אסיף מאגר המחקר החקלאי

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

Year:

2017

Source of publication :

Authors :

Volume :

10

Co-Authors:

Clevenger, J., Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
Chu, Y., Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
Chavarro, C., Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA 30602, USA
Agarwal, G., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
Bertioli, D.J., Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA 30602, USA, University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
Leal-Bertioli, S.C.M., Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA 30602, USA, Embrapa Genetic Resources and Biotechnology, 70770-917 Brasília, DF, Brazil
Pandey, M.K., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
Vaughn, J., Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA 30602, USA
Abernathy, B., Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA 30602, USA
Barkley, N.A., USDA-ARS PGRCU, Griffin, GA 30223, USA
Hovav, R., Agricultural Research Organization, Plant Sciences Institute, 7528809 Rishon LeZion, Israel
Burow, M., Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409-2122, USA
Nayak, S.N., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
Chitikineni, A., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
Isleib, T.G., Department of Crop and Soil Sciences, North Carolina State University, Box 7629, Raleigh, NC 28695-7629, USA
Holbrook, C.C., USDA-ARS, Tifton, GA 31793, USA
Jackson, S.A., Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA 30602, USA
Varshney, R.K., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
Ozias-Akins, P., Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA

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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. Genome-wide single nucleotide polymorphisms (SNPs), identified among diploid and tetraploid Arachis species and used to construct an Affymetrix 60K SNP array, provided insight into diversity across US runner-type peanut cultivars and the US mini - core collection. The frequency of fixed marker polymorphisms and identification of preferentially selected haplotypes will inform future peanut breeding to enhance diversity. © 2017 The Authors.

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