Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut

J. Clevenger; Y. Chu; C. Chavarro; G. Agarwal; D.J. Bertioli; S.C.M. Leal-Bertioli; M.K. Pandey; J. Vaughn; B. Abernathy; N.A. Barkley; R. Hovav; M. Burow; S.N. Nayak; A. Chitikineni; T.G. Isleib; C.C. Holbrook; S.A. Jackson; R.K. Varshney; P. Ozias-Akins

doi:10.1016/j.molp.2016.11.015

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Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut

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Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut

J. Clevenger, Y. Chu, C. Chavarro, G. Agarwal, D.J. Bertioli, S.C.M. Leal-Bertioli, M.K. Pandey, J. Vaughn, B. Abernathy, N.A. Barkley, …

Molecular Plant, Vol.10(2), pp.309-322

2017

DOI: https://doi.org/10.1016/j.molp.2016.11.015

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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.

Details

Title: Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut
Authors/Creators: J. Clevenger (Author/Creator) - University of Georgia
Y. Chu (Author/Creator) - University of Georgia
C. Chavarro (Author/Creator) - Applied Genetic Technologies (United States)
G. Agarwal (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
D.J. Bertioli (Author/Creator) - Applied Genetic Technologies (United States)
S.C.M. Leal-Bertioli (Author/Creator) - Applied Genetic Technologies (United States)
M.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
J. Vaughn (Author/Creator) - Applied Genetic Technologies (United States)
B. Abernathy (Author/Creator) - Applied Genetic Technologies (United States)
N.A. Barkley (Author/Creator) - Agricultural Research Service
R. Hovav (Author/Creator) - Agricultural Research Organization
M. Burow (Author/Creator) - Texas Tech University
S.N. Nayak (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
T.G. Isleib (Author/Creator) - North Carolina State University
C.C. Holbrook (Author/Creator) - Agricultural Research Service
S.A. Jackson (Author/Creator) - Applied Genetic Technologies (United States)
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P. Ozias-Akins (Author/Creator) - University of Georgia
Publication Details: Molecular Plant, Vol.10(2), pp.309-322
Publisher: Cell Press an Imprint of Elsevier
Identifiers: 991005540613807891
Copyright: © 2017 The Author.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biochemistry & Molecular Biology; Plant Sciences
ESI research areas: Plant & Animal Science