Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection.
Genetic diversity
Genome wide association
Linkage disequilibrium
Phylogenetic network tree
Population structure
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
11 Jun 2019
11 Jun 2019
Historique:
received:
29
10
2018
accepted:
21
05
2019
entrez:
13
6
2019
pubmed:
13
6
2019
medline:
8
11
2019
Statut:
epublish
Résumé
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. LD persists over long distances in the collection, decaying to r 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.
Sections du résumé
BACKGROUND
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
RESULTS
LD persists over long distances in the collection, decaying to r
CONCLUSIONS
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.
Identifiants
pubmed: 31185892
doi: 10.1186/s12864-019-5824-9
pii: 10.1186/s12864-019-5824-9
pmc: PMC6558826
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
481Subventions
Organisme : Oak Ridge Institute for Science and Education
ID : NA
Organisme : USDA-ARS
ID : Project 5030-21000-062-00D
Organisme : The Peanut Foundation
ID : 04-815-13
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