Genome Overview

Seeds of Malaysia rice varieties (Bali, Pulut Hitam 9, MRM16, MRQ100, MR297 and MRQ76) were obtained from GenBankTM, MARDI, Seberang Perai. DNA extraction was performed from leaves of each rice varieties and sent to the sequencing provider to carry out the genome sequencing. Six local rice varieties were sequenced using Illumina Hi-seq 4000 technology. A total of 88.321Gb short reads were generated from the sequencing platform. The raw short reads sequences from the six varieties were trimmed and pre-processed to produce high-quality sequence reads for further analysis. A total of 87.569Gb clean data were obtained after filtering low-quality short reads sequences and proceed for further analysis. The genome sequences of six rice varieties were mapped to Oryza sativa japonica cv. Nipponbarre reference genome, separately. BWA was used to perform the mapping sequences while SNPs calling was carried out using GATK. SnpEff was used to annotate the SNPs.

Bali, Pulut Hitam 9 (PH9), MRM16, MRQ100 and MRQ76 have been categorised under speciality rice because of their coloured and high nutritional content. In Malaysia, pigmented rice, fragrant rice, Basmati rice, and glutinous rice have been categorised as speciality rice.

Rice Varieties

  • Black rice landraces.
  • Used as parental cross to develop black rice modern variety.
  • High antioxidant properties.
  • Short maturity (110-120 days).
  • Black rice modern variety.
  • Released variety in 1990
  • Sticky texture.
  • High antioxidant properties.
  • 2x yields compare than landrace black rice.
  • Amylose texture: soft (0.3%)
Pulut Hitam 9
  • Modern red rice variety.
  • High antioxidant properties.
  • Released in 2010.
  • Parental Q72 dan ER 6275.
  • Suitable for baby’s food production and natural colouring.
  • Short maturity (110 days) compared than landrace red rice (146).
  • Modern red rice variety.
  • High antioxidant properties and high fibers.
  • Modern white rice variety.
  • Released in 2016.
  • Resistance to blast disease.
  • High yield.
  • High macro-micronutrient contents.
  • Modern white rice variety.
  • Aromatic rice variety
  • Amylose content: Intermediate

Features Summary

Oryza sativa Nipponbarre coding genes 35,825
Oryza sativa Nipponbarre coding genes 43,404
Putative SNP panels963,064
SNPs with polymorphic site981
SNPs in the flavonoid biosynthetic genes606
SNPs in the folate biosynthetic genes205