Dissecting the genetic basis of heavy panicle hybrid rice uncovered <italic>Gn1a</italic> and <italic>GS3</italic> as key genes.

Key message: Shuhui498 (R498) is an elite parent of heavy panicle hybrid rice by pyramiding the rare <italic>gn1a</italic> and null <italic>gs3</italic> alleles. This finding reveals the genetic basis and great potential application in future breeding of R498.Abstract: The heavy panicle trait, defined as 5 g or more of grain weight per panicle, is one of the target traits in super-high-yield rice breeding programs. The use of heavy panicle-type hybrid rice has been shown to be a successful strategy for super-high-yield breeding programs, particularly under the environmental conditions of high humidity and deficient solar radiation in southwestern China. However, the genetic components of the heavy panicle trait in hybrid rice remain elusive. Here, we report that the combination of loss-of-function mutations in <italic>Grain number 1a</italic> (<italic>Gn1a</italic>) and <italic>Grain Size 3</italic> (<italic>GS3</italic>) is responsible for the heavy panicle phenotype of the elite hybrid rice restorer line Shuhui498 (R498). The null <italic>gn1a</italic> allele is the determinant factor for heavy panicles through increased grain number, while <italic>gs3</italic> is associated with grain size and weight. R498 pyramided the two major null alleles, resulting in heavy panicles with a high grain number and large grains. Clustering analysis revealed that the null <italic>gn1a</italic>R498 allele is a rare haplotype which has been innovatively utilized in R498, underscoring the great potential of R498 for breeding purposes. Our research thus sheds light on the distinct genetic compositions of heavy panicle-type rice and may potentially facilitate super-high-yield rice breeding. [ABSTRACT FROM AUTHOR]