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首页> 外文期刊>Journal of Theoretical Biology >An efficient computational method for screening functional SNPs in plants.
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An efficient computational method for screening functional SNPs in plants.

机译：一种用于筛选植物中功能性SNP的有效计算方法。

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Granule Bound Starch Synthase I (GBSSI), which influences the grain quality of cereals and, particularly, rice, is one of the most important plant genes. Using GBSSI as a model plant gene in this study, we examined a number of different computational algorithm tools and programs to explore the functional SNPs of this important rice gene and the possible relationships between genetic mutation and phenotypic variation. A total of 51 SNPs/indels were retrieved from databases, including three important coding non-synonymous SNPs, namely those in exons 6, 9 and 10. Sorting Intolerant from Tolerant (SIFT) results showed that a candidate [C/A] SNP (ID: OryzaSNP2) in exon 6 (coordinate 2494) is the most important non-synonymous SNP with the highest phenotypic impact on waxy protein. This SNP can alter a tyrosine to serine residue at position 224 of waxy protein. Computational simulation of GBSSI protein with the Geno3D suggested that this mutant SNP creates a bigger loop on the surface of waxy protein and results in a shape different from that of native GBSSI. Here, we suggest a potential transcriptional binding factor site (TBF8) which has one [C/T] SNP [rs53176842] at coordinate 2777 in boundary site of intron 7/exon 8, according to Transcriptional Factor (TF) search analysis. This SNP might potentially have a major effect on regulation and function of GBSSI. Combining SNP mining data and in silico structural analysis of waxy protein led us to prepare an efficient computational pathway which can be applied for other plant genes.
机译：颗粒结合淀粉合酶I（GBSSI）是最重要的植物基因之一，它影响谷物尤其是大米的谷物品质。在这项研究中，使用GBSSI作为模型植物基因，我们研究了许多不同的计算算法工具和程序，以探索该重要水稻基因的功能性SNP以及遗传突变与表型变异之间的可能关系。从数据库中检索到总共51个SNP / indels，包括三个重要的编码非同义SNP，即外显子6、9和10中的同义核苷酸。SintingTolerant from Tolerant（SIFT）结果显示，候选[C / A] SNP（ ID：第6外显子（坐标2494）中的OryzaSNP2）是最重要的非同义词SNP，对蜡质蛋白的表型影响最大。该SNP可以将蜡质蛋白的224位的酪氨酸变为丝氨酸残基。用Geno3D对GBSSI蛋白质进行的计算模拟表明，该突变SNP在蜡质蛋白质的表面上形成了一个更大的环，并导致其形状不同于天然GBSSI。在这里，我们建议根据转录因子（TF）搜索分析，在内含子7 /外显子8边界位点的坐标2777处具有一个[C / T] SNP [rs53176842]的潜在转录结合因子位点（TBF8）。该SNP可能会对GBSSI的调节和功能产生重大影响。结合SNP挖掘数据和蜡质蛋白的计算机电子结构分析，使我们准备了可用于其他植物基因的有效计算途径。

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