Haplotype diversity at Wx and ALK loci explains starch quality in temperate rice landraces of Kashmir Valley.

Abstract

Rice kernel quality signifies cooking characteristics and ultimately determines consumer preferences. Two key genes, Wx (Waxy) and ALK (Alkali degeneration), play a crucial role in determining amylose content and gelatinization temperature, respectively. So, studying allelic variations at two of these loci is vital for designing breeding strategies aimed at enhancement of rice quality. We previously reported on the rich rice germplasm diversity panel native to temperate Kashmir Himalayas, comprising japonica, indica and the derivatives. However, the information regarding functional gene-based polymorphism underlying starch properties has not been generated on the said panel. Therefore, we performed the genotyping of 470 rice germplasm accessions using uniplex Kompetitive Allele-Specific PCR (KASP) markers. Subsequently, a subset of 36 genotypes was subjected to whole-genome re-sequencing to study Wx and ALK loci. The local landraces were found to carry Wx ⁱⁿ and Wx ^lv alleles, whereas Wx ^a was prevalent in other ruling varieties of the region. Analysis of the RM190 microsatellite locus, which harbours a (CT)_n repeat polymorphism linked to amylose content, revealed a motif repeat variation ranging between (CT)₇ to (CT)₁₉. ALK ^c allele was widely distributed across both the landraces and bred varieties. The phenotypic values for amylose content and alkali degeneration of the lines corresponded with varied allelic distribution patterns at Wx and ALK loci. The information generated can be utilized for future breeding programs aimed at quality improvement in high-altitude temperate rice.

Supplementary information: The online version contains supplementary material available at https://doi.org/10.1007/s12298-026-01823-2.