Whole-genome Sequencing Reveals Functional Genomic Variation in the Traditional Rice Landrace Iluppai Poo Samba (Oryza sativa L.)

Abstract

Background: Traditional rice landraces represent valuable reservoirs of genetic diversity associated with agronomically important traits, stress adaptation, nutritional quality and regional adaptation. Iluppai Poo Samba (Oryza sativa L.) is a traditional South Indian rice landrace cultivated in Tamil Nadu, India, valued for its characteristic aroma, grain quality and adaptation to local agroecological conditions. However, genomic information for this cultivar remains limited. The present study aimed to characterize genome-wide sequence variation in Iluppai Poo Samba through whole-genome sequencing (WGS). Methods: High-quality paired-end sequencing libraries were prepared using the NEXTflex Rapid DNA Sequencing platform and sequenced using Illumina chemistry. Sequence reads were subjected to quality assessment, genome alignment, variant calling, genome-wide SNP density analysis and functional annotation of genomic variants. Result: Sequencing quality assessment demonstrated high-quality reads with Q20 values exceeding 97% and Q30 values exceeding 94%, with an average GC content of approximately 45%. A total of 1,410,690 SNPs and 138,431 InDels were observed across the genome. Genome-wide SNP analysis revealed extensive chromosomal variation, heterogeneous SNP distribution patterns and distinct polymorphic hotspot regions. Functional annotation detected widespread intergenic, intronic and coding-region polymorphisms, including 44,070 synonymous and 51,380 non-synonymous SNPs. Transition/transversion (Ts/Tv) ratios ranging from 2.24 to 2.50 supported the reliability of variant identification. Variants associated with stress-responsive transporters, kinase signalling proteins, transcription factors and regulatory genes were also detected, indicating potentially important adaptive genomic signatures within the Iluppai Poo Samba genome.