Abstract
Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions—field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3FD and qPHS-11FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3GH, qPHS-4GH, and qPHS-11GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11GH and qPHS-11FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.
Highlights
Pre-harvest sprouting (PHS) of rice (Oryza sativa L.) is a serious economic issue causing significant reductions in grain quality and yield primarily in japonica rice-cultivating regions
These QTLs were distributed across all 12 chromosomes, and among them, a few genes have been identified via map-based cloning (Ye et al 2015; Fujino et al 2008; Sugimoto et al 2010). qSD1-2 on chromosome 1, which is associated with seed dormancy, was delimited to a 20-kb region containing OsGA20ox[2], and the naturally occurring or induced loss-of-function mutations of this gene enhance seed dormancy (Ye et al 2015). qLTG3-1, a QTL for lowtemperature germinability on chromosome 3, was found to encode a protein of unknown function, and it is strongly expressed in the embryo during seed germination (Fujino et al 2008)
10 single nucleotide polymorphism (SNP) loci were identified as significantly affecting PHS through re-sequencing 21 representative rice accessions (10 PHS resistant and 11 PHS susceptible), and a regression equation for evaluating PHS based on the genotypes of eight significant loci was constructed, which accounted for an R2 value of 0.401 in japonica rice (Lee et al 2017)
Summary
Pre-harvest sprouting (PHS) of rice (Oryza sativa L.) is a serious economic issue causing significant reductions in grain quality and yield primarily in japonica rice-cultivating regions. Regarding PHS and seed dormancy in cultivated and wild rice, several quantitative trait loci (QTLs) have been reported in the progenies of crosses between japonica and indica varieties (Lin et al 1998; Miura et al 2001; Dong et al 2003; Guo et al 2004; Wan et al 2005, 2006; Chen et al 2006; Jiang et al 2006; Gao et al 2008; Ji et al 2009; Xie et al 2011; Marzougui et al 2012; Li et al 2013; Sasaki et al 2013; Wang et al 2014; Lee and Kwon 2015) between indica varieties (Li et al 2011), between japonica varieties (Fujino et al 2004; Hori et al 2010), between weedy rice lines and cultivars (Gu et al 2004, 2005; Ye et al 2010; Subudhi et al 2012), between upland and lowland rice varieties (Mizuno et al 2018), and between a wild rice (Oryza rufipogon) line and a cultivar (Cai and Morishima 2000) These QTLs were distributed across all 12 chromosomes, and among them, a few genes have been identified via map-based cloning (Ye et al 2015; Fujino et al 2008; Sugimoto et al 2010). Better understanding of the complexity of genetic factors for PHS and seed dormancy is required to accelerate the development of PHS-resistant varieties via marker-assisted breeding
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
