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Journal of Integrative Agriculture  2018, Vol. 17 Issue (2): 265-275    DOI: 10.1016/S2095-3119(17)61712-X
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Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings
LUO Xiang-dong1, LIU Jian1, ZHAO Jun1, DAI Liang-fang1, CHEN Ya-ling1, ZHANG Ling1, ZHANG Fan-tao1, HU Biao-lin2, XIE Jian-kun1
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 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.
Keywords:  common wild rice        cold tolerance        QTL-seq        single nucleotide polymorphisms (SNP)  
Received: 17 January 2017   Accepted:

This research was partially supported by the National Natural Science Foundation of China (31260255, 31360147 and 31660384), the Natural Science Foundation of Jiangxi Province, China (20151BAB204008), the Scientific Planning Project of Jiangxi Provincial Education Department, China (GJJ12184 and KJLD12059), and the Major Projects in Jiangxi Province, China (20161ACF60022).

Corresponding Authors:  Correspondence LUO Xiang-dong, Tel: +86-791-88120392, E-mail:; XIE Jian-kun, E-mail:    

Cite this article: 

LUO Xiang-dong, LIU Jian, ZHAO Jun, DAI Liang-fang, CHEN Ya-ling, ZHANG Ling, ZHANG Fan-tao, HU Biao-lin, XIE Jian-kun . 2018. Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings. Journal of Integrative Agriculture, 17(2): 265-275.

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