Background

Breeding for genes controlling key agronomic traits is an important goal of rice genetic improvement. To gain insight into genes controlling grain morphology, we screened M₃ plants derived from 1,000 whole-genome sequenced (WGS) M₂ Kitaake mutants to identify lines with altered grain size.

Results

In this study, we isolated a mutant, named fast-neutron (FN) 60–4, which exhibits a significant reduction in grain size. We crossed FN60–4 with the parental line Kitaake and analyzed the resulting backcross population. Segregation analysis of 113 lines from the BC₂F₂ population revealed that the mutant phenotype is controlled by a single semi-dominant locus. Mutant FN60–4 is reduced 20% in plant height and 8.8% in 1000-grain weight compared with Kitaake. FN60–4 also exhibits an 8% reduction in cell number and a 9% reduction in cell length along the vertical axis of the glume. We carried out whole-genome sequencing of DNA pools extracted from segregants with long grains or short grains, and revealed that one gene, LOC_Os09g02650, cosegregated with the grain size phenotype in the BC₁F₂ and BC₂F₂ populations. This mutant allele was named grain shape 9–1 (gs9–1). gs9–1 carries a 3-bp deletion that affects two amino acids. This locus is a new allele of the BC12/GDD1/MTD1 gene that encodes a kinesin-like protein involved in cell-cycle progression, cellulose microfibril deposition and gibberellic acid (GA) biosynthesis. The GA biosynthesis-related gene KO2 is down-regulated in gs9–1. The dwarf phenotype of gs9–1 can be rescued by adding exogenous GA₃. In contrast to the phenotypes for the other alleles, the gs9–1 is less severe, consistent with the nature of the mutation, which does not disrupt the open reading frame as observed for the other alleles.

Conclusions

In this study, we isolated a mutant, which exhibits altered grain shape and identified the mutated gene, gs9–1. Our study reveals that gs9–1 is a semi-dominant gene that carries a two-amino acid mutation. gs9–1 is allelic to the BC12/GDD1/MTD1 gene involved in GA biosynthesis. These results demonstrate the efficiency and convenience of cloning genes from the whole-genome sequenced Kitaake mutant population to advance investigations into genes controlling key agronomic traits in rice.

中文翻译：

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全基因组测序鉴定出稻粒形状突变体 gs9-1。

 背景

控制关键农艺性状的基因育种是水稻遗传改良的重要目标。为了深入了解控制籽粒形态的基因，我们筛选了源自 1,000 个全基因组测序 (WGS) M ₂ Kitaake 突变体的 M ₃植物，以鉴定籽粒大小发生改变的品系。

 结果

在这项研究中，我们分离出了一种名为快中子 (FN) 60-4 的突变体，它的晶粒尺寸显着减小。我们将 FN60-4 与亲本系 Kitaake 杂交，并分析了所得的回交群体。对来自 BC ₂ F ₂群体的 113 个品系的分离分析表明，突变表型由单个半显性基因座控制。突变体FN60-4与Kitaake相比，株高降低20%，千粒重降低8.8%。 FN60-4 还表现出沿颖片垂直轴的细胞数量减少 8%，细胞长度减少 9%。我们对从长粒或短粒分离子中提取的 DNA 库进行了全基因组测序，发现一个基因 LOC_Os09g02650 与 BC ₁ F ₂和 BC ₂ F ₂群体中的粒大小表型共分离。该突变等位基因被命名为谷粒形状 9-1 ( gs9-1 )。 gs9-1携带影响两个氨基酸的 3 bp 缺失。该基因座是BC12/GDD1/MTD1基因的一个新等位基因，编码参与细胞周期进程、纤维素微纤维沉积和赤霉酸 (GA) 生物合成的驱动蛋白样蛋白。 GA生物合成相关基因KO2在gs9-1中下调。 gs9-1的矮化表型可以通过添加外源GA ₃来挽救。与其他等位基因的表型相比， gs9-1 的严重程度较低，这与突变的性质一致，不会破坏其他等位基因观察到的开放阅读框。

 结论

在这项研究中，我们分离了一个突变体，它表现出改变的颗粒形状，并鉴定了突变基因gs9-1 。我们的研究表明， gs9-1是一个携带两个氨基酸突变的半显性基因。 gs9-1是参与 GA 生物合成的BC12/GDD1/MTD1基因的等位基因。这些结果证明了从全基因组测序的 Kitaake 突变体群体中克隆基因的效率和便利性，可以推进对控制水稻关键农艺性状的基因的研究。