Identification of QTLs and candidate genes for rice seed germinability under low temperature using high-density genetic mapping and RNA-seq

Reduced temperatures during germination adversely affect rice (Oryza sativa L.) production. Little is known, however, of the genes or genetic loci involved. Here, QTLs were investigated in a recombinant inbred line (RIL) resulting from a 02428 (japonica)-YZX (indica) cross. The phenotypes of the cultivars differ significantly when exposed to low temperatures during germination. Mapping with a high-density bin map identified 11 loci associated with low-temperature germination of which loci 2 and 4 were identified by multiple traits over two seasons. Locus 2 was a major genetic locus, explaining 22.36% of phenotypic variation. The haplotype results showed that the pyramiding of favorable alleles of these two loci was beneficial to improving the rice seeds' low-temperature germinability. RNA-seq analysis was performed on the second day of germination at low temperature for both parents. Three DGEs (Os03g0119800, Os03g0120900, and Os03g0121300) were obtained for locus 2 and were confirmed as the most likely candidates by qRT-PCR verification, gene sequence alignment, and haplotype analysis. Collectively, these quantitative trait loci and candidate genes may be valuable for the breeding of cold-tolerant rice lines as well as broadening our knowledge of the genetics underlying germination at low temperatures.