Abstract
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.
Highlights
Rice (Oryza sativa L.) is the most crucial staple food crops in Asian countries
This 30× depth of sequencing was chosen as it provides sufficient coverage in identifying high-quality genetic variations such as single-nucleotide polymorphisms (SNPs), single-nucleotide variation (SNV), and insertion-deletion (InDel) [56]
Our analysis has identified that all the above genes have one nsSNP while two nsSNPs were found in Os01g0147001 that encodes for glycosyltransferase family 43 enzymes (important in the biosynthesis of cell wall [68] and Os02g0503900 that encodes for a cytochrome P450 (involved in xylan biosynthesis [69], two nsSNPs were found in Os06g0695800 that encoded for ATP-binding cassette (ABC) transporter genes
Summary
Rice (Oryza sativa L.) is the most crucial staple food crops in Asian countries. The most consumed rice is white rice, which resulted from the white pericarp. Genome resequencing of pigment rice varieties has been performed to identify potential SNPs located in the biosynthetic genes, which can be developed as molecular markers for nutritional quality traits such as high antioxidant [19, 20] and high amylose content [21]. All these efforts showed the importance of mining genetic variant, biosynthetic genes, and transcription factors in order to understand the interactions that will affect and influence the biosynthesis of antioxidant contents in rice varieties. The SNPs highlighted in this study are suggested as potential molecular markers for further validation using a genotyping platform, towards genetic improvement of pigmented rice varieties
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