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Position: Home > Articles > Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings Journal of Integrative Agriculture 2018,17 (2)

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

作者：

Luo Xiang-dong;Liu Jian;Zhao Jun;Dai Liang-fang;Chen Ya-ling;Zhang Ling;Zhang Fan-tao;Hu Biao-lin;Xie Jian-kun

单位：

Jiangxi Normal Univ, Coll Life Sci, Nanchang 330022, Jiangxi, Peoples R China;Jiangxi Acad Agr Sci, Rice Res Inst, Nanchang 330200, Jiangxi, Peoples R China

关键词：

common wild rice;cold tolerance;QTL-seq;single nucleotide polymorphisms (SNP)

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 sativaxO. rufipogon) and their parents. Single nucleotide polymorphisms (SNP)-index graphs and corresponding Delta(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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Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings

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