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 02428 (japonica)-YZX (indica) cross. The phenotypes cultivars differ significantly when exposed to low germination. Mapping with high-density bin map identified 11 associated low-temperature which 2 and 4 by multiple traits over two seasons. Locus was major locus, explaining 22.36% phenotypic variation. haplotype results showed that pyramiding favorable alleles these beneficial improving seeds' germinability. RNA-seq analysis performed on second day at temperature for both parents. Three DGEs (Os03g0119800, Os03g0120900, Os03g0121300) obtained locus confirmed as most likely candidates qRT-PCR verification, gene sequence alignment, analysis. Collectively, quantitative trait candidate may be valuable breeding cold-tolerant lines well broadening our knowledge genetics underlying temperatures.