Mapping and Validation of Quantitative Trait Loci on Yield-Related Traits Using Bi-Parental Recombinant Inbred Lines and Reciprocal Single-Segment Substitution Lines in Rice (Oryza sativa L.)

Yield-related traits have higher heritability and lower genotype-by-environment interaction, making them more suitable for genetic studies in comparison with the yield per se. Different populations have been developed and employed in QTL mapping; however, the use of reciprocal SSSLs is limited. In this study, three kinds of bi-parental populations were used to investigate the stable and novel QTLs on six yield-related traits, i.e., plant height (PH), heading date (HD), thousand-grain weight (TGW), effective tiller number (ETN), number of spikelets per panicle (NSP), and seed set percentage (SS). Two parental lines, i.e., <i>japonica</i> Asominori and <i>indica</i> IR24, their recombinant inbred lines (RILs), and reciprocal single-segment substitution lines (SSSLs), i.e., AIS and IAS, were genotyped by SSR markers and phenotyped in four environments with two replications. Broad-sense heritability of the six traits ranged from 0.67 to 0.94, indicating their suitability for QTL mapping. In the RIL population, 18 stable QTLs were identified for the six traits, 4 for PH, 6 for HD, 5 for TGW, and 1 each for ETN, NSP, and SS. Eight of them were validated by the AIS and IAS populations. The results indicated that the allele from IR24 increased PH, and the alternative allele from Asominori reduced PH at <i>qPH3-1</i>. AIS18, AIS19, and AIS20 were identified to be the donor parents which can be used to increase PH in <i>japonica</i> rice; on the other hand, IAS14 and IAS15 can be used to reduce PH in <i>indica</i> rice. The allele from IR24 delayed HD, and the alternative allele reduced HD at <i>qHD3-1</i>. AIS14 and AIS15 were identified to be the donor parents which can be used to delay HD in <i>japonica</i> rice; IAS13 and IAS14 can be used to reduce HD in <i>indica</i> rice. Reciprocal SSSLs not only are the ideal genetic materials for QTL validation, but also provide the opportunity for fine mapping and gene cloning of the validated QTLs.