Pre-harvest sprouting (PHS) is one of the important traits that not only cause serious economic issues but also lead to reduction in grain quality and yield in rice (Oryza sativa L.). To analyze the quantitative trait loci (QTLs) for PHS tolerance, we evaluated PHS, seed dormancy (SD), and low-temperature germination (LTG) of 88 F2:3 populations and their parental lines. Genotypic analysis was performed by using 441 single nucleotide polymorphisms (SNPs) detected from re-sequencing data. Seed dormancy (SD) and low-temperature germination (LTG) were identified to exhibit a positive correlation with PHS. Under the field condition, two major QTLs for PHS, qPHS1-1FC and qPHS1-2FC were identified on chromosome 1. Under the growth chamber condition, qPHS1-1GC and qPHS1-2GC had the same regions on chromosome 1. QTLs of SD and LTG (qSD1-1, qSD1-2, qLTG1-1, and qLTG1-2) had the same regions; these results suggested that candidate QTLs demonstrate pleiotropy about PHS, SD, and LTG. The major QTLs detected in this study are hypothesized to provide an important resource for molecular breeding and gain a better understanding of the genetics of traits in rice.
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