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Not AvailableA special class of rice germplasm, referred as wide-compatible can produce hybrids with enhanced spikelet fertility when crossed with japonica×indicia rice lines having neutral allele. Present study was conducted to identify the presence of neutral allele and relationship in the hybrid performance. The wide-compatible genotype screening resulted positive selection having neutral allele and responsible for increased spikelet fertility with possible utilization as donor parent in hybrid development programme for achieving higher yield. Combining ability and heterosis for grain yield and its component traits derived from japonica×indica experimental hybrids revealed higher general combining ability variance than their respective specific combining ability variances indicating the predominance of additive gene action, opened the way for fixing the yield contributing gene by breeding through transgressive selection. Most of the experimental hybrids showed significant and positive SCA effects for grain yield as well as several other yield related component traits. Wide compatibility gene investigation clearly demonstrated the utility of InDel primer in the identification of wide compatible genotypes possessing neutral allele at S5 locus. The genotypes having natural allele (281-bp) can give rise to fully fertile panicle and significant contribution towards yield and heterosis. Association index between genetic diversity and three SH of GY hybrids on the basis of microsatellite data set surprisingly exhibited significant and positive correlation indicated the possible utility of microsatellite markers for successful utilization and establishing the strong heterotic relationship.Not Availabl