Zainal-Abidin Rabiatul-Adawiah, Abu-Bakar Norliza, Sew Yun-Shin, Simoh Sanimah, Mohamed-Hussein Zeti-Azura
Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia.
Malaysian Agricultural Research & Development Institute (MARDI), Persiaran MARDI-UPM, 43300 Serdang, Selangor, Malaysia.
Int J Genomics. 2019 Oct 10;2019:4168045. doi: 10.1155/2019/4168045. eCollection 2019.
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.
最近，由于有色稻米品种对人类健康有益，水稻育种计划对其表现出了越来越浓厚的兴趣。然而，有色稻米品种的遗传变异仍然稀缺，尚未得到充分探索。因此，我们对四个马来西亚有色稻米品种（两个黑米品种和两个红米品种）进行了全基因组重测序，开展了全基因组单核苷酸多态性（SNP）分析。将四个有色品种的基因组与日本晴参考基因组序列进行比对，发现了190万个SNP。其中，在与代谢、应激反应和转运相关的258个蛋白质编码基因中，鉴定出了622个具有多态性位点的SNP。针对来自Ensembl Plants变异数据库的六个水稻SNP数据集，对622个具有多态性位点的SNP进行了比较分析，鉴定出70个新SNP。对类黄酮生物合成基因中的SNP分析揭示了40个非同义SNP，这些SNP有潜力作为水稻种子颜色鉴定的分子标记。本研究中突出的SNP显示出为水稻育种计划提供有价值的基因组资源的努力，以实现新型和改良有色稻米品种的遗传改良。
