Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff.by QTL-seq of seedlings

摘要

Cold stress is a major problem in rice production.To rapidly identify genes for cold tolerance in Dongxiang wild rice (DWR,Oryza rufipogon Griff.),sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant (R) and susceptible (S) bulks of a backcross inbred lines (BILs) population (derived from Oryza sativa×O.rufipogon)and their parents.Single nucleotide polymorphisms(SNP)-index graphs and corresponding Δ(SNP-index) graphs (at 99 and 95% confidence levels) for R- and S-bulks detected a total of 2 609 candidate SNPs,including 58 candidate cold-tolerance genes.Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O.sativa and O.rufipogon.Structural variation and functional annotations of the 5 candidate genes were also analyzed,and allowed us to identify 2 insertion-deletion (InDel) markers (12-7 and 12-16) that were linked with candidate genes on chromosome 12 in DWR.These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.