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QTLs for quantitative traits are influenced by genetic background (GB) and environment. Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection (MAS). In this study, QTLs and QTL×environment interactions affecting grain yield per plant (GY) and its component traits, filled grain number per panicle (FGN), panicle number per plant (PN) and 1000-grain weight (TGW) across six environments were dissected using two sets of reciprocal introgression lines (ILs) derived from the cross Lemont×Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs (87.4%) showed significant QTL×environment interactions (QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15 (20.8%) QTLs and 12 (16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail

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Genetic background effects on QTL and QTL×environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice