Yang Tifeng, Gu Haiyong, Yang Wu, Liu Bin, Liang Shihu, Zhao Junliang
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
Rice (N Y). 2023 Jan 17;16(1):3. doi: 10.1186/s12284-023-00620-9.
Grain shape is a key trait in rice breeding. Although many QTLs and genes of grain shape have been identified, how different combinations of alleles of these genes affect grain shape is largely unknown. It is important to understand the effects of grain shape gene combinations for breeding by design. In the present study, we performed genetic dissection of the grain shapes in Guangdong Simiao varieties, a popular kind of rice in South China, to identify the effective alleles and their combination for breeding.
We selected two hundred nineteen indica accessions with diverse grain shapes and fifty-two Guangdong Simiao varieties with long and slender grain shapes for genome-wide selection analysis. The results showed that four (GS3, GS5, GW5 and GL7) of the twenty grain shape genes fall into the regions selected for in Guangdong Simiao varieties. Allele analysis and frequency distribution of these four genes showed that GS3 and GW5 accounted for 96.2%, and GL7 and GS5 accounted for 76.9% and 74.5% of the Simiao varieties, respectively. Further analysis of the allelic combinations showed that 30 allelic combinations were identified in the whole panel, with 28 allelic combinations found in the international indica accessions and 6 allelic combinations found in Guangdong Simiao varieties. There were mainly three combinations (combinations 17, 18 and 19) in the Guangdong Simiao varieties, with combination 19 (GS3 + GW5 + GL7 + GS5) having the highest percentage (51.9%). All three combinations carried GS3 + GW5, while combinations 17 (GL7) and 19 (GL7) showed significant differences in both grain length and length/width ratio due to differences in GL7 alleles. Pedigree analysis of Guang8B, the maintainer of the first released Simiao male sterile line Guang8A, showed that the parent lines and Guang8B carried GS3 + GW5 + GS5, while the GL7 allele differed, resulting in significant differences in grain size.
The results suggest that specific alleles of GS3, GS5, GW5 and GL7 are the key grain shape genes used in the Guangdong Simiao varieties and selected for grain shape improvement. Combination 19 is the predominant allelic combination in the Guangdong Simiao varieties. Our current study is the first to dissect the genetics of grain shape in Guangdong Simiao varieties, and the results will facilitate molecular breeding of Guangdong Simiao varieties.
粒形是水稻育种中的关键性状。尽管已经鉴定出许多控制粒形的数量性状基因座（QTL）和基因，但这些基因的不同等位基因组合如何影响粒形在很大程度上仍不清楚。了解粒形基因组合的效应对于设计育种很重要。在本研究中，我们对华南地区一种受欢迎的水稻品种——广东丝苗品种的粒形进行了遗传剖析，以鉴定用于育种的有效等位基因及其组合。
我们选择了219份粒形各异的籼稻种质和52份粒形细长的广东丝苗品种进行全基因组选择分析。结果表明，20个粒形基因中的4个（GS3、GS5、GW5和GL7）位于广东丝苗品种选择的区域内。这4个基因的等位基因分析和频率分布表明，GS3和GW5在丝苗品种中的占比分别为96.2%，GL7和GS5分别占76.9%和74.5%。对等位基因组合的进一步分析表明，在整个群体中鉴定出30种等位基因组合，在国际籼稻种质中发现28种等位基因组合，在广东丝苗品种中发现6种等位基因组合。广东丝苗品种中主要有三种组合（组合17、18和19），其中组合19（GS3 + GW5 + GL7 + GS5）的占比最高（51.9%）。所有三种组合都含有GS3 + GW5，而组合17（GL7）和19（GL7）由于GL7等位基因的差异，在粒长和长宽比上均表现出显著差异。首个育成的丝苗型雄性不育系广8A的保持系广8B的系谱分析表明，亲本系和广8B携带GS3 + GW5 + GS5，而GL7等位基因不同，导致粒大小存在显著差异。
结果表明，GS3、GS5、GW5和GL7的特定等位基因是广东丝苗品种中用于粒形改良的关键粒形基因。组合19是广东丝苗品种中的主要等位基因组合。我们目前的研究首次剖析了广东丝苗品种粒形的遗传学，研究结果将有助于广东丝苗品种的分子育种。
