- Rare haplotypes show potential to improve future rice varieties.
- 210 rare haplotypes were linked to key rice traits.
- DEP1-H2 boosted yield by up to 9.87%.
Researchers from the International Rice Research Institute (IRRI) and partner institutions identified 210 haplotypes linked to important rice traits such as yield, grain quality and stress tolerance.
Haplotypes are distinct versions of a gene created by different combinations of genetic variants inherited together.
The researchers believe rare haplotypes may carry useful traits and be “central to next-generation precision breeding”.
However, they have received less attention in breeding because they are found in only a small proportion of rice accessions.
The researchers believe uncovering more rare haplotypes could be key to unlocking new opportunities in rice development.
A new source of genetic gain
The study analysed 1,644 functionally characterised rice genes across the 3,000 Rice Genomes (3K RG) dataset, one of the world’s largest rice genomic resources.
To test whether rare haplotypes could deliver practical breeding benefits, the researchers focused on DEP1, a well-characterised gene known to influence panicle architecture and grain yield.
Among the DEP1 variants identified was a rare haplotype known as DEP1-H2, found at a frequency of just 0.07 within the population studied.
The researchers introduced DEP1-H2 into Swarna, a high-yielding rice variety that is commonly grown in India.
The resulting lines produced increases of 29% to 34% in panicle length. Field evaluations also recorded yield gains of up to 9.87%, with the line producing the longest panicles delivering the highest grain yield.
The researchers said the results provide evidence that valuable alleles identified through population-scale genomic studies can be successfully translated into breeding outcomes.
“The successful introgression of the rare DEP1-H2 haplotype in the elite variety Swarna for increased PL and yield advantage provides evidence that rare haplotypes discovered at the population scale can be effectively translated for breeding purposes.”
Rare gene distribution
The team examined different haplotypes to better understand how variation is distributed across global rice germplasm.
Most of the 1,644 genes examined contained between two and 15 distinct haplotypes.
Some were broadly distributed across global rice populations, while others were restricted to specific subpopulations or geographic regions, suggesting they may have evolved in response to local environmental conditions or selection pressures.
Rare haplotypes were particularly abundant in indica and aus rice populations, while they were comparatively uncommon in japonica accessions.
According to the researchers, these patterns point to indica and aus germplasm as potentially valuable reservoirs of underutilised genetic diversity.
Several additional rare haplotypes identified in the study, particularly those associated with grain quality and abiotic stress tolerance, were highlighted as promising candidates for future validation.
The researchers also suggested combining multiple superior haplotypes.
“Stacking multiple superior haplotypes at different loci may provide an effective breeding approach to exploit additive and epistatic effects to develop optimised combinations for increased stability, adaptability, and performance in target environments.”
The study concluded: “The present study provides a framework for haplotype breeding at scale. Future work will be directed toward the comparative evaluation and stacking of multiple rare haplotypes to fully exploit their breeding potential for climate-resilient and high-performing rice varieties.”
