Identification and Characterization of LARGE EMBRYO, a New Gene Controlling Embryo Size in Rice (Oryza sativa L.)

BACKGROUND: Although embryo accounts for only 2–3% of the total weight of a rice grain, it is a good source of various nutrients for human health. Because enlarged embryo size causes increase of the amount of nutrients and bioactive compounds stored within rice grain, giant embryo mutants of rice (Oryza sativa L.) are excellent genetic resources for improving the nutritional value of rice grains. RESULTS: Three giant embryo mutants, including large embryo (le), giant embryo (ge) and super-giant embryo (ge(s)), with variable embryo size were used in this study. We investigated whether genes controlling embryo size in these mutants (le, ge and ge(s)) were allelic to each other. Although ge and ge(s) was allelic to GIANT EMBRY (GE), le was not allelic to ge and ge(s) in allelism test. The GE gene carried a unique nucleotide substitution in each of the two mutants (ge and ge(s)), resulting in non-synonymous mutations in exon 2 of GE in both mutants. However, the GE gene of the le mutant did not carry any mutation, suggesting that the enlarged embryo phenotype of le was governed by another gene. Using map-based cloning, we mapped the LE gene to the short arm of chromosome 3. The le mutant showed mild enlargement in embryo size, which resulted from an increase in the size of scutellar parenchyma cells. The LE encodes a C3HC4-type RING finger protein and was expressed to relatively high levels in seeds at a late developmental stage. Knockdown of LE expression using RNA interference increased the embryo size of rice grains, confirming the role of LE in determining the embryo size. CONCLUSION: Overall, we identified a new gene controlling embryo size in rice. Phenotypic and molecular characterization results suggest that the le mutant will serve as a valuable resource for developing new rice cultivars with large embryos and nutrient-dense grains. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12284-019-0277-y) contains supplementary material, which is available to authorized users.