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Molecular Breeding

, Volume 28, Issue 4, pp 453–462 | Cite as

Mapping two major effect grain dormancy QTL in rice

  • Bingyue Lu
  • Kun Xie
  • Chunyan Yang
  • Songfeng Wang
  • Xi Liu
  • Long Zhang
  • Ling JiangEmail author
  • Jianmin WanEmail author
Article

Abstract

The intrachromosomal positions of the two grain dormancy quantitative trait loci (QTL) qSdn-1 (chromosome 1) and qSdn-5 (chromosome 5) were obtained from the segregation analysis of the advanced backcross populations derived from the cross between rice (Oryza sativa L.) cultivars N22 (indica) and Nanjing35 (japonica). Marker-assisted selection (MAS) was applied to select derivatives carrying one or both of qSdn-1 and qSdn-5 in a genetic background which was nearly isogenic to Nanjing35. An analysis of dormancy in the BC4F2 population allowed qSdn-1 to be located between the simple sequence repeat (SSR) markers RM11669 and RM1216; the QTL explained 24.58% of the overall phenotypic variation and the most closely linked marker was RM11694. qSdn-5 was mapped between RM480 and RM3664, and explained 17.58% of the overall phenotypic variation. The SSR locus RM19080 mapped within 0.4 cM of qSdn-5. No epistasis was observed between qSdn-1 and qSdn-5. The mean germination rates of lines containing qSdn-1, qSdn-5 and both qSdn-1 and qSdn-5 were 7.9, 11.1 and 6.1%, respectively, whereas that of the check line lacking both QTL was 86.3%. The SSR loci linked most tightly to qSdn-1 and qSdn-5 are suitable for MAS for reduced pre-harvest sprouting in rice. The dormancy of both qSdn-1 and qSdn-5 could be readily broken by a 7-day post-harvest treatment at 50°C.

Keywords

Dormancy Advanced backcross population Epistatic interaction Dry heat treatment Rice (Oryza sativa L.) 

Abbreviations

AB

Advanced backcross

Chr

Chromosome

CK

Check

NIL

Near-isogenic line

PCR

Polymerase chain reaction

PHS

Pre-harvest sprouting

qSdn-*

Quantitative trait loci of seed dormancy in N22

qSdNj-*

Quantitative trait loci of seed dormancy in Nanjing35

QTL

Quantitative trait loci

SSR

Simple sequence repeat

Notes

Acknowledgments

This research was supported by grants from the National Natural Science Foundation of China (No. 30471120, 30671246), 863 Program (projects 2009AA101101) of China, the Jiangsu Cultivar Development Program (projects BE2009301-3 and BE2008352), and the 111 Project (B08025).

Supplementary material

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References

  1. Anderson JA, Sorrells ME, Tanksley SD (1993) RFLP analysis of genomic regions associated with resistance to pre-harvest sprouting in wheat. Crop Sci 33:453–459CrossRefGoogle Scholar
  2. Bernacchi D, Beck Bunn T, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley S (1998) Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum. Theor Appl Genet 97:381–397CrossRefGoogle 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. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genomewide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567CrossRefGoogle Scholar
  5. Chen CX, Cai SB, Bai GH (2008) A major QTL controlling seed dormancy and pre-harvest sprouting resistance on chromosome 4A in a Chinese wheat landrace. Mol Breed 21:351–358CrossRefGoogle Scholar
  6. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedGoogle Scholar
  7. Cui KH, Peng SB, Xing YZ, Xu CG, Yu SB, Zhang Q (2002) Molecular dissection of seedling-vigor and associated physiological traits in rice. Theor Appl Genet 105:745–753PubMedCrossRefGoogle Scholar
  8. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21CrossRefGoogle Scholar
  9. Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG31, controlling low-temperature germinability in rice. Proc Natl Acad Sci USA 105:12623–12628PubMedCrossRefGoogle Scholar
  10. Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894CrossRefGoogle Scholar
  11. Fulton TM, Grandillo S, Beck-Bunn T, Fridman E, Frampton A, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (2000) Advanced backcross QTL analysis of a Lycopersicon esculentum × Lycopersicon parviflorumcross. Theor Appl Genet 100:1025–1042CrossRefGoogle Scholar
  12. Gao FY, Ren GJ, Lu XJ, Sun SX, Li HJ, Gao YM, Lou H, Yan WG, Zhang YZ (2008) QTL analysis for resistance to preharvest sprouting in rice (Oryza sativa). Plant Breed 127:268–273CrossRefGoogle Scholar
  13. Gu XY, Chen ZX, Foley ME (2003) Inheritance of seed dormancy in weedy rice. Crop Sci 43:835–843CrossRefGoogle Scholar
  14. Gu XY, Kianian SF, Foley ME (2004) Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa L.). Genetics 166:1503–1516PubMedCrossRefGoogle Scholar
  15. Gu XY, Kianian SF, Foley ME (2005) Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice. Genetics 171:695–704PubMedCrossRefGoogle Scholar
  16. Gu XY, Kianian SF, Foley ME (2006) Isolation of three dormancy QTLs as Mendelian factors in rice. Heredity 96:93–99PubMedGoogle Scholar
  17. 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 73:97–104PubMedCrossRefGoogle Scholar
  18. Harlan JR, de Wet JMJ, Price EG (1973) Comparative evolution of cereals. Evolution 27:311–325CrossRefGoogle Scholar
  19. Hori K, Sugimoto K, Nonoue Y, Ono N, Matsubara K, Yamanouchi U, Abe A, Takeuchi Y, Yano M (2010) Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theor Appl Genet 120:1547–1557PubMedCrossRefGoogle Scholar
  20. 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(3):441–446 (in Chinese)Google Scholar
  21. Institute SAS (1988) SAS user guide: statistics. SAS Institute, GaryGoogle Scholar
  22. Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365–1369PubMedCrossRefGoogle Scholar
  23. Jing W, Jiang L, Zhang WW, Zhai HQ, Wan JM (2008) Mapping QTL for seed dormancy in weedy rice. Acta Agron Sin 34(5):737–742Google Scholar
  24. Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Curr Opin Plant Biol 5:33–36PubMedCrossRefGoogle Scholar
  25. Li CD, Ni PX, Francki M, Humter A, Zhang Y, Schibeci D, Li H, Tarr A, Wang J, Cakir M, Yu J, Bellgard M, Lance R, Appels R (2004) Genes controlling seed dormancy and preharvest sprouting in a rice-wheat-barley comparison. Funct Integr Genomics 4:84–93PubMedCrossRefGoogle Scholar
  26. Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER/EXP VER. 3.0: a tutorial and reference manual, 3rd edn. Technical Report, Whitehead Institute for Biomedical Research, CambridgeGoogle Scholar
  27. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new ssr markers for rice (Oryza sativa L.). DNA Res 9:199–207PubMedCrossRefGoogle Scholar
  28. Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H, Guimaraes E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa x Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52CrossRefGoogle Scholar
  29. Osa M, Kato K, Mori M, Shindo C, Torada A, Miura H (2003) Mapping QTLs for seed dormancy and the Vp1 homologue on chromosome 3A in wheat. Theor Appl Genet 106:1491–1496PubMedGoogle Scholar
  30. Ren ZH et al (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146PubMedCrossRefGoogle Scholar
  31. Sanguinetti CJ, Dias NE, Simpson AJG (1994) Rapid silver staining and recover of PCR products separated on polyacrylamide gels. Biotechnology 17:915–919Google Scholar
  32. Seshu DV, Sorrells ME (1986) Genetic studies on seed dormancy in rice. In: Rice genetics. IRRI, Philippines, pp 369–382Google Scholar
  33. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028PubMedCrossRefGoogle Scholar
  34. 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 USA 107(13):5792–5797PubMedCrossRefGoogle Scholar
  35. 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
  36. Tang JY, Jiang L, Wang CM, Liu SJ, Chen LM, Zhai HQ, Atsushi Y, Wan JM (2004) Analysis of QTL for seed dormancy and their response to dry heat treatment in rice (Oryza sativa L.). Sci Agric Sin 37(12):1791–1796 (in Chinese)Google Scholar
  37. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233PubMedCrossRefGoogle Scholar
  38. Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224CrossRefGoogle Scholar
  39. Thomson MJ, Tai TH, McClung AM, Hinga ME, Lobos KB, Xu Y, Martinez C, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components, and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493PubMedCrossRefGoogle Scholar
  40. Ullrich SE, Clancy JA, del Blanco IA, Lee H, Jitkov VA, Han F, Kleinhofs A, Matsui K (2008) Genetic analysis of preharvest sprouting in a six-row barley cross. Mol Breed 21:249–259CrossRefGoogle Scholar
  41. 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
  42. Wan JM, Cao YJ, Wang CM, Ikehashi H (2005) Two stable quantitative trait loci associated with seed dormancy in rice (Oryza sativa L.). Crop Sci 45:712–716CrossRefGoogle Scholar
  43. 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
  44. Wang S, Basten CJ, Zeng ZB (2007) Windows QTL Cartographer 2.5, Department of Statistics, North Carolina State University, Raleigh, NC, (http://statgen.-ncsu.edu/qtlcart/WQTLCart.htm)
  45. Xiao J, Li J, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR (1998) Identification of trait-improving QTL alleles from a wild rice relative, Oryza rufipogon. Genetics 150:899–909PubMedGoogle Scholar
  46. Xu K et al (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708PubMedCrossRefGoogle Scholar
  47. Xue WY, Xing YZ, Weng XY, Zhao Y, Tang WJ, Wang L, Zhou HJ, Yu SB, Xu CG, Li XH, Zhang QF (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767PubMedCrossRefGoogle Scholar
  48. Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Bingyue Lu
    • 1
  • Kun Xie
    • 1
  • Chunyan Yang
    • 1
  • Songfeng Wang
    • 1
  • Xi Liu
    • 1
  • Long Zhang
    • 1
  • Ling Jiang
    • 1
    Email author
  • Jianmin Wan
    • 1
    • 2
    Email author
  1. 1.National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
  2. 2.National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina

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