N'Diaye Amidou, Haile Jemanesh K, Cory Aron T, Clarke Fran R, Clarke John M, Knox Ron E, Pozniak Curtis J
Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada.
PLoS One. 2017 Jan 30;12(1):e0170941. doi: 10.1371/journal.pone.0170941. eCollection 2017.
Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.
关联作图通常通过检测单个标记与表型之间的相关性来进行。然而，由于基因组内的变异模式是以块的形式遗传的，因此将标记聚类为单倍型进行全基因组扫描可能是一种提高检测关联统计功效的有效方法。高密度分子数据的可用性使得评估这两种方法在硬粒小麦中鉴定标记-性状关联的潜力成为可能。在本研究中，我们使用基于单个标记和单倍型的方法来鉴定与硬粒小麦粗粒粉和意大利面颜色相关的位点，主要目的是评估基于单倍型分析在鉴定数量性状位点方面的潜在益处。使用Illumina 90K Infinium iSelect分析法对169个硬粒小麦品系进行基因分型，生成了12234个多态性单核苷酸多态性（SNP）标记，并用于评估群体结构和连锁不平衡（LD）模式。基于5.3 cM的平均LD距离，将先前定位到高密度共识图谱上的总共8581个SNP聚类为406个单倍型块。将多个SNP组合成单倍型块可使平均多态性信息含量（PIC）从每个SNP的0.27提高到每个单倍型的0.50。基于单倍型的分析鉴定出12个与籽粒色素颜色性状相关的位点，包括基于单个标记的分析鉴定出的5个位点。此外，与单个标记分析相比，基于单倍型的分析导致解释的表型变异（平均50.4%）和等位基因效应（平均33.7%）增加。每个单倍型位点内存在多个等位基因组合为筛选最有利的单倍型系列提供了潜力，并可能有助于硬粒小麦籽粒色素颜色的标记辅助选择。这些结果表明，基于单倍型的分析在检测硬粒小麦中与颜色性状相关的位点方面优于单个标记分析。
