Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings |
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Authors: | Xiang-dong LUO Jian LIU Jun ZHAO Liang-fang DAI Ya-ling CHEN Ling ZHANG Fantao ZHANG Biao-lin HU Jian-kun XIE |
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Institution: | 1. College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R. China;2. Rice Research Institure, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, P.R. China |
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Abstract: | 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 ρ(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. |
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Keywords: | common wild rice cold tolerance QTL-seq single nucleotide polymorphisms (SNP) |
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