Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties

Rabiatul Adawiah Zainal-Abidin, Norliza Abu-Bakar, Yun Shin Sew, Sanimah Simoh, Zeti Azura Mohamed-Hussein

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number4168045
JournalInternational Journal of Genomics
Volume2019
DOIs
Publication statusPublished - 1 Jan 2019

Fingerprint

Single Nucleotide Polymorphism
Genes
Genome
Breeding
Flavonoids
Metabolism
Seed
Oryza
Health
Color
Seeds
Databases
Proteins

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Pharmaceutical Science

Cite this

Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties. / Zainal-Abidin, Rabiatul Adawiah; Abu-Bakar, Norliza; Sew, Yun Shin; Simoh, Sanimah; Mohamed-Hussein, Zeti Azura.

In: International Journal of Genomics, Vol. 2019, 4168045, 01.01.2019.

Research output: Contribution to journalArticle

Zainal-Abidin, Rabiatul Adawiah ; Abu-Bakar, Norliza ; Sew, Yun Shin ; Simoh, Sanimah ; Mohamed-Hussein, Zeti Azura. / Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties. In: International Journal of Genomics. 2019 ; Vol. 2019.
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