The origin of Wxla provides new insights into the improvement of grain quality in rice.

Appearance and taste are important factors in rice (Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of 533 diverse cultivars to assess the relationships between-and genetic basis of-rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy (Wx) allele, Wxla , which combined two mutations from Wxb and Wxin , exhibited a unique phenotype. Reduced GBSSI activity conferred Wxla rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wxla was derived from intragenic recombination. In fact, the recombination rate at the Wx locus was estimated to be 3.34 kb/cM, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.