Rational design for rice eating and cooking quality via combination of the Waxy and ALK haplotypes

Improving rice eating and cooking quality (ECQ) through designed breeding requires a precise understanding of the functions and interactions of key gene haplotypes. Waxy and ALK are two major genes regulating ECQ, but how different combinations of their alleles interact to affect yield and quality traits remains largely unexplored. Here, we construct a set of 30 near-isogenic lines (NILs) from the elite cultivar Huanghuazhan, systematically combining 6 Waxy and 5 ALK alleles, including a recombinant-derived functional allele, ALK^e, identified in this study. Under non-extreme high temperature conditions, Waxy is associated with grain yield primarily via seed setting rate and thousand-kernel weight in our NIL populations, whereas ALK has no significant effect on yield. Compared with the Wx^b-ALK^b combination, the Wx^b-ALK^e combination improves the ECQ without compromising yield. Starch structural analysis reveals that Waxy controls chalkiness and head rice yield (HRY) via apparent amylose content, whereas ALK affects chalkiness by altering amylopectin chain-length distribution. Notably, high temperature during grain filling intensifies chalkiness and reduces HRY, particularly in the ALK^c lines. These findings provide genetic resources and facilitate the design breeding of rice varieties that meet diverse consumer preferences.