Comparative single nucleotide polymorphisms (SNPs) analysis of MR 297 and MRQ 76 rice varieties reveals potential SNPs in coding genes

Rabiatul Adawiah, Z. A.¹*, Norliza, A. B.¹, Sew, Y. S.¹, Shahril Firdaus, A. R.¹ and Sanimah, S.²

Abstract
MR 297 and MRQ 76 are commercial rice varieties in Malaysia, but the genomic information of these varieties are
scarcely reported. This study aims to unravel the genomic variations in these two rice varieties, annotate the single
nucleotide polymorphisms (SNP) and generate a list of potential SNPs in coding genes related to agronomically
important genes. In this study, the genomes of MR 297 and MRQ 76 were sequenced using Illumina HiSeq 4000.
Bioinformatics analysis was carried out to identify potential SNPs in both varieties. A total of 2,424,521 and 2,354,097
SNPs were identified in MR 297 and MRQ 76, respectively. Annotation of SNPs in coding genes identified 153,058
SNPs in MR 297 and 147,431 SNPs in MRQ 76. Deleterious SNPs analysis using SIFT4G found 12 deleterious SNPs
in genes encoding seed metabolism, salinity, cell-wall biosynthesis, and disease resistance. Identification and annotation
of SNPs in MR 297 and MRQ 76 suggested potential SNPs that valuable for PCR-based marker development or
whole-genome genotyping to facilitate marker-assisted rice breeding (MAB) and marker-assisted selection (MAS) in
rice breeding programme.

Keywords: MR 297, MRQ 76, Oryza sativa, rice, single nucleotide polymorphism

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