School of Life Sciences, Qufu Normal University, 273165, Qufu, Shandong Province, China.
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
Nat Commun. 2019 Nov 27;10(1):5399. doi: 10.1038/s41467-019-13386-w.
Cis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton (Gossypium hirsutum) and their reciprocal F hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%-64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic loci responsible for domestication traits. With respect to regulatory evolution, the two subgenomes of allotetraploid cotton are often uncoupled. Overall, our work underscores the complexity of regulatory evolution during fiber domestication and may facilitate new approaches for improving cotton and other polyploid plants.
顺式和反式调控分歧是表型和进化多样化的基础。对于作物驯化过程中伴随的调控进化的复杂性，人们相对知之甚少，特别是对于多倍体植物。在这里，我们比较了野生和驯化棉花（Gossypium hirsutum）及其正反交 F1 杂种之间的纤维转录组，揭示了在分歧和驯化过程中全基因组 (~15%)和经常补偿性顺式和反式调控变化。观察到的高水平的转进化（54%-64%）可能是多倍化后基因组冗余所允许的。我们的结果表明，调控变异与序列进化、亲本表达模式的遗传、共表达基因网络特性以及负责驯化性状的基因组位点显著相关。就调控进化而言，异源四倍体棉花的两个亚基因组通常是不相关的。总的来说，我们的工作强调了纤维驯化过程中调控进化的复杂性，并可能为改进棉花和其他多倍体植物提供新的方法。
