Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)
Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)
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DOI：
10.1007/s00122-006-0355-6
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发表时间：
2006-11-01
影响因子：
5.4
通讯作者：
Sun, M.
中科院分区：
文献类型：
--
作者：
Bao, J. S.;Corke, H.;Sun, M.
淀粉的糊化温度(GT)、表观直链淀粉含量(AAC)、糊化温度(PT)等理化特性决定了大米各种产品的品质，如食用品质、蒸煮品质和加工品质。大米粉的GT受ALK基因控制，该基因已与淀粉合成酶IIa(SSIIa)基因共同定位。本研究测定了30个水稻品种的SSIIa基因内含子6、外显子7、内含子7、外显子8和3‘非翻译区部分片段的2,051个碱基的DNA片段，这些品种具有不同的地理分布和淀粉理化特性的变异。共检测到24个单核苷酸多态(SNPs)和1个插入/缺失(Indel)，可分为9种单倍型。在这份水稻种质资源中，平均成对核苷酸多样性pi为0.00292，沃特森估计值theta为0.00296。田岛的D检验显示没有显著偏离中性期望(D=-0.04612，P>；0.10)。然而，发现7个SNP与P<；0.0001的峰值GT(P(P))显著相关，其中两个相邻的SNP(GC/TT)与T(P)有很强的相关性。除了极少数例外，这种GC/TT多态可以区分高GT和中GT水稻品种(具有GC等位基因)和低GT品种(具有TT等位基因)。相反，这些SNPs或Indel与直链淀粉含量均无显著关联。对另509个已知理化性状(如AAC和PT)和其他淀粉合成基因已知等位基因的水稻品种进行了SSIIa GC/TT等位基因的基因分型。关联分析表明，Wx基因的(CT)n简单重复序列(SSR)和G/T SNP可解释AAC总变异的82%，GC/TT多态可解释PT总变异的62.4%。对来自509个水稻品种的245个样本的子集进行了这些分子标记与温度和回生特性之间的额外关联分析。SSIIa GC/TT多态可以解释60%以上的热物性总变异，而Wx基因的SSR和SNP对回生特性总变异的解释与SSIIa GC/TT一样多。我们的研究为GC/TT多态在SSIIa中的利用提供了进一步的支持。我们对509个水稻品种的研究表明，GC/TT SNP可以在约90%的情况下区分高、中GT水稻和低GT水稻。在一次聚合酶链式反应中使用4个引物，可以进行大规模的GC/TT多态检测。因此，该SNP多态性在水稻GT等理化性状的分子标记辅助选择中具有重要的应用价值。
The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3' untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise nucleotide diversity pi was 0.00292, and Watterson's estimator theta was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = -0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T (p)) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T (p) (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.