Discovery of single nucleotide polymorphisms via rice whole-genome resequencing and development of molecular markers in Malaysian rice accessions with varying amylose contents

Rice amylose content (AC) is a critical determinant of grain quality, influencing cooking, eating, and dietary preferences, which vary across Asia. A key challenge for the rice breeding programme is tailoring rice varieties to meet these diverse consumer preferences. Although single nucleotide polymorphism (SNP) markers have emerged as powerful tools for improving rice traits through marker-assisted breeding (MAB) and marker-assisted selection (MAS), SNP markers associated with AC in Malaysian rice accessions remain largely unexplored, limiting the precision and efficiency of breeding efforts targeting the AC trait. To address this gap, we conducted genome resequencing of 13 rice varieties, identifying 902 SNPs within starch biosynthetic genes (SBGs). We further developed the 66 SNP markers and validated them experimentally in 155 Malaysian rice accessions using the MassARRAY iPLEX™ platform. After SNP quality control, 59 SNPs were retained, achieving an 89.4% genotyping success rate. The identified SNPs showed moderate diversity among accessions, with polymorphic information content (PIC) values ranging from 0.05 to 0.37 and an overall mean of 0.26. Functional annotation highlighted six deleterious SNPs in Wx , ADP-glucose pyrophosphorylase (AGPase), starch synthase IIIa (SSIIIa), and starch phosphorylase (SPho). Using the general linear model (GLM), we identified two SNPs within the Wx locus that exhibit significant associations with low and high AC levels across the rice accessions. This study provides valuable SNP markers to facilitate molecular breeding for AC traits, addressing the current limitations in developing rice varieties tailored to consumer preferences in Malaysia and beyond.