Regulatory sequence diversity in the wheat genome

Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. We used diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluated their effects on the population-scale variation in homoeolog expression dosage. The genetic diversity in the wheat genome was characterized using combination of complexity reduced genome sequencing, array-based genotyping, transcriptome sequencing and targeted re-sequencing of promoter regions. To better understand the functional properties of variants associated with homoeolog expression variation, we investigated the distribution of cis- and trans-acting eQTL across genomic regions showing distinct epigenetic marks and chromatin architecture. Finally, summary-level eQTL and GWAS mapping data, and gene co-expression networks were analyzed jointly to investigate the role of variants linked with homoeologous gene regulation in shaping variation in major agronomic traits in wheat landraces and cultivars.