A novel functional gene associated with cold tolerance at the seedling stage in rice.
Identification and cloning of cold-tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold-tolerant QTL at the seedling stage, qCTS-9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold-tolerant variety Lijiangxintuanheigu (LTH) and a cold-sensitive variety Shanhuangzhan 2 (SHZ-2). In this study, eight candidate genes within the qCTS-9 interval were identified through integrated analysis of QTL mapping with genomewide differential expression profiling of LTH. The qRT-PCR assay showed that only Os09g0410300 exhibited different expression patterns between LTH and SHZ-2 during cold stress, and significantly positive correlation was found between cold induction of Os09g0410300 and seedling cold tolerance in the RI lines. Five SNPs and one InDel in the promoters of Os09g0410300 were detected between LTH and SHZ-2, and the InDel marker ID410300 designed based on the insertion-deletion polymorphism in the promoter was significantly associated with seedling cold tolerance in RIL population. Further, Os09g0410300 over-expression plants exhibited enhanced cold tolerance at the seedling stage compared with the wild-type plants. Thus, our results suggest that Os09g0410300 is the functional gene underlying qCTS-9. To our knowledge, it is a novel gene contributed to enhance cold tolerance at the seedling stage in rice. Identification of the functional gene underlying qCTS-9 and development of the gene-specific marker will facilitate molecular breeding for cold tolerance at the seedling stage in rice through transgenic approach and marker-assisted selection (MAS).
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Junliang
J
Zhao
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Shaohong
S
Zhang
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Jingfang
J
Dong
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Tifeng
T
Yang
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Xingxue
X
Mao
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Qing
Q
Liu
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Xiaofei
X
Wang
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Bin
B
Liu
D001483:Base Sequence; D001947:Breeding; D002874:Chromosome Mapping; D003080:Cold Temperature; D015870:Gene Expression; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D030821:Plants, Genetically Modified; D040641:Quantitative Trait Loci / Q000235:genetics*; D036226:Seedlings / Q000235:genetics / Q000502:physiology; D016415:Sequence Alignment; D013312:Stress, Physiological
D005819:Genetic Markers; D010940:Plant Proteins
QTL mapping; cold tolerance; expression profiling; gene cloning; quantitative trait locus (QTL); rice