Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform.
Genetic diversity
Linkage disequilibrium
Population structure
SNP
SilicoDArT
Wheat
Journal
3 Biotech
ISSN: 2190-572X
Titre abrégé: 3 Biotech
Pays: Germany
ID NLM: 101565857
Informations de publication
Date de publication:
Feb 2020
Feb 2020
Historique:
received:
13
06
2019
accepted:
08
12
2019
entrez:
1
2
2020
pubmed:
1
2
2020
medline:
1
2
2020
Statut:
ppublish
Résumé
In this study, 129 wheat genotypes from globally diverse origins were genotyped using DArTseq (SilicoDArT and SNP) markers. After filtering markers for quality-filtering, 14,270 SilicoDArTs and 6484 SNPs were retained and used for genetic diversity, population structure and linkage disequilibrium analyses. The highest number of SilicoDArT and SNP markers mapped on genome A and B compared to genome D. In both marker types, polymorphism information content (PIC) values ranged from 0.1 to 0.5, while > 0.80% of SilicoDArTs and > 0.44% SNPs showed PIC value more than median (0.25%). Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped wheat genotypes into three and four clusters, respectively. Principal component analysis and discriminant analysis of principal component results showed highly match with cluster and population structure analysis. Linkage disequilibrium (LD) was more extensive in both marker types, while graphical display of LD decay for both marker types showed that LD declined in the region close to 15 kbp, where
Identifiants
pubmed: 32002339
doi: 10.1007/s13205-019-2014-z
pii: 2014
pmc: PMC6960278
doi:
Types de publication
Journal Article
Langues
eng
Pagination
48Informations de copyright
© King Abdulaziz City for Science and Technology 2020.
Déclaration de conflit d'intérêts
Conflict of interestThe authors declare no conflict of interest.
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