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是控制粒長(zhǎng)最重要的QTL，對(duì)其比較測(cè)序發(fā)現(xiàn)，水稻粒長(zhǎng)差異主要是由于其第2外顯子的一個(gè)單核苷酸多態(tài)性（SNP）C/A造成的。以代表廣大水稻種質(zhì)的180個(gè)水稻品種，用作C-A突變和粒長(zhǎng)關(guān)聯(lián)分析，來確定潛在的因果突變。SF28可以用作區(qū)別GS3 C-A多態(tài)的酶切擴(kuò)增多態(tài)性序列（CAPS）標(biāo)記。142個(gè)水稻品種SNP位點(diǎn)是C，粒長(zhǎng)6.4mm~8.8mm；其余38個(gè)品種SNP位點(diǎn)是A，粒長(zhǎng)8.8mm~10.7mm。選用24個(gè)不連鎖的SSR標(biāo)記對(duì)這180個(gè)水稻品種基因分型，以進(jìn)行群體結(jié)構(gòu)分析。當(dāng)群體被分為3個(gè)亞群時(shí)，能檢測(cè)到群體結(jié)構(gòu)。盡管在180個(gè)水稻品種中秈稻的平均粒長(zhǎng)大于粳稻，但是基因型同為A/C時(shí)，秈稻和粳稻的平均粒長(zhǎng)沒有明顯差異。然而，在三個(gè)亞群中，基因型是C時(shí)，其平均粒長(zhǎng)要比基因型是A的粒長(zhǎng)短（原文中是“l(fā)onger”，可能是筆誤）。該突變分別可以解釋三個(gè)亞群中79.1%，66.4%，34.7%粒長(zhǎng)變異率。這些結(jié)果明確表明C/A突變與粒長(zhǎng)密切相關(guān)。SF28可以作為提高水稻粒長(zhǎng)的功能標(biāo)記。