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.

异源多倍性极大拓展了功能冗余的部分同源基因（homoeologous genes）间潜在的调控互作范围。然而，新兴的调控复杂性与多倍体作物的表达及表型多样性之间的关联仍尚不明确。本研究利用多样化的小麦种质资源绘制了表达数量性状位点（expression quantitative trait loci）图谱，并评估了其对部分同源基因表达剂量的群体水平变异的调控效应。研究通过整合简化基因组测序、芯片基因分型、转录组测序及启动子区域靶向重测序等技术，对小麦基因组的遗传多样性进行了系统表征。为深入解析与部分同源基因表达变异相关的遗传变异的功能属性，我们探究了顺式和反式作用eQTL在具有独特表观遗传标记和染色质结构的基因组区域中的分布特征。最后，本研究联合分析了汇总级eQTL与全基因组关联分析（genome-wide association study, GWAS）定位数据及基因共表达网络，以探究与部分同源基因调控相关的变异位点在塑造小麦地方品种与栽培品种主要农艺性状变异中的作用。