Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2018, Vol. 44 ›› Issue (01): 15-23.doi: 10.3724/SP.J.1006.2018.00015


Mapping of QTLs for Seed Dormancy in Oryza Rufipogon Griff.

SUN Ai-Ling1,WU Hong-Ming1,CHEN Gao-Ming1,ZHANG Tian-Yu1,CAO Peng-Hui1,LIU Shi-Jia1,JIANG Ling1,*,WAN Jian-Min1,2   

  1. 1State Key Loboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture / Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; 2National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2017-04-06 Revised:2017-09-10 Online:2018-01-12 Published:2017-10-31
  • Supported by:

    This study was supported by the National Key Research and Development Program of China (2016YFD0100101-08), the Agricultural Science and Technology Independent Innovation Fund Project of Jiangsu Province (CX[16]1029), Science and Technology Major Project of Anhui Province (16030701068), and Jiangsu Collaborative Innovation Center for Modern Crop Production.


Seed dormancy of rice is an important agronomic trait related to rice quality and quantity. Studies on genetics and molecular mechanisms of rice seed dormancy are of great significance in breeding fine rice varieties with moderate dormancy. In this research, a set of chromosome segment substitution lines (CSSLs), derived from an indica rice variety 9311 as the recurrent parent and the Oryza rufipogon Griff. as the donor parent, were used to detect the QTLs for dormancy of seeds at different storage dates after harvest. A total of 14 QTLs were detected on chromosomes 3, 4, 5, 6, 7, 10, 11, and 12. The lines with significantly stronger dormancy than the background parent 9311 were selected, showing the more dormancy loci in the lines the more strong dormancy. The F2 population of the cross between Q14 and 9311 was used to verify the QTLs for seed dormancy. A significant dormancy locus qSD-7-2 was mapped on chromosome 7 between the markers RM180 and RM21323, its LOD was 18.49 and the phenotypic variation rate was 33.53%. On this major stable inherited QTL, the allele gene from Oryza rufipogon Griff. significantly increased the dormancy of seeds. These results are available for map-based cloning of major QTLs for seed dormancy, and provide the breeding materials for cultivating appropriate dormant rice varieties.

Key words: Oryza rufipogon Griff., seed dormancy, CSSL, QTL

[1] Bewley J D. Seed germination and dormancy. Plant Cell, 1997, 9: 1055–1066 [2] Dong Y J, Tsuzuki E, Kamiunten H, Terao H, Lin D Z, Matsuo M, Zheng Y F. Identification of quantitative trait loci associated with pre-harvest sprouting resistance in rice (Oryza sativa L.). Field Crops Res, 2003, 81: 133–139 [3] 卢丙越. 水稻品种强休眠性的定位及遗传解析. 南京农业大学博士学位论文, 江苏南京, 2011 Lu B Y. QTL Mapping and genetic dissection of strong seed dormancy in N22 (Oryza sativa L.). PhD Dissertation of Nanjing Agricultural University, Nanjing, China, 2011 (in Chinese with English abstract) [4] Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci USA, 2010, 107: 5792–5797 [5] Takeuchi Y, Lin S Y, Sasaki T, Yano M. Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice. Theor Appl Genet, 2003, 107: 1174–1180 [6] Gu X Y, Kianian S F, Hareland G A, Hoffer B L, Foley M E. Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet, 2005, 110: 1108–1118 [7] Gu X Y, Liu T L, Feng J H, Suttle J C, Gibbons J. The qSD12 underlying gene promotes abscisic acid accumulation in early developing seeds to induce primary dormancy in rice. Plant Mol Biol, 2010, 73: 97–104 [8] Lu B Y, Xie K, Yang C Y, Wang S F, Liu X, Zhang L, Jiang L, Wan J M. Mapping two major effect grain dormancy QTL in rice. Mol Breed, 2011, 28: 453–462 [9] 罗正良. 水稻抗穗发芽主效QTL qPSR8的精细定位及候选基因分析. 四川农业大学硕士学位论文, 四川雅安, 2012 Luo Z L. Fine mapping and candidate gene analysis of qPSR8, a major QTL for pre-harvest sprouting resistance in rice. MS Thesis of Sichuan Agricultural University, Ya’an, China, 2012 (in Chinese with English abstract) [10] 钟代彬, 罗利军, 应存山. 野生稻有利基因转移研究进展. 中国水稻科学, 2000, 14: 103–106 Zhong D B, Luo L J, Ying C S. Advances on transferring elite gene from wild rice species into cultivated rice. Chin J Rice Sci, 2000, 14: 103–106 (in Chinese with English abstract) [11] Wan J M, Cao Y J, Wang C M, Ikehashi H. Quantitative trait loci associated with seed dormancy in rice. Crop Sci, 2005, 45: 712–716 [12] Porebski S, Bailey L G, Baum B R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep, 1997, 15: 8–15 [13] Sanguinetti C J, Dias N E, Simpson A J. RAPD silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques, 1994, 17: 914–918 [14] Meng L, Li H H, Zhng L Y, Wang J K. QTL IciMapping Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J, 2015, 3: 269–283 [15] McCouch S R, Cho Y G, Yno M, Paul E, Blinstrub M, Morishima H, Kinoshita T. Report on QTL nomenclature. Rice Genet Newsl, 1997, 14: 11-13 [16] Tanksley S D, Grandillo S, Fulton T M, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T. Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet, 1996, 92: 213–224 [17] Cai H W, Morishima H. Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet, 2000, 100: 840–846 [18] Miura K, Lin S, Yano M, Nagamine T. Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet, 2002, 104: 981–986 [19] Wang L, Cheng J, Lai Y Y, Du W L, Huang X, Wang Z F, Zhang H S. Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice. Planta, 2014, 239: 411–420 [20] Li W, Xu L, Bai X F, Xing Y Z. Quantitative trait loci for seed dormancy in rice. Euphytica, 2011, 178: 427–435 [21] Marzougui S, Sugimoto K, Yamanouchi U, Shimono M, Hoshino T, Hori K, Kobayashi M, Ishiyama K, Yano M. Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice. Theor Appl Genet, 2012, 124: 893–902 [22] Gu X Y, Kianian S F, Foley M E. Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics, 2004, 166: 1503–1516 [23] Sasaki K, Kazama Y, Chae Y, Sato T. Confirmation of novel quantitative trait loci for seed dormancy at different ripening stages in rice. Rice Sci, 2013, 20: 207–212 [24] Rathi S, Baruah A R, Chowdhury R K, Sarma R N. QTL analysis of seed dormancy in indigenous rice of Assam, India. Cereal Res Commun, 2011, 39: 137–146

[1] HU Wen-Jing, LI Dong-Sheng, YI Xin, ZHANG Chun-Mei, ZHANG Yong. Molecular mapping and validation of quantitative trait loci for spike-related traits and plant height in wheat [J]. Acta Agronomica Sinica, 2022, 48(6): 1346-1356.
[2] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[3] HUANG Li, CHEN Yu-Ning, LUO Huai-Yong, ZHOU Xiao-Jing, LIU Nian, CHEN Wei-Gang, LEI Yong, LIAO Bo-Shou, JIANG Hui-Fang. Advances of QTL mapping for seed size related traits in peanut [J]. Acta Agronomica Sinica, 2022, 48(2): 280-291.
[4] ZHANG Yan-Bo, WANG Yuan, FENG Gan-Yu, DUAN Hui-Rong, LIU Hai-Ying. QTLs analysis of oil and three main fatty acid contents in cottonseeds [J]. Acta Agronomica Sinica, 2022, 48(2): 380-395.
[5] ZHANG Bo, PEI Rui-Qing, YANG Wei-Feng, ZHU Hai-Tao, LIU Gui-Fu, ZHANG Gui-Quan, WANG Shao-Kui. Mapping and identification QTLs controlling grain size in rice (Oryza sativa L.) by using single segment substitution lines derived from IAPAR9 [J]. Acta Agronomica Sinica, 2021, 47(8): 1472-1480.
[6] LUO Lan, LEI Li-Xia, LIU Jin, ZHANG Rui-Hua, JIN Gui-Xiu, CUI Di, LI Mao-Mao, MA Xiao-Ding, ZHAO Zheng-Wu, HAN Long-Zhi. Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.) [J]. Acta Agronomica Sinica, 2021, 47(7): 1391-1401.
[7] HAN Yu-Zhou, ZHANG Yong, YANG Yang, GU Zheng-Zhong, WU Ke, XIE Quan, KONG Zhong-Xin, JIA Hai-Yan, MA Zheng-Qiang. Effect evaluation of QTL Qph.nau-5B controlling plant height in wheat [J]. Acta Agronomica Sinica, 2021, 47(6): 1188-1196.
[8] WANG Wu-Bin, TONG Fei, KHAN Mueen-Alam, ZHANG Ya-Xuan, HE Jian-Bo, HAO Xiao-Shuai, XING Guang-Nan, ZHAO Tuan-Jie, GAI Jun-Yi. Detecting QTL system of root hydraulic stress tolerance index at seedling stage in soybean [J]. Acta Agronomica Sinica, 2021, 47(5): 847-859.
[9] ZHOU Xin-Tong, GUO Qing-Qing, CHEN Xue, LI Jia-Na, WANG Rui. Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of pink petal trait in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 587-598.
[10] LI Shu-Yu, HUANG Yang, XIONG Jie, DING Ge, CHEN Lun-Lin, SONG Lai-Qiang. QTL mapping and candidate genes screening of earliness traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 626-637.
[11] SHEN Wen-Qiang, ZHAO Bing-Bing, YU Guo-Ling, LI Feng-Fei, ZHU Xiao-Yan, MA Fu-Ying, LI Yun-Feng, HE Guang-Hua, ZHAO Fang-Ming. Identification of an excellent rice chromosome segment substitution line Z746 and QTL mapping and verification of important agronomic traits [J]. Acta Agronomica Sinica, 2021, 47(3): 451-461.
[12] MENG Jiang-Yu, LIANG Guang-Wei, HE Ya-Jun, QIAN Wei. QTL mapping of salt and drought tolerance related traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(3): 462-471.
[13] WANG Rui-Li, WANG Liu-Yan, LEI Wei, WU Jia-Yi, SHI Hong-Song, LI Chen-Yang, TANG Zhang-Lin, LI Jia-Na, ZHOU Qing-Yuan, CUI Cui. Screening candidate genes related to aluminum toxicity stress at germination stage via RNA-seq and QTL mapping in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(12): 2407-2422.
[14] LYU Guo-Feng, BIE Tong-De, WANG Hui, ZHAO Ren-Hui, FAN Jin-Ping, ZHANG Bo-Qiao, WU Su-Lan, WANG Ling, WANG Zun-Jie, GAO De-Rong. Evaluation and molecular detection of three major diseases resistance of new bred wheat varieties (lines) from the lower reaches of the Yangtze River [J]. Acta Agronomica Sinica, 2021, 47(12): 2335-2347.
[15] MA Meng, YAN Hui, GAO Run-Fei, KOU Meng, TANG Wei, WANG Xin, ZHANG Yun-Gang, LI Qiang. Construction linkage maps and identification of quantitative trait loci associated with important agronomic traits in purple-fleshed sweetpotato [J]. Acta Agronomica Sinica, 2021, 47(11): 2147-2162.
Full text



No Suggested Reading articles found!