of Georgia
item CHAVARRO, C - University Of Georgia
item AGARWAL, G - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item BERTIOLI, D - University Of Georgia
item LEAL-BERTIOLI, SCM - University Of Georgia
item PANDEY, M - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item VAUGHN, J - University Of Georgia
item ABERNATHY, B - University Of Georgia
item Anglin, Noelle
item HOVAV, R - Agricultural Research Organization Of Israel
item BUROW, M - Texas Tech University
item NAYAK, S - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item CHITIKINENI, A - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item ISLEIB, T - North Carolina State University
item Holbrook, Carl - Corley
item JACKSON, S - University Of Georgia
item VARSHNEY, R - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item OZIAS-AKINS, P - University Of Georgia

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2017
Publication Date: 12/30/2017
Citation: Clevenger, J., Chu, Y., Chavarro, C., Agarwal, G., Bertioli, D.J., Leal-Bertioli, S., Pandey, M.K., Vaughn, J., Abernathy, B., Barkley, N.L., Hovav, R., Burow, M., Nayak, S.N., Chitikineni, A., Isleib, T.G., Holbrook Jr, C.C., Jackson, S.A., Varshney, R.K., Ozias-Akins, P. 2017. Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut. Molecular Plant. 10:309-322.

Interpretive Summary: Here, we report deployment of the first large-scale SNP genotyping array for peanut to assess allelic diversity between cultivated/wild germplasm and among cultivated sets of germplasm representing global diversity on the one hand and focused breeding programs on the other. Cultivated germplasm with importance in India, Israel, Africa, and the United States was utilized in this study. SNPs from diploid wild species were included for flexibility in genotyping interspecific hybrid populations. The utility of this array was demonstrated by assaying 384 genotypes, including elite U.S. germplasm, the USDA mini core germplasm collection, interspecific hybrids, diploid wild species, and recombinant inbred line populations. By genetically following the breeding history runner market type cultivars, which are the most widely grown and economically important in the United States, genomic regions for which breeders have positively selected were unveiled. By sampling these genotypes of direct relevance to breeders, the efficiency of crosses for the development of future populations for gene discovery can be predicted.

Technical 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 iterspecific 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 U.S. 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.