, Volume 164, Issue 3, pp 699–708 | Cite as

Identification of four genes for stable hybrid sterility and an epistatic QTL from a cross between Oryza sativa and Oryza glaberrima



To further understand the nature of hybrid sterility between Oryza sativa and Oryza glaberrima, quantitative trait loci (QTL) controlling hybrid sterility between the two cultivated rice species were detected in BC1F1 and advanced backcross populations. A genetic map was constructed using the BC1F1 population derived from a cross between WAB450-16, an O. sativa cultivar, and CG14, an O. glaberrima cultivar. Seven main-effect QTLs for pollen and spikelet sterility were detected in the BC1F1. Forty-four sterility NILs (BC6F1) were developed via successive backcrosses using pollen sterility plants as female and WAB450-16 as the recurrent parent. Seven NILs, in which the target QTL regions were heterozygous while the other QTL regions as well as most of the reminder of the genome were homozygous for the WAB450-16 allele, were selected as the QTL identification materials. BC7F1 for the seven NILs showed a continuous variation in pollen and spikelet fertility. The four identified pollen sterility QTLs were located one each on chromosomes 1, 3, 7 and 7. Pollen sterility loci qSS-3 and qSS-7a were on chromosomes 3 and 7, respectively, which coincides with the previously identified S19, and S20, while loci qSS-1 and qSS-7b on chromosomes 1 and 7L appear distinct from all previously reported loci. An epistatic interaction controlling the hybrid sterility was detected between qSS-1 and qSS-7a.


Epistasis Hybrid sterility Near isogenic line (NIL) Oryza sativa O. glaberrima 



This research was funded partially by grants from Ministry of Science and Technology (2006CB708207), and Yunnan Department of Science and Technology (2002C0009Z, 2003RC02, 2004PY01-21, 2006GP09), the People’s Republic of China.


  1. Basten CJ, Weir BS, Zeng ZB (1998) QTL CARTOGRAPHER: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, RaleighGoogle Scholar
  2. Bernardo R (2004) What proportion of declared QTL in plants are false? Theor Appl Genet 109:419–424PubMedCrossRefGoogle Scholar
  3. Carlborg O, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5:618–625PubMedCrossRefGoogle Scholar
  4. Chu YE, Morishima H, Oka HI (1969) Reproductive barriers distributed in cultivated rice species and their wild relatives. Jap J Genet 44:207–223CrossRefGoogle Scholar
  5. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedGoogle Scholar
  6. Doebley J, Stec A, Gustus C (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333–346PubMedGoogle Scholar
  7. Doi K, Taguchi K, Yoshimura A (l998a) A new locus affecting high F1 pollen sterility found in backcross progenies between Japonica rice and African rice. Rice Genet Newsl 15:146–148Google Scholar
  8. Doi K, Yoshimura A, Iwata N (1998b) RFLP mapping and QTL analysis of heading date and pollen sterility using backcross population between Oryza sativa L. and Oryza glaberrima Steud. Breed Sci 48:395–399Google Scholar
  9. Doi K, Taguchi K, Yoshimura A (1999) RFLP mapping of S20 and S21 for F1 pollen semi-sterility found in backcross progeny of Oryza sativa and O. glaberrima. Rice Genet Newsl 16:65–68Google Scholar
  10. Eshed Y, Zamir D (1996) Less-than-additive epistatic interaction of quantitative trait loci in tomato. Genetics 143:1807–1817PubMedGoogle Scholar
  11. Fan CC, Xing YZ, HL, Lu TT, Han B, Xu CG, Li XH, Zhang QF (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171PubMedCrossRefGoogle Scholar
  12. Flint J, Mott R (2001) Finding the molecular basis of quantitative traits: successes and pitfalls. Nat Rev Genet 2:437–445PubMedCrossRefGoogle Scholar
  13. Frary A, Nesbitt TC, Frary A, Grandillo S, Knaap EVD, Cong B, Liu JP, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: A quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88PubMedCrossRefGoogle Scholar
  14. Ghesquiere A, Sequier J, Second G, Lorieux M (1997) First steps towards a rational use of African rice, Oryza glaberrima, in rice breeding through a ‘contig line’ concept. Euphytica 96:31–39CrossRefGoogle Scholar
  15. Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298:2345–2349PubMedCrossRefGoogle Scholar
  16. Hu FY, Xu P, Deng XN, Zhou JW, Li J, Tao DY (2006) Molecular mapping of a pollen killer gene S29(t) in Oryza glaberrima and co-linear analysis with S22 in O. glumaepatula. Euphytica 151:273–278CrossRefGoogle Scholar
  17. Jones MP, Dingkuhn M, Aluko GK, Senmon M (1997) Interspecific Oryza sativa L. × O. glaberrima Steud. progenies in upland rice improvement. Euphytica 92:237–246CrossRefGoogle Scholar
  18. Kitamura E (1962) Genetic studies on sterility observed in hybrids between distantly related varieties of rice, Oryza sativa L. Bull Chugoku Agric Exp Station A8:141–205Google Scholar
  19. Kroymann J, Mitchell-Olds T (2005) Epistasis and balanced polymorphism influencing complex trait variation. Nature 435:95–98PubMedCrossRefGoogle Scholar
  20. Kubo T, Yoshimura A (2005) Epistasis underlying female sterility detected in hybrid breakdown in a Japonica-Indica cross of rice (Oryza sativa L.). Theor Appl Genet 110:346–355PubMedCrossRefGoogle Scholar
  21. Lander E, Green P (1987) Construction of multilocus genetic maps in Humans. Proc Natl Acad Sci USA 84:2363–2367PubMedCrossRefGoogle Scholar
  22. Li ZB (1980) A preliminary discussion about the classification of male sterile lines of rice in China. Acta Agron Sin 6(1):17–26Google Scholar
  23. Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021–1028CrossRefGoogle Scholar
  24. Lincoln S, Daly M, Lander ES (1992) Constructing genetic maps with MAPMAKER/EXP3.0. Whitehead Institute Technical Report (3rd edn)Google Scholar
  25. Liu JP, Eck JV, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shape tomato fruit. Proc Natl Acad Sci USA 99:13302–13306PubMedCrossRefGoogle Scholar
  26. Lorieux M, Ndjiondjop MN, Ghesquière A (2000) A first interspecific Oryza sativa × Oryza glaberrima microsatellite based genetic linkage map. Theor Appl Genet 100:593–601Google Scholar
  27. Mackay TF (2001) The genetic architecture of quantitative traits. Ann Rev Genet 35:303–339PubMedCrossRefGoogle Scholar
  28. Manly KF, Cudmore Jr RH, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932PubMedCrossRefGoogle Scholar
  29. Mizuta Y, Harushima Y, Kurata N (2006) Mapping of a pair of reproductive barrier loci observed in a cross between Nipponbare and Kasalath. Rice Genet Newsl 23:33–35Google Scholar
  30. Morinaga T, Kuriyama H (1957) Cytogenetical studies on Oryza sativa L. IX. The F1 hybrid of O. sativa L and O. glaberrima. Steud. Jpn J Breed 12:153–165Google Scholar
  31. Morishima H, Hinata K, Oka HI (1962) Comparison between two cultivated rice species, Oryza sativa L. and O. glaberrima Steud. Jap J Breed 12(3):153–165Google Scholar
  32. Oka HI (1974) Analysis of genes controlling F1 sterility in rice by the use of isogenic lines. Genetics 77:521–534PubMedGoogle Scholar
  33. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete map of restriction fragment length polymorphisms. Nature 335:721–726PubMedCrossRefGoogle Scholar
  34. Sano Y (1983) A new gene controlling sterility in F1 hybrids of two cultivated rice species. J Hered 74: 435–439Google Scholar
  35. Sano Y (1986) Sterility barriers between Oryza sativa and O. glaberrima. In: International Rice Research Institute (eds) Rice genetics. International Rice Research Institute, Manila, pp 109–118Google Scholar
  36. Sano Y (1990) The genic nature of gamete eliminator in rice. Genetics 125:183–191PubMedGoogle Scholar
  37. Sano Y, Chu YE, Oka HI (1979) Genetic studies of speciation in cultivated rice. 1. Genic analysis for the F1sterility between Oryza sativa L. and O. glaberrima Steud. Jpn J Genet 54:121–132CrossRefGoogle Scholar
  38. Shinjyo C (1975) Genetical studies of cytoplasmic male sterility and fertility restoration in rice, Oryza sativa L. Sci Bull Coll Agr Univ Ryukyus 22:1–57Google Scholar
  39. Sinha H, Nicholson BP, Steinmetz LM, McCusker JH (2006) Complex genetic interactions in a quantitative trait locus. PLOS Genet 2(2):140–147CrossRefGoogle Scholar
  40. Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416:326–330PubMedCrossRefGoogle Scholar
  41. Taguchi K, Doi K, Yoshimura A (1999) RFLP mapping of S19, a gene for F1 pollen semi-sterility found in backcross progeny of Oryza sativa and O. glaberrima. Rice Genet Newsl 16:70–71Google Scholar
  42. Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd-6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the a subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927PubMedCrossRefGoogle Scholar
  43. 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 107:1174–1180PubMedCrossRefGoogle Scholar
  44. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233PubMedCrossRefGoogle Scholar
  45. Tao DY, Hu FY, Yang G, Yang J, Tao H (1997) Exploitation and utilization of interspecific hybrid vigor between Oryza sativa and O. glaberrima. In: Jones MP, M Dingkuhn, Johnson DE, Fagade SO (eds) Interspecific hybridization: progress and prospects. WARDA/ADRAO, Cote d’Ivoire, pp 103–112Google Scholar
  46. Tao DY, Xu P, Hu FY, Yang YQ, Li J, Zhou JW, Jones MP (2002) Hybrid sterility among near-isogenic lines derived from interspecific hybrid between cultivated rice species Oryza sativa and O. glaberrima. Chinese J Rice Sci 16(2):106–110Google Scholar
  47. Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ, Weng JF, Wang HL, Lei CL, Wang JL, Zhang X, Cheng ZJ, Guo XP (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258–1270PubMedCrossRefGoogle Scholar
  48. Xu Y, Zhu L, Xiao J, Ning N, McCouch SR (1997) Chromosomal region associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred population in rice (Oryza sativa L.). Mol Gen Genet 253:535–545PubMedCrossRefGoogle Scholar
  49. Yabuno T (1995) A gametocidal factor of Oryza galberrima Steud. in O. sativa L. Euphytica 45:191–195Google Scholar
  50. Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet 97:37–44CrossRefGoogle Scholar
  51. Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6, and characterization of its epistatic interaction with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891PubMedGoogle Scholar
  52. Yan LL, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268PubMedCrossRefGoogle Scholar
  53. Yan LL, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644PubMedCrossRefGoogle Scholar
  54. Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153PubMedCrossRefGoogle Scholar
  55. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd-1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant cell 12:2473–2483PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Nanjing Agricultural UniversityNanjingP.R. China
  2. 2.Food Crops Research InstituteYunnan Academy of Agricultural SciencesKunmingP.R. China

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