Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.

中文翻译：

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通过马来西亚色素水稻品种的全基因组探索发现功能性SNP。

最近，稻米育种计划由于对有色稻米品种有益于人类健康，因此显示出对它们的浓厚兴趣。但是，有色水稻品种的遗传变异仍然很稀少，尚未开发。因此，我们从代表两个黑色和两个红色水稻品种的四个马来西亚有色水稻品种的基因组重测序中进行了全基因组SNP分析。根据日本晴参考基因组序列对四个有色品种的基因组进行了定位，并发现了190万个SNP。其中，在与代谢，应激反应和转运蛋白有关的258个蛋白质编码基因中鉴定出622个具有多态性位点的SNP。对Ensembl Plants变异数据库中的622个SNP与6个水稻SNP数据集进行了比较分析，70个SNP被鉴定为新型SNP。对类黄酮生物合成基因中的SNP进行分析后发现，有40个非同义SNP，它们有可能作为水稻种子颜色鉴定的分子标记。这项研究中突出显示的SNP显示了努力生产有价值的基因组资源以用于水稻育种计划，以期对新的和改良的有色水稻品种进行遗传改良。