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Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection

BACKGROUND: Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to c...

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Autores principales: Otyama, Paul I., Wilkey, Andrew, Kulkarni, Roshan, Assefa, Teshale, Chu, Ye, Clevenger, Josh, O’Connor, Dan J., Wright, Graeme C., Dezern, Stanley W., MacDonald, Gregory E., Anglin, Noelle L., Cannon, Ethalinda K. S., Ozias-Akins, Peggy, Cannon, Steven B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558826/
https://www.ncbi.nlm.nih.gov/pubmed/31185892
http://dx.doi.org/10.1186/s12864-019-5824-9
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author Otyama, Paul I.
Wilkey, Andrew
Kulkarni, Roshan
Assefa, Teshale
Chu, Ye
Clevenger, Josh
O’Connor, Dan J.
Wright, Graeme C.
Dezern, Stanley W.
MacDonald, Gregory E.
Anglin, Noelle L.
Cannon, Ethalinda K. S.
Ozias-Akins, Peggy
Cannon, Steven B.
author_facet Otyama, Paul I.
Wilkey, Andrew
Kulkarni, Roshan
Assefa, Teshale
Chu, Ye
Clevenger, Josh
O’Connor, Dan J.
Wright, Graeme C.
Dezern, Stanley W.
MacDonald, Gregory E.
Anglin, Noelle L.
Cannon, Ethalinda K. S.
Ozias-Akins, Peggy
Cannon, Steven B.
author_sort Otyama, Paul I.
collection PubMed
description BACKGROUND: Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. RESULTS: LD persists over long distances in the collection, decaying to r(2) = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. CONCLUSIONS: Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5824-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-65588262019-06-13 Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection Otyama, Paul I. Wilkey, Andrew Kulkarni, Roshan Assefa, Teshale Chu, Ye Clevenger, Josh O’Connor, Dan J. Wright, Graeme C. Dezern, Stanley W. MacDonald, Gregory E. Anglin, Noelle L. Cannon, Ethalinda K. S. Ozias-Akins, Peggy Cannon, Steven B. BMC Genomics Research Article BACKGROUND: Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. RESULTS: LD persists over long distances in the collection, decaying to r(2) = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. CONCLUSIONS: Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5824-9) contains supplementary material, which is available to authorized users. BioMed Central 2019-06-11 /pmc/articles/PMC6558826/ /pubmed/31185892 http://dx.doi.org/10.1186/s12864-019-5824-9 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Otyama, Paul I.
Wilkey, Andrew
Kulkarni, Roshan
Assefa, Teshale
Chu, Ye
Clevenger, Josh
O’Connor, Dan J.
Wright, Graeme C.
Dezern, Stanley W.
MacDonald, Gregory E.
Anglin, Noelle L.
Cannon, Ethalinda K. S.
Ozias-Akins, Peggy
Cannon, Steven B.
Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
title Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
title_full Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
title_fullStr Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
title_full_unstemmed Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
title_short Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
title_sort evaluation of linkage disequilibrium, population structure, and genetic diversity in the u.s. peanut mini core collection
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558826/
https://www.ncbi.nlm.nih.gov/pubmed/31185892
http://dx.doi.org/10.1186/s12864-019-5824-9
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