Population structure and association analyses of the core collection of hexaploid accessions conserved ex situ in the Japanese gene bank NBRP-Wheat
| Autor: | Shotaro Takenaka, Miyuki Nitta, Shuhei Nasuda |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
0301 basic medicine Genetics Genetic diversity Quantitative Trait Loci food and beverages Single-nucleotide polymorphism General Medicine Biology Quantitative trait locus Polymorphism Single Nucleotide 01 natural sciences Polyploidy 03 medical and health sciences 030104 developmental biology Gene bank Genetic marker Genotype Genetic variation Molecular Biology Triticum 010606 plant biology & botany Genetic association |
| Zdroj: | Genes & Genetic Systems. 93:237-254 |
| ISSN: | 1880-5779 1341-7568 |
| Popis: | In this study, we investigated the genetic diversity and population structure of the core collection of hexaploid wheat accessions in the Japanese wheat gene bank NBRP-Wheat. The core collection, consisting of 188 accessions of Triticum aestivum, T. spelta, T. compactum, T. sphaerococcum, T. macha and T. vavilovii, was intensively genotyped by DArTseq markers and consisted of 20,186 SNPs and 60,077 present and absent variations (PAVs). Polymorphic markers were distributed in all chromosomes, with a tendency for smaller numbers on the D-genome chromosomes. We examined the population structure by Bayesian clustering and principal component analysis with a general linear model. Overall, the core collection was divided into seven clusters. Non-admixture accessions in each cluster indicated that the clusters reflect the geographic distribution of the accessions. Both structure analyses strongly suggested that the cluster consisting of T. spelta and T. macha is out-grouped from other hexaploid wheat accessions. We performed genome-wide association analysis pilot studies for nine quantitative and seven qualitative traits and found marker-trait associations for all traits but one, indicating that the current core collection will be useful for detecting uncharacterized QTLs associated with phenotypes of interest. |
| Databáze: | OpenAIRE |
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