eprintid: 9944
rev_number: 17
eprint_status: archive
userid: 1305
dir: disk0/00/00/99/44
datestamp: 2017-04-10 06:34:12
lastmod: 2017-04-10 06:34:12
status_changed: 2017-04-10 06:34:12
type: article
metadata_visibility: show
creators_name: Clevenger, J
creators_name: Chu, Y
creators_name: Chavarro, C
creators_name: Agarwal, G
creators_name: Bertioli, D J
creators_name: Leal-Bertioli, S C M
creators_name: Pandey, M K
creators_name: Vaughn, J
creators_name: Abernathy, B
creators_name: Barkley, N A
creators_name: Hovav, R
creators_name: Burow, M
creators_name: Nayak, S N
creators_name: Chitikineni, A
creators_name: Isleib, T G
creators_name: Holbrook, C C
creators_name: Jackson, S A
creators_name: Varshney, R K
creators_name: Ozias-Akins, P
icrisatcreators_name: Agarwal, G
icrisatcreators_name: Pandey, M K
icrisatcreators_name: Nayak, S N
icrisatcreators_name: Chitikineni, A
icrisatcreators_name: Varshney, R K
affiliation: Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia (Tifton)
affiliation: Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia (Athens)
affiliation: ICRISAT (Patancheru)
affiliation: University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro (Brasília)
affiliation: Embrapa Genetic Resources and Biotechnology (Brasília)
affiliation: USDA-ARS PGRCU (Griffin)
affiliation: Agricultural Research Organization, Plant Sciences Institute (Rishon LeZion)
affiliation: Department of Plant and Soil Science, Texas Tech University (Lubbock)
affiliation: Department of Crop and Soil Sciences, North Carolina State University (Raleigh)
affiliation: USDA-ARS (Tifton)
country: USA
country: India
country: Brazil
country: Israel
title: Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut
ispublished: pub
subjects: s1.3
subjects: s2.13
divisions: CRPS3
crps: crp1.5
full_text_status: public
keywords: Single nucleotide polymorphism; Groundnut; Arachis hypogaea; Peanut; SNPs
note: 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.
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.
date: 2017-02-13
date_type: published
publication: Molecular Plant
volume: 10
number: 2
publisher: Oxford University Press
pagerange: 309-322
id_number: 10.1016/j.molp.2016.11.015
refereed: TRUE
issn: 1674-2052
official_url: http://dx.doi.org/10.1016/j.molp.2016.11.015
related_url_url: https://scholar.google.co.in/scholar?q=+Genome-wide+SNP+Genotyping+Resolves+Signatures+of+Selection+and+Tetrasomic+Recombination+in+Peanut&btnG=&hl=en&as_sdt=0%2C5
related_url_type: pub
funders: Open Access funded by Bill & Melinda Gates Foundation
citation:   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     
document_url: http://oar.icrisat.org/9944/1/1-s2.0-S1674205216303008-main.pdf