Genetic Control of Germination Ability under Cold Stress in Rice

doi:10.1016/S1672-6308(08)60076-1

Abstract

Abstract: An F₉ recombinant inbred lines (RIL) population, derived from a cross between IR28 (Oryza sativa L. spp. indica) and Daguandao (O. sativa L. spp. japonica), was used to construct a molecular linkage map and to identify germination ability including the traits of imbibition rate, germination rate, germination index, root length, shoot length and seed vigor at 14°C for 23 d. A composite interval mapping approach was applied to conduct genetic analysis for germination ability. The frequency distributions of the germination ability traits under the cold stress in the RIL population showed continuous segregation, suggesting they were quantitative traits controlled by several genes. A total of seven QTLs were identified on chromosomes 4, 6 and 9, including two for imbibition rate (qIR-6, qIR-9), one for germination rate (qGR-4), two for germination index (qGI-4-1, qGI-4-2) and two for root length (qRL-4-1, qRL-4-2). There were no detected QTLs controlling shoot length and seed vigor. The phenotypic variance explained by a single QTL ranged from 9.1% to 37.0%, and two major QTLs, qIR-6 and qGI-4-2, accounted for over 30% of the phenotypic variance. The expressions of QTLs were developmentally regulated and growth stage-specific. Most of the QTLs observed here were located in the regions similar to the QTLs for rice cold tolerance reported previously, indicating that these QTLs were reliable. However, qRL-4-2 is not reported before.

Key words: rice, cold stress, germination ability, quantitative trait locus

WANG Zhou-fei, WANG Jian-fei, WANG Fu-hua, BAO Yong-mei, WU Yun-yu, ZHANG Hong-sheng. Genetic Control of Germination Ability under Cold Stress in Rice[J]. RICE SCIENCE, 2009, 16(3): 173-180 .

References

1 Nakagahra M, Okuno K, Vaughan D. Rice genetic resources: History, conservation, investigative characterization and use in Japan. Plant Mol Biol, 1997, 35: 69–77.
2 Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin S, Yano M. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet, 2004, 108: 794–799.
3 Han L Z, Kou H J, Piao Z Z. Status and prospects of genetic and QTLs analysis for cold tolerance in rice. Chinese J Rice Sci, 2002, 16(2): 193–198. (in Chinese with English abstract)
4 Lou Q J, Chen L, Sun Z X, Xing Y Z, Li J, Xu X Y, Mei H W, Luo L J. A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica, 2007, 158: 87–94.
5 Kuroki M, Saito K, Matsuba S, Yokogami N, Shimizu H, Ando I, Sato Y. A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8. Theor Appl Genet, 2007, 115: 593–600.
6 Dai L, Lin X, Ye C, Ise K, Saito K, Kato A, Xu F Yu T, Zhang D. Identification of quantitative trait loci controlling cold tolerance at the reproductive stage in Yunnan landrace of rice, Kunmingxiaobaigu. Breeding Sci, 2004, 54: 253–258.
7 Miura K, Lin S Y, Yano M, Nagamine T. Mapping quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Breeding Sci, 2001, 51: 293–299.
8 Chen L, Lou Q J, Sun Z X, Xing Y Z, Yu X Q, Luo L J. QTL mapping of low temperature on germination rate of rice. Rice Sci, 2006, 13(2): 93–98.
9 Ji S L, Jiang L, Wang Y H, Liu S J, Liu X, Zhai H Q, Wan J M. Detection and analysis of QTL for germination rate at low temperature in rice (Oryza sativa L.) using backcross inbred lines. J Nanjing Agric Univ, 2007, 30: 1–6. (in Chinese with English abstract)
10 Yan C J, Li X, Cheng Z K, Yu H X, Gu M H, Zhu L H. Identification of QTL for cold tolerance at early seeding stage in rice (Oryza sativa L.) via RFLP markers. Chinese J Rice Sci, 1999, 13(2): 134–138. (in Chinese with English abstract)
11 Zhang Z H, Li S, Wei L, Wei C, Zhu Y G. A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci, 2005, 168: 527–534.
12 Qiao Y L, Han L Z, An Y P, Zhang Y Y, Cao G L, Kou H J. Molecular mapping of QTLs for cold tolerance at the bud bursting period in rice. Sci Agric Sin, 2005, 38: 217–221. (in Chinese with English abstract)
13 Zhang L X, Wang S F, Jiang L, Wan J M. QTL analysis of cold tolerance at the bud bursting period in rice (Oryza sativa L. ) by using recombinant inbred lines. J Nanjing Agric Univ, 2007, 30: 1–5. (in Chinese with English abstract)
14 Jiang L, Liu S J, Hou M Y, Tang J Y, Chen L M, Zhai H Q, Wan J M. Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crop Res, 2006, 98: 68–75.
15 Miura K, Lin S Y, Araki H, Nagamine T, Kuroki M, Shimizu H, Ando I, Yano M. Genetical studies on germination of seed and seedling establishment for breeding of improved rice varieties suitable for direct seeding culture. JARQ, 2004, 38: 1–5.
16 Hu J, Cai S Q. Physiological and biochemical changes of supersweet corn seeds imbibed at low temperature. Acta Agron Sin, 2001, 27: 371–376. (in Chinese with English abstract)
17 Fujino K. A major gene for low temperature germinability in rice (Oryza sativa L.). Euphytica, 2004, 136: 63–68.
18 Dellaporta S L, Wood T, Hicks T B. A plant DNA mini preparation. Version II. Plant Mol Biol Rep, 1983, 1: 19–21.
19 Temnykh S, Park W D, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho Y G, Ishii T, McCouch S R. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet, 2000, 100: 697–712.
20 McCouch S R, Teytelman L, Xu Y B, Lobos K B, Clare K, Walton M, Fu B Y, Maghirang R, Li Z K, Xing Y Z, Zhang Q F, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 2002, 6: 199–207.
21 Chen X, Temnykh S, Xu Y, Cho Y G, McCouch S R. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet, 1997, 95: 553–567.
22 Sanguinetti C J, Neto E D, Simpson A J. Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques, 1994, 17: 914–921.
23 Lander E S, Green P, Abrahamson J, Barlow A, Daly M J, Lincoln S E, Newburg L. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1987, 1: 174–181.
24 Qi B, Korir P, Zhao T J, Yu D Y, Chen S Y, Gai J Y. Mapping quantitative trait loci associated with aluminum toxin tolerance in NJRIKY recombinant inbred line population of soybean (Glycine max). J Integr Plant Biol, 2008, 50(9): 1089–1095.
25 McCouch S R, Cho Y G, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T. Report on QTL nomenclature. Rice Genet Newsl, 1997, 14: 11–13.
26 Ye C C, Kato A, Saito K, Ise K, Dai L Y, Yang Q Z. QTL analysis of cold tolerance at the booting stage in Yunnan rice variety Chongtui. Chinese J Rice Sci, 2001, 15(1): 13–16. (in Chinese with English abstract)
27 Andaya V C, Mackill D J. QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica×indica cross. Theor Appl Genet, 2003, 106: 1084– 1090.
28 Zhan Q C, Zeng S Z, Xiong F X, Sado K, Kato A. Molecular mapping of QTLs for seedling cold tolerance in rice. J Hunan Agric Univ: Nat Sci, 2003, 29: 7–11. (in Chinese with English abstract)
29 Andaya V C, Tai T H. Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Breeding, 2007, 20: 349–358.
30 Xu L M, Zhou L, Zeng Y W, Wang F M, Zhang H L, Shen S Q, Li Z C. Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice near- isogenic line. Plant Sci, 2008, 174: 340–347.
31 Hou M Y, Wang C M, Jiang L, Wan J M, Hideshi Y, Atsushi Y. Inheritance and QTL mapping of low temperature germinability in rice (Oryza sativa L.). Acta Genet Sin, 2004, 31: 701–706.
32 Chen W, Li W. Mapping of QTL conferring cold tolerance at early seedling stage of rice by molecular markers. J Wuhan Bot Res, 2005, 23: 116–120. (in Chinese with English abstract)
33 Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M. Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc Natl Acad Sci USA, 2008, 105: 12623–12628.
34 Cui K H, Peng S B, Xing Y Z, Xu C G, Yu S B, Zhang Q. Molecular dissection of seedling-vigor and associated physiological traits in rice. Theor Appl Genet, 2002, 105: 745–753.
35 Lin H X, Zhu M Z, Yano M J, Gao P, Liang Z W, Su W A, Hu X H, Ren Z H, Chao D Y. QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet, 2004, 108: 253–260.

[1]	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-.
[2]	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-.
[3]	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-.
[4]	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-.
[5]	Sundus ZAFAR, XU Jianlong. Recent Advances to Enhance Nutritional Quality of Rice [J]. Rice Science, 2023, 30(6): 4-.
[6]	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-.
[7]	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-.
[8]	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-.
[9]	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-.
[10]	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-.
[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]	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.
[14]	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.
[15]	Lu Xuedan, Li Fan, Xiao Yunhua, Wang Feng, Zhang Guilian, Deng Huabing, Tang Wenbang. Grain Shape Genes: Shaping the Future of Rice Breeding [J]. Rice Science, 2023, 30(5): 379-404.