Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, China.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
Sci China Life Sci. 2020 Oct;63(10):1565-1579. doi: 10.1007/s11427-019-1618-7. Epub 2020 Feb 24.
Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization. However, the global gene pattern variation during early fiber development was unknown. In this study, through RNA-seq technology, we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton (G. hirsutum) and its diploid progenitors (G. arboreum and G. raimondii) at the fiber early development stage. In tetraploid cotton, genes showed expression level dominance (ELD) bias toward the A genome. This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor (D genome). Gene ontology (GO) enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession, and the ELD-D genes might be involved in transcription regulation and stress inducement. In addition, the number and proportion of completely A- and D-subfunctionalized gene were similar at different fiber development stages. However, for neofunctionalization, the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA. Eventually, we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process, further making the fiber property meet the human demands. Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages, providing new insights into the mechanism of cotton fiber evolution.
天然异源四倍体棉花被广泛用作研究多倍化导致基因表达重塑的理想模型。然而，早期纤维发育过程中全局基因模式的变化尚不清楚。在这项研究中，我们通过 RNA-seq 技术，全面研究了异源四倍体棉花（G. hirsutum）与其二倍体祖先（G. arboreum 和 G. raimondii）在纤维早期发育阶段同源基因的表达模式。在四倍体棉花中，基因表现出表达水平优势（ELD）偏向 A 基因组。这种现象可以通过非优势祖先（D 基因组）同源物的上调/下调来解释。基因本体（GO）富集结果表明，ELD-A 基因可能是通过调节脂肪酸生物合成/代谢和微管进程导致纤维特性变化的主要原因，而 ELD-D 基因可能参与转录调控和应激诱导。此外，在不同的纤维发育阶段，完全 A-和 D-亚功能化基因的数量和比例相似。然而，对于新功能化，在 3 和 5 DPA 时，重新激活的 D 衍生基因的数量和比例大于 A。最终，我们发现，在多倍化和驯化过程中，一些属于几个特定途径的同源基因可能在两个亚基因组之间产生新的不对称转录本，进一步使纤维特性满足人类需求。我们的研究在早期纤维发育阶段确定了异源四倍体棉花与其祖先之间的决定途径及其涉及的基因，为棉花纤维进化的机制提供了新的见解。
