Work

Whole genome resequencing dataset of weedy rice variants

Year: 2025

Type: data-paper

Abstract: Weedy rice (Oryza sativa f. spontanea) is a major problematic weed in rice-growing regions, causing significant yield losses and reducing grain quality. To generate genomic resources that can aid in the understanding and management of this weed, we performed whole genome resequencing (WGRS) of 10 weedy rice variants exhibiting differences in selected phenotypic traits, collected from various rice cultivation areas in Peninsular Malaysia. Genomic DNA from each accession was extracted and sequenced using the Illumina NovaSeq 6000 platform, generating a total of ∼138 Giga base (Gb) of high-quality paired-end reads. The raw reads were processed to remove adapters, low-quality bases, and ambiguous sequences, producing a total of ∼136.9 Gb clean read datasets. The clean reads have been deposited in the European Nucleotide Archive (ENA) under accession number [PRJEB96009]. This dataset provides a valuable genomic resource for future investigations into weedy rice genetics and the development of molecular markers to differentiate weedy rice from cultivated rice varieties. Furthermore, the identified molecular markers, such as single nucleotide polymorphism (SNP), can be screened within genic regions that encode genes related to domestication traits in weedy rice. Additionally, genome-wide analysis of genetic variation in weedy rice provides insights into the molecular mechanisms underlying its evolution.

Source: Data in Brief

DOI: 10.1016/j.dib.2025.112252