Identification of QTLs for Rice Cold Tolerance at Plumule and 3-Leaf-Seedling Stages by Using QTLNetwork Software

doi:10.1016/S1672-6308(09)60028-7

Abstract

Abstract: A doubled haploid (DH) population consisted of 120 lines, derived from a cross between an indica variety, TN1, and a japonica variety, Chunjiang 06, was used to identify QTLs controlling rice cold tolerance at the plumule and 3-leaf-seedling stages by using the QTLNetwork software. The percentages of normal plumules after 4°C treatments for 7 d, 9 d, 11 d, and 14 d, as well as the cold stress tolerance index (CSTI) and the withering index (WI) of rice seedling were investigated. A total of five single-effect QTLs, each for percentages of normal plumules after 4°C treatments for 9 d, 11 d and 14 d, and CSTI and WI, respectively were identified. The QTLs for the percentages of normal plumules after low temperature treatments for 9 d, 11 d and 14 d were on chromosomes 4, 2 and 11, accounting for 14.1%, 17.3% and 21.5% of the phenotypic variation, respectively. QTLs for CSTI and WI were on chromosomes 10 and 1, respectively. Two pairs of epistatic loci were identified, but none of the epistatic loci involved the single-effect QTLs. The RM528–RM340 interval on chromosome 6 interacted with the RM278–RM3919B interval on chromosome 9 for CSTI, and the epistatic interaction accounted for 17.7% of the phenotypic variation. A pair of epistatic loci was identified for WI, the RM246–RM5461 interval on chromosome 1 interacted with the ISA–RM447 interval on chromosome 8, which accounted for 22.6% of the phenotypic variation.

Key words: rice, cold tolerance, quantitative trait loci, plumule, QTLNetwork software

JI Zhi-juan, ZENG Yu-xiang, ZENG Da-li, MA Liang-yong, LI Xi-ming, LIU Bing-xin, YANG Chang-deng. Identification of QTLs for Rice Cold Tolerance at Plumule and 3-Leaf-Seedling Stages by Using QTLNetwork Software[J]. RICE SCIENCE, 2010, 17(4): 282-287 .

References

Andaya V C, Mackill D J. 2003a. Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot, 54: 2579–2585.
Andaya V C, Mackill D J. 2003b. QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica×indica cross. Theor Appl Genet, 106: 1084–1090.
Andaya V C, Tai T H. 2006. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet, 113: 467–475.
Cheng H T, Jang H, Xue D W, Guo L B, Zeng D L, Zhang G H, Qian Q. 2008. Mapping of QTLs underlying tolerance to alkali at germination and early seedling stages in rice. Acta Agron Sin, 34: 1719–1727. (in Chinese with English abstract)
de los Reyes B G, Morsy M, Gibbons J, Varma T S N, Antoine W, McGrath J M, Halgren R, Redus M. 2003. A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library. Theor Appl Genet, 107: 1071–1082.
Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin S Y, Yano M. 2004. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet, 108: 794–799.
Gong Y J, Ruan W J, Xun X, Dong Y J, Lin D Z, Ye S H, Zhang X M. 2009. QTL analysis of cold tolerance for two bud traits in rice. Mol Plant Breeding, 7: 273–278. (in Chinese with English abstract)
Ji S L, Jiang L, Wang Y H, Liu S J, Liu X, Zhai H Q, Atsushi Y, Wan J M. 2008. QTL and epistasis for low temperature germinability in rice. Acta Agron Sin, 34: 551–556. (in Chinese with English abstract)
Ji S L, Jiang L, Wang Y H, Zhang W W, Liu X, Liu S J, Chen L M, Zhai H Q, Wan J M. 2009. Quantitative trait loci mapping and stability for low temperature germination ability of rice. Plant Breeding, 128: 387–392.
Kaneda C, Beachell H M. 1974. Response of indica-japonica rice hybrids to low temperatures. SABRAO J, 6: 17–32.
Mackill D J, Lei X M. 1997. Genetic variation for traits related to temperate adaptation of rice cultivars. Crop Sci, 37: 1340– 1346.
McCouch S R, Cho Y G, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T. 1997. Suggestion for QTL nomenclature. Rice Genet Newsl, 14: 11–13.
Miura K, Lin S Y, Yano M, Nagamine T. 2001. Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.). Breeding Sci, 51: 293–299.
Nakagahra M, Okuno K, Vaughan D. 1997. Rice genetic resources: History, conservation, investigative characterization and use in Japan. Plant Mol Biol, 35: 69–77.
Qian Q, Zeng D L, He P, Zheng X W, Chen Y, Zhu L H. 2000. QTL analysis of the rice seedling cold tolerance in a double haploid population derived from anther culture of a hybrid between indica and japonica rice. Chin Sci Bull, 45: 448–453.
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. J Wuhan Bot Res, 21: 385–389. (in Chinese with English abstract)
Teng S, Zeng D L, Qian Q, Kunihifo Y, Huang D N, Zhu L H. 2001. QTL analysis of rice low temperature germinability. Chin Sci Bull, 46: 1800–1803.
Wang D L, Zhu J, Li Z K, Paterson A H. 1999. Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches. Theor Appl Genet, 99: 1255– 1264.
Yan C J, Li X, Cheng Z K, Yu H X, Gu M H, Zhu L H. 1999. Identification of QTL for cold tolerance at early seedling stage in rice (Oryza sativa L.) via RFLP markers. Chin J Rice Sci, 13: 134–138. (in Chinese with English abstract)
Yang J, Hu C C, Hu H, Yu R D, Xia Z, Ye X Z, Zhu J. 2008. QTLNetwork: Mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 24: 721–723.
Yoshida R, Kanno A, Sato T, Kameya T. 1996. Cool temperature- induced chlorosis in rice plants. Plant Physiol, 110: 997–1005.
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 Sci, 168: 527–534.

[1]	Prathap V, Suresh KUMAR, Nand Lal MEENA, Chirag MAHESHWARI, Monika DALAL, Aruna TYAGI. Phosphorus Starvation Tolerance in Rice Through a Combined Physiological, Biochemical and Proteome Analysis [J]. Rice Science, 2023, 30(6): 8-.
[2]	Serena REGGI, Elisabetta ONELLI, Alessandra MOSCATELLI, Nadia STROPPA, Matteo Dell’ANNO, Kiril PERFANOV, Luciana ROSSI. Seed-Specific Expression of Apolipoprotein A-I_Milano Dimer in Rice Engineered Lines [J]. Rice Science, 2023, 30(6): 6-.
[3]	Sundus ZAFAR, XU Jianlong. Recent Advances to Enhance Nutritional Quality of Rice [J]. Rice Science, 2023, 30(6): 4-.
[4]	Kankunlanach KHAMPUANG, Nanthana CHAIWONG, Atilla YAZICI, Baris DEMIRER, Ismail CAKMAK, Chanakan PROM-U-THAI. Effect of Sulfur Fertilization on Productivity and Grain Zinc Yield of Rice Grown under Low and Adequate Soil Zinc Applications [J]. Rice Science, 2023, 30(6): 9-.
[5]	FAN Fengfeng, CAI Meng, LUO Xiong, LIU Manman, YUAN Huanran, CHENG Mingxing, Ayaz AHMAD, LI Nengwu, LI Shaoqing. Novel QTLs from Wild Rice Oryza longistaminata Confer Rice Strong Tolerance to High Temperature at Seedling Stage [J]. Rice Science, 2023, 30(6): 14-.
[6]	LIN Shaodan, YAO Yue, LI Jiayi, LI Xiaobin, MA Jie, WENG Haiyong, CHENG Zuxin, YE Dapeng. Application of UAV-Based Imaging and Deep Learning in Assessment of Rice Blast Resistance [J]. Rice Science, 2023, 30(6): 10-.
[7]	Md. Forshed DEWAN, Md. AHIDUZZAMAN, Md. Nahidul ISLAM, Habibul Bari SHOZIB. Potential Benefits of Bioactive Compounds of Traditional Rice Grown in South and South-East Asia: A Review [J]. Rice Science, 2023, 30(6): 5-.
[8]	Raja CHAKRABORTY, Pratap KALITA, Saikat SEN. Phenolic Profile, Antioxidant, Antihyperlipidemic and Cardiac Risk Preventive Effect of Chakhao Poireiton (A Pigmented Black Rice) in High-Fat High-Sugar induced Rats [J]. Rice Science, 2023, 30(6): 11-.
[9]	LI Qianlong, FENG Qi, WANG Heqin, KANG Yunhai, ZHANG Conghe, DU Ming, ZHANG Yunhu, WANG Hui, CHEN Jinjie, HAN Bin, FANG Yu, WANG Ahong. Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages [J]. Rice Science, 2023, 30(6): 7-.
[10]	JI Dongling, XIAO Wenhui, SUN Zhiwei, LIU Lijun, GU Junfei, ZHANG Hao, Tom Matthew HARRISON, LIU Ke, WANG Zhiqin, WANG Weilu, YANG Jianchang. Translocation and Distribution of Carbon-Nitrogen in Relation to Rice Yield and Grain Quality as Affected by High Temperature at Early Panicle Initiation Stage [J]. Rice Science, 2023, 30(6): 12-.
[11]	Nazaratul Ashifa Abdullah Salim, Norlida Mat Daud, Julieta Griboff, Abdul Rahim Harun. Elemental Assessments in Paddy Soil for Geographical Traceability of Rice from Peninsular Malaysia [J]. Rice Science, 2023, 30(5): 486-498.
[12]	Monica Ruffini Castiglione, Stefania Bottega, Carlo Sorce, Carmelina SpanÒ. Effects of Zinc Oxide Particles with Different Sizes on Root Development in Oryza sativa [J]. Rice Science, 2023, 30(5): 449-458.
[13]	Tan Jingyi, Zhang Xiaobo, Shang Huihui, Li Panpan, Wang Zhonghao, Liao Xinwei, Xu Xia, Yang Shihua, Gong Junyi, Wu Jianli. ORYZA SATIVA SPOTTED-LEAF 41 (OsSPL41) Negatively Regulates Plant Immunity in Rice [J]. Rice Science, 2023, 30(5): 426-436.
[14]	Ammara Latif, Sun Ying, Pu Cuixia, Noman Ali. Rice Curled Its Leaves Either Adaxially or Abaxially to Combat Drought Stress [J]. Rice Science, 2023, 30(5): 405-416.
[15]	Liu Qiao, Qiu Linlin, Hua Yangguang, Li Jing, Pang Bo, Zhai Yufeng, Wang Dekai. LHD3 Encoding a J-Domain Protein Controls Heading Date in Rice [J]. Rice Science, 2023, 30(5): 437-448.