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.