Identification of a novel mutant allele of the <i>LIKE EARLY STARVATION 1</i> gene in rice ( <i>Oryza sativa</i> L.) using QTL-seq

Starch characteristics are of paramount importance for the eating and cooking quality of rice (Oryza sativa L.), and many genes act in concert to regulate starch biosynthesis. In this study, we investigated the seed morphology, starch structure, and genetic basis of the endosperm cavity mutant "KDS-1830C". The "KDS-1830C" mutant displayed an opaque endosperm with a central cavity, in contrast to normal translucent endosperm of wild-type "Kitaake." Scanning electron microscopy analysis revealed distinct starch granule morphologies with "Kitaake" grains exhibiting polygonal granules and "KDS-1830C" showing irregularly-shaped, rounded granules. Comparison of yield-related and starch physico-chemical traits revealed significant differences in grain width, thickness, weight, and protein content, with "KDS-1830C" having lower seed hardness. QTL-seq analysis identified a significant locus on chromosome 11 associated with the cavity phenotype. A non-synonymous SNP in the LOC_Os11g37560 gene was detected as the candidate causal mutation and is predicted to generate a premature stop codon. This gene's ortholog in Arabidopsis, LESV, is known to influence starch granule structure. Protein structure prediction suggests that the nonsense mutation in "KDS-1830C" results in a truncated β sheet structure, potentially impairing amylopectin binding and granule crystallization. These findings enhance our understanding of the genetic and structural factors influencing rice endosperm development and starch biosynthesis, which are of critical importance to maintaining and improving rice grain quality.