| Sumario: | Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits and both determining farmers’ final profit. More than one population under multiple environments may provide valuable information for breeding selection on this MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our objectives were (1) to provide a set of reciprocal introgression lines (composed by two BC2RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test mapping effect by MQ-GS correlation dissection by different mapping methods; (3) to perform genetic and breeding simulation to pyramid favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci in average for MQ-GS traits. It’s notable that 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful data for rice molecular breeding.
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