Mining rare haplotypes to accelerate precision breeding in rice

Rice (Oryza sativa L.) genomics has made significant progress, with over 13000 genome sequences available and more than 4500 genes functionally characterized. However, limited haplotype-level information has constrained the effective deployment of these genes in breeding programs. Here, we investigated haplotype variation of 1644 functionally characterized genes representing six major trait categories using the 3000 Rice Genome panel. High haplotypic diversity was observed, with more than 300 haplotypes, which clustered into 2-15 major haplogroups. Several haplotypes showed subpopulation or region-specific distributions, whereas others were broadly distributed across the panel. To identify rare haplotypes (frequency < 0.1) with potential breeding value, we prioritized 180 genes relevant to defined product concepts and identified 210 rare haplotypes across 51 genes. Notably, a rare haplotype of DEP1 (DEP1-H2: frequency 0.07) associated with increased panicle length was introgressed into the mega rice variety Swarna through haplotype-based backcross breeding. The resulting introgression lines showed a 29%-34% increase in panicle length compared to the recurrent parent, confirming the functional advantage of the rare haplotype.