Data from: Estimating parent-specific QTL effects through cumulating linked identity-by-state SNP effects in multi-parental populations

The emergence of multi-parental mapping populations enabled plant geneticists to gain deeper insights into the genetic architecture of major agronomic traits and to map quantitative trait loci (QTL) controlling the expression of those traits. Although the investigated mapping populations are similar, one open question is whether genotype data should be modelled as identical-by-state (IBS) or identical-by-descent (IBD). While IBS simply makes use of raw genotype scores to distinguish alleles, IBD data are derived from parental offspring information. We report on comparing IBS and IBD by applying two multiple regression models on four traits studied in the barley nested association mapping (NAM) population HEB-25. We observed that modelling parent-specific IBD genotypes produced a lower number of significant QTL with increased prediction abilities compared to modelling IBS genotypes. However, at lower trait heritabilities the IBS model produced higher prediction abilities. We developed a method to estimate multi-allelic QTL effects in multi-parental populations from simple bi-allelic IBS data. This method is based on cumulating IBS-derived SNP effect estimates in a defined genetic region surrounding a QTL. Comparing the resulting parent-specific QTL effects with those obtained from IBD approaches revealed high accordance that could be confirmed through simulations. The method turned out to be also applicable to a barley multi-parent advanced generation inter-cross (MAGIC) population. The ‘cumulation method’ represents a universal approach to differentiate parent-specific QTL effects in multi-parental populations, even if no IBD information is available. In future, the method could further benefit from the availability of much denser SNP maps.多亲本作图群体的出现，使植物遗传学家得以更深入地解析主要农艺性状的遗传架构，并定位调控这些性状表达的数量性状位点（quantitative trait loci, QTL）。尽管所研究的作图群体具有相似性，但仍存在一个悬而未决的问题：基因型数据应按照状态同源（identical-by-state, IBS）还是血统同源（identical-by-descent, IBD）进行建模。状态同源仅利用原始基因型得分区分等位基因，而血统同源数据则源于亲本-后代信息。本研究通过对大麦巢式关联作图（nested association mapping, NAM）群体HEB-25中的4个性状应用两种多元回归模型，对比了IBS与IBD两种建模方式。 我们观察到，相较于对状态同源基因型进行建模，对亲本特异性血统同源基因型建模得到的显著QTL数量更少，但预测能力更高；不过在性状遗传率较低的情况下，状态同源模型的预测能力反而更高。我们开发了一种方法，可从简单的双等位基因状态同源数据中估算多亲本群体中的多等位基因QTL效应。该方法基于对QTL侧翼特定遗传区域内由状态同源数据得到的单核苷酸多态性（single nucleotide polymorphism, SNP）效应估计值进行累积。将得到的亲本特异性QTL效应与通过血统同源方法得到的效应进行对比，结果显示二者高度一致，该结论可通过模拟试验验证。该方法还被证实可应用于大麦多亲本高级世代互交（multi-parent advanced generation inter-cross, MAGIC）群体。“累积法”（cumulation method）是一种可在多亲本群体中区分亲本特异性QTL效应的通用方法，即便无法获取血统同源信息也可使用。未来，更高密度的单核苷酸多态性图谱将进一步助力该方法的优化与应用。