Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm

Low-temperature germinability (LTG) is an important trait for breeding of varieties for use in direct-seeding rice production systems. Although rice (Oryza sativa L.) is generally sensitive to low temperatures, genetic variation for LTG exists and several quantitative trait loci (QTLs) have been reported. Most notably, the gene underlying the major effect QTL qLTG3-1 has been cloned and implicated in tissue weakening. The objective of this study was to develop molecular markers for use in selecting rice germplasm with enhanced LTG. A panel of japonica rice accessions (n = 180) from temperate regions in Asia was evaluated for LTG and genotyped with markers from qLTG3-1 and regions previously reported to harbor other LTG QTLs. In addition to the germplasm evaluation using these markers, an association analysis was conducted using SNP data generated by reduced representation sequencing of the panel. Eight SNP markers were found to be significantly associated with LTG using general and mixed linear models. Two of these markers were in close proximity (similar to 35 kb) to each other on chromosome 4 in a region previously linked to LTG in rice. The identification of several markers strongly associated with LTG in locations not previously reported provides a foundation for further genetic dissection of this complex trait.