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

Authors: SHIM, KYU-CHAN - Chungnam National University; KIM, HYUNJUNG - University Of California, Davis; YOON, MI-RA - Rural Development Administration - Korea; NA, SUNG-HO - Chungnam National University; PARK, SA-EUN - Chungnam National University; AHN, SANG-NAG - Chungnam National University; Tai, Thomas

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2026
Publication Date: 4/28/2026
Citation: Shim, K., Kim, H., Yoon, M., Na, S., Park, S., Ahn, S., Tai, T. 2026. Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq. G3: Genes, Genomes, Genetics. 16(7). Article jkag108. https://doi.org/10.1093/g3journal/jkag108.
DOI: https://doi.org/10.1093/g3journal/jkag108

Interpretive Summary: Most rice is consumed in the form of whole, milled rice kernels which are made up mostly of starch. As such, starch characteristics largely govern various rice grain qualities (e.g., eating, cooking, milling, appearance). In this study, we identified a rice grain mutant based on appearance. The grains of this mutant were opaque or chalky rather than the translucent appearance of normal rice grains and upon further inspection, it was observed that a central cavity wax was present within the grain. Using a method called quantitative trait loci (QTL)-seq, we were able to identify the likely cause of this abnormal rice grain as a single base change in the gene encoding the Like Early Starvation 1 (LESV1) gene, which has previously been reported in the plant Arabidopsis thaliana and in rice. The LESV1 gene is able to bind starch (specifically the component of starch called amylopectin) and is involved in starch granule formation. Although there have been previous reports of rice LESV1 mutants, the mutation underlying the mutant in our study results in a less severe effect, likely due to the fact that the effect of the mutation is predicted to result in the production of a much larger protein than the other reported mutants of rice LESV1. A possible use of this novel mutant of LESV1 for rice breeding is discussed.

Technical Abstract: 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 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 ß 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.