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（SNPindex） 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.
LUO Xiang-dongLIU JianZHAO JunDAI Liang-fangCHEN Ya-lingZHANG LingZHANG Fan-taoHU Biao-linXIE Jian-kun
Cold stress is one of the major restraints for rice production. Cold tolerance is controlled by complex genetic factor. In this study, a backcross inbred lines （BILs） population derived from an inter-specific cross （Oryza sativa L.xO. rufipogon Griff.） was used for genetic linkage map construction and quantitative trait locus （QTL） mapping. A linkage map consisting of 153 markers was constructed, spanning 1 596.8 cM with an average distance of 11.32 cM between the adjacent markers. Phenotypic evaluation of the parents and BILs under （6±1）℃ cold stress revealed that the ability of cold tolerance in BILs at early seedling obeyed a skewed normal and continuous distribution. Fifteen QTLs on chromosomes 6, 7, 8, 11, and 12 were identified using survival percent （SP） and non death percent （NDP） as indicators of cold tolerance, which could explain 5.99 to 40.07% of the phenotypic variance, of which the LOD values ranged from 3.04 to 11.32. Four QTLs on chromosomes 3, 5 and 7 were detected using leaf conductivity （LC） and root conductivity （RC） as indicators of cold tolerance, ranging from 19.54 to 33.53% for the phenotypic variance explained and 2.54 to 6.12 for the LOD values. These results suggested that there might be multi major QTLs in O. rufipogon and some useful genes for cold tolerance have been transferred into cultivated rice, which would be helpful for cloning and utilizing the cold tolerance-responsive genes from wild rice.
LUO Xiang-dongZHAO JunDAI Liang-fangZHANG Fan-taoZHOU YiWAN YongXIE Jian-kun
