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

Clevenger, J and Chu, Y and Chavarro, C and Agarwal, G and Bertioli, D J and Leal-Bertioli, S C M and Pandey, M K and Vaughn, J and Abernathy, B and Barkley, N A and Hovav, R and Burow, M and Nayak, S N and Chitikineni, A and Isleib, T G and Holbrook, C C and Jackson, S A and Varshney, R K and Ozias-Akins, P (2017) Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut. Molecular Plant, 10 (2). pp. 309-322. ISSN 1674-2052

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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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Single nucleotide polymorphism; Groundnut; Arachis hypogaea; Peanut; SNPs
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 10 Apr 2017 06:34
Last Modified: 10 Apr 2017 06:34
URI: http://oar.icrisat.org/id/eprint/9944
Official URL: http://dx.doi.org/10.1016/j.molp.2016.11.015
Projects: UNSPECIFIED
Funders: Open Access funded by Bill & Melinda Gates Foundation
Acknowledgement: Funding: This project was funded by the Feed the Future Innovation Lab for Collaborative Research on Peanut Productivity and Mycotoxin Control (Peanut and Mycotoxin Innovation Lab), supported by funding from the United States Agency for International Development (USAID) (P.O.-A., S.A.J., D.J.B., R.K.V., M.B.); the US-Israel Binational Agricultural R&D Fund (BARD) project, IS-4540-12 (P.O.-A., R.H., S.A.J.); the Agriculture and Food Research Initiative competitive grant2012-85117-19435 of the USDA National Institute of Food and Agriculture (P.O.-A., C.C.H.); the Peanut Foundation (P.O.-A., S.A.J., R.K.V.), and Bill & Melinda Gates Foundation (grant no. OPP1114827) funded Tropical Legumes III project (R.K.V.). Acknowledgments: This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium. No conflict of interest declared.
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