Rice breeders may be overlooking a useful source of improvement: rare versions of genes that are already well known. Researchers from the International Rice Research Institute (IRRI) and partner institutions have identified 210 such rare haplotypes linked to yield, grain quality and stress tolerance, AgNavigator reports.
A haplotype is a distinct version of a gene, formed by a combination of genetic variants that are inherited together. Rare haplotypes have received little attention from breeders because they turn up in only a small share of rice accessions, but the researchers argue they may be "central to next-generation precision breeding".
The team analysed 1,644 rice genes whose functions are already characterised, across the 3,000 Rice Genomes (3K RG) dataset, one of the largest genomic resources for the crop. Most of those genes carried between two and 15 distinct haplotypes. Some were spread across rice populations worldwide; others were confined to particular subpopulations or regions, which suggests they evolved under local conditions.
To test whether a rare haplotype could deliver in the field, the researchers turned to DEP1, a gene known to shape the panicle and influence grain yield. One version, DEP1-H2, occurs at a frequency of just 0.07 in the population studied. Bred into Swarna, a high-yielding variety widely grown in India, it produced panicles 29% to 34% longer, and field trials recorded yield gains of up to 9.87%, with the longest-panicle line giving the most grain.
Rare haplotypes were especially common in indica and aus rice and comparatively scarce in japonica, so the authors point to indica and aus germplasm as reservoirs of under-used diversity. Several more rare haplotypes, mainly for grain quality and tolerance of abiotic stress, were flagged for validation.
The researchers also suggest stacking several superior haplotypes at different loci to build varieties with greater stability and adaptability. The study describes itself as a framework for haplotype breeding at scale, with future work aimed at comparing and combining rare haplotypes for climate-resilient, high-performing rice.
Photo: International Rice Research Institute / Wikimedia Commons (CC BY 2.0)
Source: AgNavigator
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