Please wait a minute...
Journal of Integrative Agriculture  2016, Vol. 15 Issue (12): 2703-2711    DOI: 10.1016/S2095-3119(16)61465-X
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
Linkage map construction and QTL mapping for cold tolerance in Oryza rufipogon Griff. at early seedling stage
LUO Xiang-dong1, ZHAO Jun1, DAI Liang-fang1, ZHANG Fan-tao1, ZHOU Yi1, WAN Yong2, XIE Jian-kun1
1 College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R.China
2 Rice Research Institute, Jiangxi Academy of Agricultural Science, Nanchang 330200, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract      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.×O. 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)°C 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.
Keywords:  common wild rice        cold tolerance        quantitative trait loci (QTL)        introgression  
Received: 08 April 2016   Accepted:
Fund: 

This research was partially supported by the National Natural Science Foundation of China (31260255, 31360327 and 31360147), the Development Program for Young Scientists of Jiangxi Province, China (20112BCB23007) and the Scientific Planning Project of Jiangxi Provincial Education Department, China (GJJ12184 and KJLD12059).

Corresponding Authors:  LUO Xiang-dong, Tel: +86-791-88120390, E-mail: xdluolf@163.com; XIE Jian-kun, Tel: +86-791-88120396, E-mail: xiejiankun@yahoo.com   

Cite this article: 

LUO Xiang-dong, ZHAO Jun, DAI Liang-fang, ZHANG Fan-tao, ZHOU Yi, WAN Yong, XIE Jian-kun. 2016. Linkage map construction and QTL mapping for cold tolerance in Oryza rufipogon Griff. at early seedling stage. Journal of Integrative Agriculture, 15(12): 2703-2711.

Andaya V C, Mackill D J. 2003. Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. Journal of Experimental Botany, 54, 2579–2585.

Andaya V C, Tai T H. 2006. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theoretical and Applied Genetics, 113, 467–475.

Andaya V C, Tai T H. 2007. Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Molecular Breeding, 20, 349–358.

Chen D Z, Zhong P A, Xiao Y Q, Huang Y J, Xie J K. 2002. Identification of QTLs for cold tolerance at seedling stage in dongxiang wild rice (Oryza rufipogon Griff.) by SSR markers. Acta Agriculturae Universitatis Jiangxiensis, 24, 753–756. (in Chinese)

Chen J, Bughio H, Chen D Z, Liu G J, Zheng K L, Zhuang J Y. 2006. Development of chromosomal segment substitution lines from a backcross recombinant inbred population of interspecific rice cross. Rice Science, 13, 15–21.

Chen X R, Yang K S, Fu J R, Zhu C L, Peng X S, He X P, He H H. 2008. Identification and genetic analysis of fertility restoration ability in Dongxiang wild rice (Oryza rufipogon). Rice Science, 15, 21–28.

Churchill G A, Doerge R W. 1994. Empirical threshold value for quantitative trait mapping. Genetics, 138, 963–971.

Farrell T C, Fox K M, Williams R L, Fukai S, Reinke R F, Lewin L G. 2001. Temperature constraint to rice production in Australia and Laos: a shared problem. In: Increased Lowland Rice Production in the Mekong Region, Proceedings of an International Workshop Held in Vientiane. ACIAR Proceedings 101, Laos. pp. 129–137.

Fujino K. 2004. A major gene for low temperature germinability in rice (Oryza sativa L.). Euphytica, 136, 63–68.

Han L Z, Qiao Y L, Cao G L, Zhang Y Y, An Y P, Ye J D, Koh H J. 2005. QTL analysis on cold tolerance during early growth period in rice. Chinese Journal of Rice Science, 19, 122–126. (in Chinese)

Huang L S, Liu L F, Liu Z X. 2008. Advances and prospects of cold tolerance in rice. Hunan Agricultural Sciences, 1, 3–6. (in Chinese)

Kim S M, Suh J P, Lee C K, Lee J H, Kim Y G, Jena K K. 2014. QTL mapping and development of candidate gene?derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.). Molecular Genetics and Genomics, 289, 333–343.

Kosambi D D. 1943. The estimation of map distance from recombination values. Annals of Eugenics, 12, 172–175.

Koseki M, Kitazawa N, Yonebayashi S, Maehara Y, Wang Z, Minobe Y. 2010. Identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage. Molecular Genetics and Genomics, 284, 45–54.

Lander E S, Green P, Abrahamson J, Barlow A, Daly M J, Lincoln S E, Newburg L. 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1, 174–181.

Lee T M, Lur H S, Chu C. 1995. Abscisic acid and putrescine accumulation in chilling-tolerant rice cultivars. Crop Science, 35, 502–508.

Liu F X, Sun C Q, Tan L B, Fu Y C, Li D J, Wang X K. 2003. Identification of QTL for cold tolerance at booting and flowering stage in Jiangxi Dongxiang wild rice. Chinese Science Bulletin, 48, 1864–1867.

Liu F X, Xu W Y, Song Q, Tan L B, Liu J Y, Zhu Z F, Fu Y C, Sun C Q. 2013. Microarrayassisted fine-mapping of quantitative trait loci for cold tolerance in rice. Molecular Plant, 6, 757–767.

Lou Q J, Chen L, Sun Z X, Xing Y Z, Li J, Xu X Y, Mei H W, Luo L J. 2007. A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica, 158, 87–94.

Luo X D, Dai L F, Cao J F, Jian S R, Chen Y L, Hu B L, Xie J K. 2012. Identification and molecular cytology analysis of cold tolerance introgression lines derived from Oryza sativa L. mating with O. rufipogon Griff. Euphytica, 187, 461–469.

Lü Y, Guo Z L, Li X K, Ye H Y, Li X H, Xiong L Z. 2016. New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome-wide association analysis. Plant, Cell and Environment, 39, 556–570.

Mao D, Yu L, Chen D, Li L, Zhu Y, Xiao Y, Zhang D, Chen C. 2015. Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theoretical and Applied Genetics, 128, 1359–1371.

McCouch S R, CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative). 2008. Gene nomenclature system for rice. Rice, 1, 72–84.

Murashige T, Skoog F. 1962. A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiologia Plantarum, 15, 473–497.

Murray H G, Thompson W F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321–4326.

Orvar B L, Sangwan V, Omann F, Dhindsa R S. 2000. Early steps in cold sensing by plant cells: The role of actin cytoskeleton and membrane fluidity. The Plant Journal, 23, 785–794.

Qu T T, Chen L Y, Zhang Z H, Hu Z L, Li P, Zhu L H, Zhu Y G. 2003. Molecular mapping of genes conferring cold tolerance at seedling stage using doubled haploid lines from an indica×japonica cross in rice. Journal of Wuhan Botanical Research, 21, 385–389. (in Chinese)

Rahman L, Khanam M S, Koh H J. 2008. QTL analysis for yield related traits using populations derived from an indica japonica hybrid in rice (Oryza sativa L.). Czech Journal of Genetics and Plant Breeding, 44, 93–104.

Saito K, Hayano-Saito Y, Maruyama-Funatsuki W, Sato Y, Kato A. 2004. Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice. Theoretical and Applied Genetics, 109, 515–522.

Suh J P, Lee C K, Lee J H, Kim J J, Kim S M, Cho Y C, Park S H, Shin J C, Kim Y G, Jena K K. 2012. Identification of uantitative trait loci for seedling cold tolerance using RILs derived from a cross between japonica and tropical japonica rice cultivars. Euphytica, 184, 101–108.

Tan L B, Liu F X, Xue W, Wang G J, Ye S, Zhu Z F, Fu Y C, Wang X K, Sun C Q. 2007. Development of Oryza rufipogon and O. sativa introgression lines and assessment for yield-related quantitative trait loci. Journal of Integrative Plant Biology, 49, 871–884.

Wang S, Basten C J, Zeng Z B. 2007. Windows QTL cartographer 2.5. department of statistics, north carolina state university, raleigh, NC, USA. [2012-04-23]. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm

Xia R X, Xiao N, Hong Y H, Zhang C, Su Y, Zhang X M, Chen J M. 2010. QTLs mapping for cold tolerance at seedling stage in Dongxiang Wild Rice (Oryza rufipogon Griff.). Scientia Agricultura Sinica, 43, 443–451. (in Chinese)

Xiao N, Huang W N, Zhang X, Gao Y, Li A L, Dai Y, Yu L, Liu G Q, Pan C H, Li Y H, Dai Z Y, Chen J M. 2014. Fine mapping of qRC10-2, a quantitative trait locus for cold tolerance of rice roots at seedling and mature stages. PLOS ONE, 9, 95–104.

Xie J, Agrama H A, Kong D, Zhuang J, Hu B, Wan Y, Yan W. 2010. Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon). Genetic Resources and Crop Evolution, 57, 597–609.

Xie J K, Hu B L, Wan Y, Zhang T, Li X, Liu R N, Huang Y H, Dai L F, Luo X D. 2010a. Comparison of the drought resistance characters at seedling stage between Dongxiang common wild rice (Oryza rufipogon Griff.) and cultivars (Oryza sativa L.). Acta Eclolgica sinica, 30, 1665–1674.

Xu L M, Zhou L, Zeng Y W, Wang F M, Zhang H L, Shen S Q, Li Z C. 2008. Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice nearisogenic line. Plant Science, 174, 340–347.

Yang T F, Zhang S H, Zhao J L, Huang Z H, Zhang G Q, Liu B. 2015. Meta-analysis of QTLs underlying cold tolerance in rice (Oryza sativa L.). Molecular Plant Breeding, 13, 1–15.

Yoshida H, Kato A. 1994. Cold-induced accumulation of RNAs and cloning of cDNAs related to chilling injury in rice. Japanese Journal of Breeding, 44, 361–365.

Zeng Y W, Yang S M, Cui H, Yang X J, Xu L M, Du J, Pu X Y, Li Z C, Cheng Z Q, Huang X Q. 2009. QTLs of cold tolerance-related traits at the booting stage for NIL-RILs in rice revealed by SSR. Genes & Genomics, 31, 143–154.

Zhang S H, Zheng J S, Liu B, Peng S B, Leung H, Zhao J L, Wang X F, Yang T F, Huang Z H. 2014. Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment. Euphytica, 195, 95–104.

Zhang X, Zhou S X, Fu Y C, Zhen S, Wang X K. Sun C Q. 2006. Identification of a drought tolerant introgression line derived from Dongxiang common wild rice (O. rufipogon Griff.). Plant Molecular Biology, 62, 247–259.

Zhang Y S, Luo L J, Liu T M, Xu C G, Xing Y Z. 2009. Four rice QTL controlling number of spikelets per panicle expressed the characteristics of single Mendelian gene in near isogenic backgrounds. Theoretical and Applied Genetics, 118, 1035–1044.

Zhang Z H, Su L, Li W, Chen W, Zhu Y G. 2005. A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Science, 168, 527–534.
[1] Jianjun Wang, Yanan Shao, Xin Yang, Chi Zhang, Yuan Guo, Zijin Liu, Mingxun Chen.

Heterogeneous expression of stearoyl-acyl carrier protein desaturase genes SAD1 and SAD2 from Linum usitatissimum enhances seed oleic acid accumulation and seedling cold and drought tolerance in Brassica napus [J]. >Journal of Integrative Agriculture, 2024, 23(6): 1864-1878.

[2] Akmaral Baidyussen, Gulmira Khassanova, Maral Utebayev, Satyvaldy Jatayev, Rystay Kushanova, Sholpan Khalbayeva, Aigul Amangeldiyeva, Raushan Yerzhebayeva, Kulpash Bulatova, Carly Schramm, Peter Anderson, Colin L. D. Jenkins, Kathleen L. Soole, Yuri Shavrukov. Assessment of molecular markers and marker-assisted selection for drought tolerance in barley (Hordeum vulgare L.)[J]. >Journal of Integrative Agriculture, 2024, 23(1): 20-38.
[3] XU Peng-yue, XU Li, XU Hai-feng, HE Xiao-wen, HE Ping, CHANG Yuan-sheng, WANG Sen, ZHENG Wen-yan, WANG Chuan-zeng, CHEN Xin, LI Lin-guang, WANG Hai-bo.

MdWRKY40is directly promotes anthocyanin accumulation and blocks MdMYB15L, the repressor of MdCBF2, which improves cold tolerance in apple [J]. >Journal of Integrative Agriculture, 2023, 22(6): 1704-1719.

[4] Tahmina SHAR, SHENG Zhong-hua, Umed ALI, Sajid FIAZ, WEI Xiang-jin, XIE Li-hong, JIAO Gui-ai, Fahad ALI, SHAO Gao-neng, HU Shi-kai, HU Pei-song, TANG Shao-qing. Mapping quantitative trait loci associated with starch paste viscosity attributes by using double haploid populations of rice (Oryza sativa L.)[J]. >Journal of Integrative Agriculture, 2020, 19(7): 1691-1703.
[5] ZHAO Chen-chen, YUE Lei, WANG Yao, GUO Jian-ying, ZHOU Zhong-shi, WAN Fang-hao. Relationship between copulation and cold hardiness in Ophraella communa (Coleoptera: Chrysomelidae)[J]. >Journal of Integrative Agriculture, 2019, 18(4): 900-906.
[6] LUO Xiang-dong, LIU Jian, ZHAO Jun, DAI Liang-fang, CHEN Ya-ling, ZHANG Ling, ZHANG Fan-tao, HU Biao-lin, XIE Jian-kun . Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings[J]. >Journal of Integrative Agriculture, 2018, 17(2): 265-275.
[7] ZHAO Jie, QIN Jing-jing, SONG Qian, SUN Chuan-qing, LIU Feng-xia. Combining QTL mapping and expression profile analysis to identify candidate genes of cold tolerance from Dongxiang common wild rice (Oryza rufipogon Griff.)[J]. >Journal of Integrative Agriculture, 2016, 15(9): 1933-1943.
No Suggested Reading articles found!