Molecular Breeding

, 39:123 | Cite as

Identification of QTL for seed dormancy from weedy rice and its application to elite rice cultivar ‘Ninggeng 4’

  • Thanhliem Nguyen
  • Chunlei Zhou
  • Tianyu Zhang
  • Jiangfeng Yu
  • Rong Miao
  • Yunshuai Huang
  • Xingjie Zhu
  • Weihan Song
  • Xi Liu
  • Changling Mou
  • Jie Lan
  • Shijia Liu
  • Yunlu Tian
  • Zhigang Zhao
  • Ling JiangEmail author
  • Jianmin WanEmail author


Seed dormancy is a complex agronomic trait that is not only controlled by genetics but also influenced by environmental conditions. Novel seed dormancy genes could improve rice yield and quality by preventing losses due to pre-harvest sprouting (PHS). Although there have been many reported studies related to seed dormancy in rice, little is known about seed dormancy genes derived from weedy rice. We used a weedy rice line ‘Ludao’ (with strong seed dormancy) as the donor parent and elite japonica variety ‘Ninggeng 4’ (with weak seed dormancy) as a recurrent parent for backcrossing. A BC4F2 population was developed for gene mapping, and germination percentage was used as the phenotype. Four quantitative trait loci (QTLs), qSdr7-1, qSdr7-2, qSdr7-3, and qSdr7-4, were identified on chromosome 7. Seed dormancy alleles of the QTLs were all derived from ‘Ludao.’ Located between markers RM21103 and RM5672, qSdr7-2 had the largest effect and explained 27.2% of the phenotypic variation with a LOD score of 14.5. Based on the closest linked marker for locus qSdr7-2, we developed near-isogenic lines (NILs) with the qSdr7-2 allele from ‘Ludao’ in ‘Ninggeng 4’ background. The qSdr7-2-NILs, which have strong seed dormancy and elite agronomic traits, should be useful as a parent in breeding for PHS resistance.


Fine mapping Near-isogenic line Pre-harvest sprouting QTL Oryza sativa 



pre-harvest sprouting


analysis of variance


logarithm of odds


near-isogenic line


quantitative trait locus


marker-assisted backcrossing


advanced backcross


polymerase chain reaction


phenotypic variance explained


single nucleotide polymorphism


simple sequence repeat




basic helix-loop-helix


National Center for Biotechnology Information


Rice Annotation Project Database



We gratefully acknowledge support from the Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-Lower Yangtze River, Ministry of Agriculture, P. R. China, and Jiangsu Collaborative Innovation Center for Modern Crop Production.

Authors’ contributions

NTL, JL, and WJM conceived and designed the experiments. NTL, ZJL, ZTY, YJF, MR, HYS, ZXJ, SWH, LX, MCL, LJ, and ZZG performed the experiments and analyzed the data. LSJ and TYL were responsible for material plant and field management. NTL wrote the manuscript. JL and WJM revised the manuscript. All authors read and approved the manuscript.


This research was supported by the grants from the National Transformation Science and Technology Program (2016ZX08001006), the National Key Research and Development Program of China (2016YFD0100101-08), the National Natural Science Foundation of China (31871712), the Jiangsu Science and Technology Development Program (BE2018388), and the Project for Major New Varieties of Agriculture in Jiangsu Province (PZCZ201701).

Compliance with ethical standards

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Supplementary material

11032_2019_1031_MOESM1_ESM.docx (16 kb)
Table S1 (DOCX 15 kb)
11032_2019_1031_MOESM2_ESM.docx (583 kb)
Figure S1 (DOCX 583 kb)
11032_2019_1031_MOESM3_ESM.docx (236 kb)
Figure S2 (DOCX 235 kb)


  1. Bewley JD, Bradford KJ, Hilhorst HWM, Nonogaki H (2013) Seeds: physiology of development, germination and dormancy. Springer, New YorkCrossRefGoogle Scholar
  2. Black M, Bewley JD, Halmer P (2006) Preharvest sprouting – economic importance. In The Encyclopedia of Seeds Science, Technology and Uses. CABI, Wallingford, Oxfordshire, UK, pp 528Google Scholar
  3. Cai HW, Morishima H (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet 100:840–846CrossRefGoogle Scholar
  4. Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228CrossRefGoogle Scholar
  5. Chang TT (1976) The origin, evolution, cultivation, disseminationand diversification of Asian and African rice. Euphytica 25:425–441CrossRefGoogle Scholar
  6. Clarke JD (2009) Cetyltrimethyl ammonium bromide (CTAB) DNA miniprep for plant DNA isolation. Cold Spring Harb Protoc 2009:pdb.prot5177PubMedGoogle Scholar
  7. Depauw RM, Mccaig TN (1991) Components of variation, heritabilities and correlations for indexes of sprouting tolerance and seed dormancy in Triticum spp. Euphytica 52:221–229CrossRefGoogle Scholar
  8. Dong Y, Tsozuki E, Kamiunten H, Terao H, Lin D, Matsuo M, Zheng Y (2003) Identification of quantitative trait loci associated with pre-harvest sprouting resistance in rice (Oryza sativa L.). Field Crops Res 81:133–139CrossRefGoogle Scholar
  9. Furukawa T, Maekawa M, Oki T, Suda I, Iida S, Shimada S, Takamure I, Kadowaki K (2007) The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant J 49:91–102CrossRefGoogle Scholar
  10. Gao FY, Ren GJ, Liu XJ, Sun SX, Li HJ, Gao YM, Luo H, Yan WG, Zhang YZ (2008) QTL analysis for resistance to pre-harvest sprouting in rice (Oryza sativa). Plant Breed 127:268–273CrossRefGoogle Scholar
  11. Groos CG, Gay MR, Perretant L, Gervais M, Bernard F, Dedryver CG (2002) Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white × red grain bread-wheat cross. Theor Appl Genet 104:39–47CrossRefGoogle Scholar
  12. Gu XY, Chen ZX, Foley ME (2003) Inheritance of seed dormancy in weedy rice. Crop Sci 43:835–843CrossRefGoogle Scholar
  13. Gu XY, Kianian SF, Foley ME (2004) Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics 166:1503–1516CrossRefGoogle Scholar
  14. Gu XY, Kianian SF, Foley ME (2005a) Seed dormancy imposed by covering tissues interrelates to shattering and seed morphological characteristics in weedy rice. Crop Sci 45:948–955CrossRefGoogle Scholar
  15. Gu XY, Kianian SF, Hareland GA, Hoffer BL, Foley ME (2005b) Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet 110:1108–1118CrossRefGoogle Scholar
  16. Gu XY, Liu T, Feng J, Suttle JC, Gibbons J (2010) The qSD12 underlying gene promotes abscisic acid accumulation in early developing seeds to induce primary dormancy in rice. Plant Mol Biol 73:97–104CrossRefGoogle Scholar
  17. Gu XY, Foley ME, Horvath DP, Anderson JV, Feng J, Zhang L, Mowry CR, Ye H, Suttle JC, Kadowaki K, Chen Z (2011) Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates ABA and flavonoid synthesis in weedy red rice. Genetics 189:1515–1524CrossRefGoogle Scholar
  18. Guo L, Zhu L, Xu Y, Zeng D, Wu P, Qian Q (2004) QTL analysis of seed dormancy in rice (Oryza sativa L.). Euphytica 140:155–162CrossRefGoogle Scholar
  19. Hu WM, Ma HS, Fan LJ, Ruan SL (2003) Characteristics of pre-harvest sprouting in sterile lines in hybrid rice seeds production. Acta Agron Sin 29:441–446 (in Chinese)Google Scholar
  20. Jiang H, Wu JL, Wang GL (1985) Studies on Ludao of Lianyungang. Crop Genetic Res 2:4–7Google Scholar
  21. Jiang L, Cao YJ, Wang CM, Zhai HQ, Wan JM, Yoshimura A (2003) Detection and analysis of QTL for seed dormancy in rice (Oryza sativa L.) using RIL and CSSL populations. Acta Genet Sin 30:453–458PubMedGoogle Scholar
  22. Jing W, Jiang L, Zhang WW, Zhai HQ, Wan JM (2008) Mapping QTL for seed dormancy in weedy rice. Acta Agron Sin 34:737–742Google Scholar
  23. Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Curr Opin Plant Biol 5:33–36CrossRefGoogle Scholar
  24. Lee SJ, Oh CS, Suh JP, McCouch SR, Ahn SN (2005) Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa × O. rufipogon BC1F7 population. Plant Breed 124:209–219CrossRefGoogle Scholar
  25. Li CB, Zhou AL, Sang T (2006) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–193CrossRefGoogle Scholar
  26. Lin S, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theor Appl Genet 96:997–1003CrossRefGoogle Scholar
  27. Meng L, Li HH, Zhang LY, Wang JK (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:269–283CrossRefGoogle Scholar
  28. Mispan MS, Zhang L, Feng J, Gu X-Y (2013) Quantitative trait locus and haplotype analyses of wild and crop-mimic traits in U.S. weedy rice. G3 3:1049–1059CrossRefGoogle Scholar
  29. Mortimer M, Pandey S, Piggin C (2000) Weedy rice: approaches to ecological appraisal and implications for research priorities. In: Baki BB, Chin DV, Mortimer M (eds) Proceedings of wild and weedy rice in rice ecosystems in Asia–a review. Limited Proceedings No. 2. International Rice Research Institute, Los Banos, pp 97–105Google Scholar
  30. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefGoogle Scholar
  31. Ogbonnaya FCM, Imtiaz G, Ye PR, Hearnden E, Hernandez RF, Eastwood M, Van Ginkel S, Shorter C, Winchester JM (2008) Genetic and QTL analyses of seed dormancy and pre-harvest sprouting resistance in the wheat germplasm CN10955. Theor Appl Genet 116:891–902CrossRefGoogle Scholar
  32. Oka HI (1958) Intervarietal variation and classification of cultivated rice. Indian J Genet Plant Breed 18:79–89Google Scholar
  33. Rodríguez M, Barrero JM, Corbineau F, Gubler F, Benech-Arnold RL (2015) Dormancy in cereals (not too much, not so little): about the mechanisms behind this trait. Seed Sci Res 25:99–119CrossRefGoogle Scholar
  34. Sakamoto T, Sakakibara H, Kojima M, Yamamoto Y, Nagasaki H, Inukai Y, Sato Y, Matsuoka M (2006) Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice. Plant Physiol 142:54–62CrossRefGoogle Scholar
  35. Sanguinetti CJ, Dias EN, Simpson AJ (1994) Rapid silver staining and recovery of PCR products separated on poly-acrylamide gels. Biotechniques 17:914–992PubMedGoogle Scholar
  36. Subudhi PK, Parco A, Singh PK, DeLeon T, Karan R, Biradar H, Cohn MA, Brar DS, Sasaki T (2012) Genetic architecture of seed dormancy in U.S. weedy rice in different genetics backgrounds. Crop Sci 52:2564–2575CrossRefGoogle Scholar
  37. Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci U S A 107:5792–5797CrossRefGoogle Scholar
  38. Sun J, Qian Q, Ma DR, Xu ZJ, Liu D, Du HB, Chen WF (2013) Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. New Phytol 197:290–299CrossRefGoogle Scholar
  39. Sweeney MT, Thomson MJ, Pfeil BE, McCouch SR (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18:283–294CrossRefGoogle Scholar
  40. Takeuchi Y, Lin SY, Sasaki T, Yano M (2003) Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice. Theor Appl Genet 101:1174–1180CrossRefGoogle Scholar
  41. Tang LH, Morishima H (1988) Characteristics of weed rice strains. Rice Genet Newsl 5:70–72Google Scholar
  42. Veasey EA, Karasawa MG, Santos PP, Rosa MS, Mamani E, Oliveira GC (2004) Variation in the loss of seed dormancy during after-ripening of wild and cultivated rice species. Ann Bot (Lond) 94:875–882CrossRefGoogle Scholar
  43. Wan JM, Nakazaki T, Kawaura K, Ikehashi H (1997) Identification of marker loci for seed dormancy in rice (Oryza sativa L.). Crop Sci 37:1759–1763CrossRefGoogle Scholar
  44. Wan JM, Cao YJ, Wang CM, Ikehashi H (2005) Quantitative trait loci associated with seed dormancy in rice. Crop Sci 45:712–716CrossRefGoogle Scholar
  45. Wan JM, Jiang L, Tang JY, Wang CM, Hou MY, Jing W, Zhang LX (2006) Genetic dissection of the seed dormancy trait in cultivated rice (Oryza sativa L.). Plant Sci 170:786–792CrossRefGoogle Scholar
  46. Xie K, Jiang L, Lu B, Yang C, Li L, Liu X, Zhang L, Zhao Z, Wan J (2010) Identification of QTLs for seed dormancy in rice (Oryza sativa L.). Plant Breed 130:328–332CrossRefGoogle Scholar
  47. Ye H, Foley ME, Gu X-Y (2010) New seed dormancy loci detected from weedy rice-derived advanced populations with major QTL alleles removed from the background. Plant Sci 179:612–619CrossRefGoogle Scholar
  48. Ye H, Beighley DH, Feng J, Gu X-Y (2013) Genetic and physiological characterization of two clusters of quantitative trait loci associated with seed dormancy and plant height in rice. G3 3:323–331CrossRefGoogle Scholar
  49. Ye H, Feng J, Zhang L, Zhang J, Mispan MS, Cao Z, Beighley DH, Yang J, Gu X-Y (2015) Map-based cloning of seed dormancy1-2 identified a gibberellin synthesis gene regulating the development of endosperm-imposed dormancy in rice. Plant Physiol 169:2152–2165PubMedPubMedCentralGoogle Scholar
  50. Zhang L, Lou J, Foley ME, Gu X-Y (2017) Comparative mapping of seed dormancy loci between tropical and temperate ecotypes of weedy rice (Oryza sativa L.). G3 7:2605–2614CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Thanhliem Nguyen
    • 1
    • 2
  • Chunlei Zhou
    • 1
  • Tianyu Zhang
    • 1
  • Jiangfeng Yu
    • 1
  • Rong Miao
    • 1
  • Yunshuai Huang
    • 1
  • Xingjie Zhu
    • 1
  • Weihan Song
    • 1
  • Xi Liu
    • 1
  • Changling Mou
    • 1
  • Jie Lan
    • 1
  • Shijia Liu
    • 1
  • Yunlu Tian
    • 1
  • Zhigang Zhao
    • 1
  • Ling Jiang
    • 1
    Email author
  • Jianmin Wan
    • 1
    • 3
    Email author
  1. 1.State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
  2. 2.Department of Biology and Agricultural EngineeringQuy Nhon UniversityQuy NhonVietnam
  3. 3.National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina

Personalised recommendations