Genomic analysis for the selection of superior donor genotypes in rice improvement

The field experiment was conducted following a Randomized Block Design (RBD) with three replications, involving 30 advanced breeding lines, with BPT-5204 included as a standard quality check. For molecular characterization, a set of seven genes (Gs3, Gw5, Gn2, Gn1, SCM3, SCM2, and Spl14) and three yield-related QTLs (Yld12.1 and Yld2.1) associated with grain yield were employed. Among these, Gn1 and Gn2 were linked to grain number, SCM2 and SCM3 to culm strength, Gw5 to grain weight, Gs3 to grain size, and Spl14 to the number of filled grains per panicle. Genotyping results revealed that only one advanced breeding line, SP-08, possessed all seven yield-associated genes and QTLs, suggesting a strong potential for enhanced yield performance. Two breeding lines exhibited the presence of six yield-contributing loci: SP-69, which carried Gn2, Gn1, Gw5, SCM3, Yld2.1, and Spl14, and SP-70, which harbored Gn1, SCM3, Gw5, Gs3, Yld2.1, and Yld12.1. In addition, four advanced breeding lines were identifies with 5 yield-related genes/QTLs, line SP-37 (Gn2, SCM3, Gw5, Yld2.1, Yld12.1), SP-55 (Gn2, SCM2, SCM3, Gw5, Yld2.1), SP-75 (Gn2, Gn1, SCM3, Gw5, Yld12.1), and SP-61 (Gn2, Gn1, SCM2, Gw5, Yld2.1).