Data on genome resequencing of pigmented and non-pigmented Malaysian rice varieties.

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

doi:10.1016/j.dib.2020.105806

Abstract

The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage. We aimed to identify and annotate single nucleotide polymorphisms (SNPs) from the genome of these four pigmented and two non-pigmented rice varieties. The potential SNPs will be used in developing the functional SNP markers related to nutritional (i.e. antioxidant, folate, amylose) and quality (i.e. aromatic) traits. Raw data of the pigmented and non-pigmented rice varieties have been deposited into the European Nucleotide Archive (ENA) database with accession number PRJEB29070 and PRJEB32344, respectively.

Highlights

The genomics and genetic data of pigmented and nonpigmented Malaysian rice varieties are still limited
Agricultural and Biological Sciences Plant sciences Genome sequence data Illumina HiSeq 4000 sequencing platform Clean raw reads (FASTQ) Total DNA was extracted from leaves of two weeks old germinated seedlings using Murray and Motou protocols and Sigma DNA extraction kit
City/Town/Region: Serdang, Selangor Country: Malaysia Latitude and longitude for collected samples/data:] 2.9885871 N 101.697955417 E The raw reads of pigmented and non-pigmented rice varieties have been deposited at European Nucleotide Archive (ENA) under the studies accession numbers PRJEB29070 and PRJEB32344. https://www.ebi.ac.uk/ena/data/view/PRJEB29070 https://www.ebi.ac.uk/ena/data/view/PRJEB32344

Summary

Introduction

The genomics and genetic data of pigmented and nonpigmented Malaysian rice varieties are still limited. Agricultural and Biological Sciences Plant sciences Genome sequence data Illumina HiSeq 4000 sequencing platform Clean raw reads (FASTQ) Total DNA was extracted from leaves of two weeks old germinated seedlings using Murray and Motou protocols and Sigma DNA extraction kit. The leaves of two-week-old germinated seedlings were obtained from each pigmented and non-pigmented Malaysian rice varieties and quickly frozen in liquid nitrogen before stored in a −80C freezer.

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