Abstract
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.
Highlights
Soybean [Glycine max (L.) Merr.], the most important crop among legumes, providing ~70% of dietary proteins and ~30% of edible oil worldwide (Lam et al, 2010), was domesticated from its annual wild relative, Glycine soja, in China 5000 years ago (Hymowitz, 1970; Carter et al, 2004)
A soybean pan-genome analysis has identified genes, such as senescenceassociated gene 101 (SAG101), with amino acid changes resulting from large-effect single nucleotide polymorphisms (SNPs) and/ or indels (Li et al, 2014).These results indicate that changes affecting protein sequences are a source of genetic variation in soybean domestication
The four wild accessions were abbreviated to Y1,Y2, Y3, and Y4, while the four cultivated soybeans were abbreviated to DN, HF, HN, and NF.They displayed a rich diversity in flower color, seed coat color, seed size, oil content, protein content, and isoflavone content (Supplementary Dataset S1), suggesting full representation of wild and cultivated soybeans in this geographic region
Summary
Soybean [Glycine max (L.) Merr.], the most important crop among legumes, providing ~70% of dietary proteins and ~30% of edible oil worldwide (Lam et al, 2010), was domesticated from its annual wild relative, Glycine soja, in China 5000 years ago (Hymowitz, 1970; Carter et al, 2004). A few genes have been found to be involved in soybean domestication and improvement through various strategies, such as mapping of quantitative trait loci (QTLs). These genes include early maturity 1 (E1), GIGANTEA (GI), and the juvenile (J) locus, which regulate maturity and flowering time (Watanabe et al, 2011; Xia et al, 2012; Wang et al, 2016; Lu et al, 2017); GmHs1-1, which controls hard seededness (Sun et al, 2015); pod dehiscence 1(PDH1), which confers pod-shattering resistance (Funatsuki et al, 2014); and determinate stem locus (Dt1 and Dt2), which controls determinate growth (Liu et al, 2010; Ping et al, 2014). Increasing advances in sequencing technology have provided a genomic platform (Metzker, 2010) to predict the domesticated genes in various crops, such as rice (Huang et al, 2012;Wang et al, 2018), maize (Swanson-Wagner et al, 2012), and tomato (Koenig et al, 2013).This is having a significant impact on molecular breeding programs (Poland and Rife, 2012)
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