Influence of natural and artificial selection on the yield differences among progeny derived from crossing between subspecies in cultivated rice

Extended natural and artificial selection have introduced pronounced differences throughout the genomes, morphological traits, and geographical distributions of the two predominant rice strains, Oryza sativa Xian/indica (XI) and O. sativa Geng/japonica (GJ). However, the unique roles of natural and artificial selection in strain differentiation remain uncharacterized. Therefore, we independently produced advanced inbreeding populations in typical GJ- and XI-cultivated areas, beginning from the F₂ generation. We utilized pedigree and bulk-selective methods to characterize artificial and natural selection, respectively. Our examination uncovered preferences between artificial and natural selection. Artificial selection was favored by individuals with increased grain count per panicle but reduced panicle number, while natural selection favored traits like greater panicle number, reduced grains per panicle, and higher thousand-grain weight, especially in the XI cultivation areas. Notably, in the XI regions, natural selection produced a preference for wider grains, indicating that the elongated grains in XI rice may be caused by artificial rather than natural selection. Using de novo assembly of a high-quality parental genome, we observed an increased prevalence of the GJ genotype in GJ areas compared to XI areas, segregation distortion in the advanced inbreeding population could be attributed to loci regulating hybrid sterility. Notably, the semi-dwarf allele sd1-d, linked to the “Green Revolution”, was not favored in either selection paradigm in northern areas, possibly due to its disadvantages on grain yield per plant and NH₄⁺ uptake rate. Our study offers novel perspectives into the contributions of natural and artificial selection to the divergence between XI and GJ subspecies.