Background

Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers.

Result

In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F₂ population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio.

Conclusions

The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

中文翻译：

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使用针对水稻 14 个基因的新型功能标记进行粒度选择。

 背景

籽粒大小是水稻育种极其重要的一个方面，影响籽粒产量和品质性状。它由多个基因控制，在育种计划中跟踪这些基因应能加快选择具有优异谷物产量和品质的品系，因此开发稳健、高效的标记至关重要。

 结果

在本研究中，选择了14个与籽粒大小相关的基因（ GW2 、 GS2 、 qLGY3 、 GS3 、 GL3.1 、 TGW3 、 GS5 、 GW5 、 GS6 、 TGW6 、 GW6a 、 GLW7 、 GL7和GW8 ）用于功能标记开发。开发了二十一个基于PCR凝胶的标记来对这些基因的候选功能核苷酸多态性（FNP）进行基因分型，并且所有标记都可以有效识别相应的等位基因类型。为了测试不同 FNP 的等位基因效应，使用了包括来自水稻多样性组 1 的 257 个种质在内的全球水稻品种进行等位基因挖掘，并在两个种植地点调查了四种与颗粒大小相关的性状。 GW2 、 GS2和GL3.1的三个FNP被基因分型为仅在具有明显大粒的品种中发现的稀有等位基因，并且其余FNP的等位基因贡献在籼稻和粳稻亚种中均得到阐明。大多数 FNP 都具有显着的性状贡献，尤其是GS3 、 GW5和GL7 。值得注意的是， GW5可以作为协调其他粒度基因性能的关键调节因子。还利用F ₂群体通过QTL分析测试了几个FNP的等位基因效应，并进一步确定GW5是对粒宽和长宽比贡献最大的主要位点。

 结论

这些功能标记对于不同品种的基因分型来说是稳健的，并且可以促进籽粒大小的合理设计，以在未来的水稻育种工作中实现籽粒产量和品质之间的平衡。