A causal C–A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker

3.363
Chuchuan Fan, Sibin Yu, Chongrong Wang, Yongzhong Xing
Theoretical and Applied Genetics, 2009, 118(3): 465-472  DOI: 10.1007/s00122-008-0913-1     追溯原文......本站官方QQ群:62473826

Comparative sequencing of GS3, the most important grain length (GL) QTL, has shown that differentiation of rice GL might be principally due to a single nucleotide polymorphism (SNP) between C and A in the second exon. A total of 180 varieties representing a wide range of rice germplasm were used for association analysis between C–A mutation and GL in order to confirm the potential causal mutation. A cleaved amplified polymorphic sequence (CAPS) marker, SF28, was developed based on the C–A polymorphism in the GS3 gene. A total of 142 varieties carried allele C with GL from 6.4 to 8.8 mm, while the remaining 38 varieties carried allele A with GL from 8.8 to 10.7 mm. Twenty-four unlinked SSR markers were selected to genotype 180 varieties for population structure analysis. Population structure was observed when the population was classified to three subpopulations. Average GL of either genotype A or genotype C within japonica among the three subpopulations had no significant difference from that in indica, respectively, although indica rice had longer grains on average than japonica in the 180 varieties. However, genotype C always had longer grain length on average than genotype A among three subpopulations. The mutation could explain 79.1, 66.4 and 34.7% of GL variation in the three subpopulations, respectively. These results clearly confirmed the mutation between C and A was highly associated with GL. The SF28 could be a functional marker for improvement of rice grain length.

GS3第2外显子C-A突变与水稻粒长相关,经验证可以作为一个功能标记

GS3是控制粒长最重要的QTL,对其比较测序发现,水稻粒长差异主要是由于其第2外显子的一个单核苷酸多态性(SNP)C/A造成的。以代表广大水稻种质的180个水稻品种,用作C-A突变和粒长关联分析,来确定潜在的因果突变。SF28可以用作区别GS3 C-A多态的酶切扩增多态性序列(CAPS)标记。142个水稻品种SNP位点是C,粒长6.4mm~8.8mm;其余38个品种SNP位点是A,粒长8.8mm~10.7mm。选用24个不连锁的SSR标记对这180个水稻品种基因分型,以进行群体结构分析。当群体被分为3个亚群时,能检测到群体结构。尽管在180个水稻品种中籼稻的平均粒长大于粳稻,但是基因型同为A/C时,籼稻和粳稻的平均粒长没有明显差异。然而,在三个亚群中,基因型是C时,其平均粒长要比基因型是A的粒长短(原文中是“longer”,可能是笔误)。该突变分别可以解释三个亚群中79.1%,66.4%,34.7%粒长变异率。这些结果明确表明C/A突变与粒长密切相关。SF28可以作为提高水稻粒长的功能标记。


基因列表
  粒长粒重主效控制基因 GS3