A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication,Journal of Integrative Plant Biology

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A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication
Journal of Integrative Plant Biology ( IF 9.3 ) Pub Date : 2023-08-27 , DOI: 10.1111/jipb.13559
Siming Wei _{1,

2,

3} , Bin Yong _{1,

2,

3} , Hongwei Jiang _{4,

5} , Zhenghong An _{1,

2,

3} , Yan Wang _{1,

2} , Bingbing Li _{1,

2,

3} , Ce Yang _{1,

2,

3} , Weiwei Zhu _{1,

2,

3} , Qingshan Chen ₄ , Chaoying He _{1,

2,

3,

6}

Affiliation

The resultant DNA from loss-of-function mutation can be recruited in biological evolution and development. Here, we present such a rare and potential case of “to gain by loss” as a neomorphic mutation during soybean domestication for increasing seed weight. Using a population derived from a chromosome segment substitution line of Glycine max (SN14) and Glycine soja (ZYD06), a quantitative trait locus (QTL) of 100-seed weight (qHSW) was mapped on chromosome 11, corresponding to a truncated β-1, 3-glucosidase (βGlu) gene. The novel gene hsw results from a 14-bp deletion, causing a frameshift mutation and a premature stop codon in the βGlu. In contrast to HSW, the hsw completely lost βGlu activity and function but acquired a novel function to promote cell expansion, thus increasing seed weight. Overexpressing hsw instead of HSW produced large soybean seeds, and surprisingly, truncating hsw via gene editing further increased the seed size. We further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed size. Transcriptomic variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size control. Moreover, the hsw allele underwent selection and expansion during soybean domestication and improvement. Our work cloned a likely domesticated QTL controlling soybean seed weight, revealed a novel genetic variation and mechanism in soybean domestication, and provided new insight into crop domestication and breeding, and plant evolution.

中文翻译：

糖基水解酶基因的功能丧失突变等位基因已被用于大豆驯化过程中的种子重量控制

功能丧失突变产生的 DNA 可以在生物进化和发育中被招募。在这里，我们提出了这种罕见且潜在的“以失而得”的案例，作为大豆驯化过程中增加种子重量的新形态突变。使用源自大豆(SN14) 和大豆(ZYD06) 染色体片段替换系的群体，将 100 粒种子重 ( qHSW ) 的数量性状位点 (QTL) 映射到 11 号染色体上，对应于截短的 β- 1、3-葡萄糖苷酶（βGlu）基因。新基因hsw源自 14 bp 缺失，导致移码突变和βGlu中的过早终止密码子。与HSW相比， hsw完全丧失了 βGlu 活性和功能，但获得了促进细胞扩张的新功能，从而增加了种子重量。过度表达hsw而不是HSW产生了大的大豆种子，令人惊讶的是，通过基因编辑截断hsw进一步增加了种子的大小。我们进一步发现hsw及其变体的核心21-aa肽充当种子大小的启动子。这些转基因大豆品系的转录组变异证实了 hsw 与细胞和种子大小控制的整合。此外， hsw等位基因在大豆驯化和改良过程中经历了选择和扩增。我们的工作克隆了一个可能控制大豆种子重量的驯化QTL，揭示了大豆驯化的新遗传变异和机制，并为作物驯化和育种以及植物进化提供了新的见解。

更新日期：2023-08-27

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