In a study published in Nature Genetics, researchers collected 2,839 hybrid rice cultivars and conducted phenotyping as well as sequencing, providing the largest reported collection of hybrid rice germplasm resources to date (data resource are available at http://ricehybridresource.cemps.ac.cn/#/). From them, 18 representative hybrid cultivars were selected to construct an F2 population comprising 9,839 individuals. Among all the collections, there were 2,724 indica-indica, 68 indica-japonica and 47 japonica-japonica hybrid varieties, as well as 4,497 and 5,342 F2 individuals from indica-indica and indica-japonica hybrid cultivars. Based on indica-indica materials, genome-wide selection and genetic improvement were searched, and based on indica-japonica samples, the genetic basis of intersubspecific heterosis was explored. 

 

The breeding trends of hybrid rice were summarized as follows: enlarged source and sink organ, slightly shortened heading date and improved grain cooking and appearance quality. 

 

By analyzing the genetic structure of rice hybrid, an increasing genetic diversity was observed during the improvement breeding process. It mainly resulted from the increase of Twoline-Jap hybrids, which had higher japonica-introgression level than Wild-Abortive hybrids due to founder varieties. And the introgression event also introduced breeding-favorable alleles from japonica subspecies.

 

Genome-wide analysis (GWAS) and composite interval mapping (CIM) method were conducted to identify breeding signatures. The magnitude of dominance and phenotypic variation explained (PVE) were subsequently estimated to quantitatively evaluate genetic effect of loci associated with breeding signatures, and demonstrated that improvement breeding selected the optimal genotypes according to their genetic effect: both heterozygous and breeding-favorable homozygous genotypes were selected for loci representing partial or complete dominance, but only breeding-favorable homozygous genotype was preferred for loci having additive or negative dominant effect. 

 

Overall, the results indicated that creation new germplasm and selection for optimal genotypes pyramided advantageous alleles and promoted improvement in hybrid rice.

 

Although there is only a small subset of intersubspecific (indica-japonica) hybrids, it has great yield potential. The genetic basis of intersubspecific heterosis was quantitatively analyzed in this research. Genome-wide genetic complementation was prevalent in intersubspecific hybrids. Among genetically complementary region, both dominant and overdominant loci contributed to intersubspecific heterosis in yield traits, with dominant loci playing a more crucial role in terms of phenotypic variation contribution.

 

Besides, a genomic selection model was constructed based upon the comprehensive dataset. The model conducted multi-trait selection by integrating the genomic estimated breeding value (GEBV) of 7 important agronomic traits, which could help to screen heterotic combinations and formulate hybrid plans. The model demonstrated robust performance when tested on a validation population.

 

This research mainly conducted by Prof. Han Bin’s group from the CAS Center for Excellence in Molecular Plant Sciences of the Chinese Academy of Sciences, collaborating with Prof. Yang Shihua and Associate Prof. Gong Junyi from China National Rice Research Institute.