Whole-genome polymorphisms and relatedness of rice varieties circulating in the Mediterranean market

Abstract

Rice cultivation in Europe is declining as consumers increasingly prefer imported exotic varieties, such as aromatic and basmati rice, which are prone to fraudulent varietal claims due to their higher market value. To address this issue, we sequenced 20 high-value rice cultivars circulating in the Mediterranean market, analyzing their phylogeny and whole-genome polymorphisms. Our results revealed that two basmati varieties are genetically closer to two Mediterranean varieties, and that no direct link exists between genome-wide single nucleotide polymorphism (SNP) patterns and the rice commercial category. We further discuss genes located in previously described quantitative trait loci (QTLs) related to eating quality and seed properties. A variant in the WX1 gene, associated with higher amylose content, was found in both the Basmati group and Mediterranean varieties. Additionally, a SNP that could disrupt the drought tolerance gene OsbHLH148 was identified in five European varieties, while a variant affecting splicing of OsPol lambda, related to drought response, was present in four of those. This data could assist certification offices in reducing fraud in the rice market and provide valuable insights for researchers and breeders, particularly regarding the production, consumption, and adaptation of these cultivars to the Mediterranean region.