Abstract
BackgroundThe genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach.ResultsMore than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs.ConclusionsOur results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.
Highlights
The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding
The mapping quality assessed according to the number of Basic Local Alignment Search Tool (BLAST) hits per marker and the maximum similarity score was lower for single nucleotide polymorphisms (SNP) (Table 1, Fig. 1)
A comparative analysis of the distribution of trimmed sequences classified by the sequence length and maximum BLAST score indicated that most of the SNP and silicoDArT markers between 20 and 50 bp had a maximum score below 95%, which corresponded to decreased specificity
Summary
The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the highdensity genotyping-by-sequencing approach. Various approaches are currently being used to increase wheat yields to satisfy the expected demand for food sources. Doubling the wheat yield by 2050 [2] is a challenging goal and will require the application of the increased genetic diversity of landraces well adapted to different stresses [3], synthetic wheat varieties [4], and wild relatives [2]. One of the milestones toward the development of high-yielding and climate-smart ‘ generation varieties’ was the sequencing of the 17 Gb allohexaploid wheat (AABBDD) genome [5, 6]. The wheat reference sequence was annotated with various genetic markers that were historically used for evaluating genetic resources to enhance wheat production
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