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

Abstract

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.