Analysis on the spectra and level of wide-compatibility conferred by three neutral alleles in inter-subspecific hybrids of rice (Oryza sativa L.) using near isogenic lines

Wide‐compatibility varieties are a special class of rice germplasm that is able to produce fertile hybrids when crossed to either indica or japonica subspecies. Previous studies determined the f5 allele from ‘Dular’ (f5‐Du), f6 allele from ‘Dular’ (f6‐Du) and S5 allele from ‘02428’ (S5‐08) as neutral alleles conferring wide‐compatibility. However, the possible extent of the effect of the three neutral alleles has not been fully characterized because of the narrow range of the tester varieties used and the highly complex differentiation in Asian cultivated rice. In this study, we further developed the five near‐isogenic lines with higher recovery rates of the recurrent parent genome, and testcrossed to 14 japonica varieties, which have been widely used in rice breeding programmes in China. The results clearly revealed that all three neutral alleles exhibited substantial effects on spikelet fertility in most of the indica–japonica testcrosses, which indicated that these hybrid sterility loci have been extensively differentiated between indica and japonica varieties. The magnitudes of effects on spikelet fertility averaged over various crosses seem to be similar among the three neutral alleles, with f5‐Du, f6‐Du and S5‐08 alleles increasing spikelet fertility by 15.09%, 13.99% and 14.25%, respectively. The testcrosses involving f5‐Du allele generally showed much smaller variation in pollen fertility than others. The pyramiding lines with two neutral alleles showed a wider spectrum and a higher level of wide compatibility than others, whereas most of the increases in hybrid fertility couldn’t be simply explained by additive effects, suggesting the very complexity of wide compatibility and hybrid sterility. The indica–japonica hybrids involving restorer lines as one of their parents showed much higher pollen fertility (almost normal) and also higher spikelet fertility. The implications of the findings in rice breeding programmes are also discussed.