State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
J Exp Bot. 2018 Oct 12;69(21):5089-5104. doi: 10.1093/jxb/ery291.
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestication. Moreover, the most divergent stage in gene expression between wild and cultivated soybeans occurred during seed development around the cotyledon stage (15 d after fertilization, G15). A module in which the co-expressed genes were significantly down-regulated at G15 of wild soybeans was identified. The divergent clusters and modules included substantial differentially expressed genes (DEGs) between wild and cultivated soybeans related to cell division, storage compound accumulation, hormone response, and seed maturation processes. Chromosomal-linked DEGs, quantitative trait loci controlling seed weight and oil content, and selection sweeps revealed candidate DEGs at G15 in the fruit-related divergence of G. max and G. soja. Our work establishes a transcriptomic selection mechanism for altering gene expression during soybean domestication, thus shedding light on the molecular networks underlying soybean seed development and breeding strategy.
大豆（Glycine max）是由其野生近缘种大豆（Glycine soja）驯化而来。然而，大豆驯化的遗传变异尚不清楚。比较转录组学表明，一小部分直系同源基因可能进化得很快。相比之下，有三个基因表达簇因其表达模式而被鉴定为差异表达，它们占据了总基因的 37.44%，暗示基因表达改变在大豆驯化中起着重要作用。此外，在野生和栽培大豆之间，基因表达最具差异的阶段发生在种子发育过程中，大约在子叶期（受精后 15 天，G15）。鉴定到一个模块，其中在 G15 时，野生大豆中的共表达基因显著下调。差异表达基因（DEGs）在野生和栽培大豆之间存在大量差异，涉及细胞分裂、储存化合物积累、激素反应和种子成熟过程。与果实相关的 G. max 和 G. soja 分化中的染色体连锁 DEGs、控制种子重量和油含量的数量性状位点以及选择清扫揭示了 G15 时的候选 DEGs。我们的工作建立了一个在大豆驯化过程中改变基因表达的转录组选择机制，从而为大豆种子发育和育种策略的分子网络提供了新的认识。
