2010
DOI: 10.1186/1471-2164-11-727
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Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

Abstract: BackgroundSingle nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.ResultsMost of the wheat oligo pool assay (OPA) SNPs that… Show more

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citations
Cited by 209 publications
(233 citation statements)
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References 75 publications
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“…The D-genome exhibited the highest extent of LD decay distance as compared to A and B genomes. Similar results were also reported in a previous study on wheat genotypes (Chao et al, 2010). More extended LD decay distance in the D-genome than in the A and B genomes could be due to the introduction of new haplotype, which can increase the extent of LD from Aegilops tauschii (D-genome donor) into the Dgenome of hexaploid wheat.…”
Section: Determination Of Population Structure and Estimation Of Ld Dsupporting
confidence: 89%
“…The D-genome exhibited the highest extent of LD decay distance as compared to A and B genomes. Similar results were also reported in a previous study on wheat genotypes (Chao et al, 2010). More extended LD decay distance in the D-genome than in the A and B genomes could be due to the introduction of new haplotype, which can increase the extent of LD from Aegilops tauschii (D-genome donor) into the Dgenome of hexaploid wheat.…”
Section: Determination Of Population Structure and Estimation Of Ld Dsupporting
confidence: 89%
“…Low genetic differentiation between landraces and modern cultivars suggests that selection during wheat breeding, when we consider the total population, has not dramatically altered allele frequency genome-wide, but may have been accomplished by selection on a relatively limited number of loci. At the same time strong geographic differentiation among wheat populations found in the current and previously published studies (25)(26)(27)(28) and the relatedness of landraces and cultivars suggest that the use of distinct founders as well as allele-frequency divergence from the ancestral population of landraces could have contributed to the development of regional breeding populations. Relatively few alleles were exclusive to to wheat cultivars.…”
Section: Discussionsupporting
confidence: 48%
“…Although multiple studies have reported the genetic basis of individual phenotypes associated with wheat improvement and adaptation (9,12,(20)(21)(22)(23)(24) or sought to characterize the structure of genetic variation in regional populations (25)(26)(27)(28), the genome-scale impact of selection for improvement on the patterns of genetic variation in wheat remains largely unknown. Here we performed single-nucleotide polymorphism (SNP) discovery in the wheat transcriptome and developed a high-throughput SNP genotyping array.…”
mentioning
confidence: 99%
“…However, several variations in the LD pattern of the germplasm reflected a complexity of the evolutionary and breeding history of wheat (Dubcovsky and Dvorak 2007). The lower values of LD observed in WSHs are in concordance of what has been previously reported by Chao et al (2010) using the SNP marker system. They reported that CIMMYT wheat populations with the lowest LD among completely linked loci and the slowest rate of LD decay was possibly a consequence of an intensive use of synthetic wheat lines.…”
Section: Ld-based Diversitysupporting
confidence: 86%
“…A number of LD-based mapping and diversity studies in wheat have been conducted at the genome or chromosome levels (Breseghello and Sorrells 2006, Chao et al 2007, Somers et al 2004, Horvath et al 2009, Chao et al 2010, Hao et al 2011, Maccaferri et al 2011. Nevertheless it is important to characterize germplasm for examining the extent of LD to study the genetic diversity.…”
Section: Ld-based Diversitymentioning
confidence: 99%