Structural Variations Contribute to Subspeciation and Yield Heterosis in Rice

Area of Science:

• Genomics
• Plant Breeding
• Molecular Biology

Background:

• Yield heterosis in hybrid breeding, particularly in intersubspecific rice hybrids, is significant but challenging to achieve.
• The genetic underpinnings of heterosis have remained elusive due to a lack of high-quality rice genomes.

Purpose of the Study:

• To assemble high-quality genomes for diverse rice accessions.
• To investigate the role of structural variants (SVs) in rice subspeciation and heterosis.

Main Methods:

• Genome assembly of 12 indica, intermediate, and japonica rice accessions.
• Comparative genomics to identify sequence and structural variations.
• Functional validation of SVs impacting traits like phenol reaction, seed setting, and yield.

Main Results:

• Extensive sequence and structural variations identified, highlighting SVs' role in rice subspeciation.
• Number of SVs between parental lines correlated with heterosis across 17 agronomic traits.
• Identified and validated SVs associated with S5-ORF5 and OsBZR1, influencing seed setting and yield heterosis.
• Transcriptional changes induced by SVs explained heterosis variance; translocations showed significant effects.

Conclusions:

• Structural variants are key drivers of rice subspeciation and heterosis.
• Overdominance of heterozygous SV haplotypes is a crucial mechanism for harnessing rice heterosis in breeding.