W7984 x Opata M85 fine-mapping chromosome 5AS structural variation

In this study, we sought to positionally clone the causal genetic variant of a thousand grain weight, TGW, quantitative trait loci, QTL, on wheat chromosome 5AL. We developed a heterogenous inbred family, HIF, of more than 5,000 plants for enhanced genotypic resolution and fine-mapped the QTL to a ten Mbp region. The transcriptome of developing grains from four positive and negative control HIF haplotypes revealed chromosome 5AS genomic structural variation of presence or absence, previously identified by Gutierrez-Gonzalez et al., 2019, and unexpectedly no differential expression of genes within the 5AL candidate region. Evaluation of genomic, transcriptomic, and phenotypic data, and predicted function of genes, identified that the 5AL QTL was an artifact of strong linkage disequilibrium with chromosome 5AS presence and absence. Structural variation is common in wheat, and our results highlight that the redundant polyploid genome masking of such variation is a significant barrier to positional cloning.

在本项研究中，我们旨在对小麦5AL染色体上影响千粒重（TGW）的因果遗传变异进行定位克隆。我们构建了一个包含超过5,000个植株的异质近交系（HIF），以提升基因型的分辨率，并将数量性状位点（QTL）精细定位至一个10 Mbp的区域内。通过对四个阳性及阴性控制HIF单倍型的发育籽粒转录组进行分析，揭示了5AS染色体的基因组结构变异，即存在与否，这一变异已由Gutierrez-Gonzalez等人于2019年发现，且令人意外的是，5AL候选区域内未观察到基因表达的差异。对基因组、转录组、表型数据以及基因预测功能的评估表明，5AL QTL是5AS存在与否的强连锁不平衡的产物。结构变异在小麦中普遍存在，我们的研究强调了此类变异被冗余的多倍体基因组掩盖，从而成为定位克隆的重大障碍。