Table_2_Gene Duplication and Evolution Dynamics in the Homeologous Regions Harboring Multiple Prolamin and Resistance Gene Families in Hexaploid Wheat.PDF

Improving end-use quality and disease resistance are important goals in wheat breeding. The genetic loci controlling these traits are highly complex, consisting of large families of prolamin and resistance genes with members present in all three homeologous A, B, and D genomes in hexaploid bread wheat. Here, orthologous regions harboring both prolamin and resistance gene loci were reconstructed and compared to understand gene duplication and evolution in different wheat genomes. Comparison of the two orthologous D regions from the hexaploid wheat Chinese Spring and the diploid progenitor Aegilops tauschii revealed their considerable difference due to the presence of five large structural variations with sizes ranging from 100 kb to 2 Mb. As a result, 44% of the Ae. tauschii and 71% of the Chinese Spring sequences in the analyzed regions, including 79 genes, are not shared. Gene rearrangement events, including differential gene duplication and deletion in the A, B, and D regions, have resulted in considerable erosion of gene collinearity in the analyzed regions, suggesting rapid evolution of prolamin and resistance gene families after the separation of the three wheat genomes. We hypothesize that this fast evolution is attributed to the co-evolution of the two gene families dispersed within a high recombination region. The identification of a full set of prolamin genes facilitated transcriptome profiling and revealed that the A genome contributes the least to prolamin expression because of its smaller number of expressed intact genes and their low expression levels, while the B and D genomes contribute similarly.

提升小麦加工品质与抗病性是小麦育种的重要目标。调控上述性状的遗传位点极为复杂，由多组醇溶蛋白（prolamin）基因家族与抗病基因家族构成，在六倍体普通小麦的三个部分同源A、B、D基因组中均存在同源成员。本研究构建了同时包含醇溶蛋白与抗病基因位点的同源（orthologous）区域并开展比较分析，以解析不同小麦基因组内的基因重复与进化模式。通过对比六倍体小麦中国春与二倍体祖先种节节麦（Aegilops tauschii）的两个同源D基因组区域，研究发现二者存在显著差异：二者共携带5个长度介于100 kb至2 Mb的大型结构变异。受此影响，分析区域内节节麦序列的44%与中国春序列的71%（包含79个基因）均无同源共享序列。A、B、D基因组区域内发生的基因重排事件（包括差异化的基因重复与缺失）已大幅削弱了分析区域内的基因共线性，这表明三个小麦基因组分化后，醇溶蛋白与抗病基因家族经历了快速进化。我们推测该快速进化源于两个基因家族在高重组区域内的协同演化。通过系统鉴定全部醇溶蛋白基因，本研究完成了转录组分析（transcriptome profiling），结果显示A基因组对醇溶蛋白总表达量的贡献最低——这是由于A基因组中表达的完整醇溶基因数量更少，且单基因表达水平更低；而B与D基因组的贡献程度相近。