Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
권호 표지

Identification of QTLs for Some Agronomic Traits in Rice Using an Introgression Line from Oryza minuta

  • Rahman, Md Lutfor (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Chu, Sang Ho (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Choi, Min-Sun (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Qiao, Yong Li (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Jiang, Wenzhu (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Piao, Rihua (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Khanam, Sakina (Department of Biological and Environmental Science, Kobe University) ;
  • Cho, Young-Il (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Jeung, Ji-Ung (IRRI- Korea Office, National Institute of Crop Science, Rural Development Administration) ;
  • Jena, Kshirod K. (IRRI- Korea Office, National Institute of Crop Science, Rural Development Administration) ;
  • Koh, Hee-Jong (Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University)
  • Received : 2006.09.08
  • Accepted : 2007.04.17
  • Published : 2007.08.31
⟨ Previous Next ⟩

Abstract

Wild progenitor species provide potential gene sources for complex traits such as yield and multiple resistances to biotic and abiotic stresses, and thus are expected to contribute to sustainable food supplies. An introgression line 'IR71033-121-15' was derived from a wild species Oryza minuta (2n = 48, BBCC, Acc No. 101141) at IRRI. Introgression analysis using 530 SSR and STS markers revealed that at least 14 chromosomal segments distributed over 12 chromosomes had been introgressed from O. minuta. An $F_{2:3}$ population from the cross between IR71033 and Junambyeo (a Korean japonica cultivar) consisting of 146 lines was used for quantitative trait loci (QTL) analysis of 16 agronomic traits. A total of 36 single-locus QTLs (S-QTLs) and 45 digenic epistasis (E-QTLs) were identified. In spite of it's inferiority of O. minuta for most of the traits studied, its alleles contributed positively to 57% of the QTLs. The other QTLs originated from either parent, IR71033 or Junambyeo. QTLs for phenotypically correlated traits were mostly detected on introgressed segments. Fourteen QTLs corresponded to QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Twenty-two QTLs controlling yield and its components had not been detected in previous QTL studies. Of these, thirteen consisted of potentially novel alleles from O. minuta. QTLs from O. minuta introgression could be new sources of natural variation for the genetic improvement of rice.

Keywords

Acknowledgement

Supported by : Rural Development Administration

References

  1. Aluko, G. C., Martinez, J., Tohme, C., Castano, C., Bergman, C., et al. (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa X O. glaberrima. Theor. Appl. Genet. 109, 630-639
  2. Amante, A. D., Sitch, L. A., Nelson, R., Dalmacio, R. D., Oliva, N. P., et al. (1998) Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice O. sativa. Theor. Appl. Genet. 84, 345-354
  3. Ammiraju, J. S. S., Luo, M., Goicoechea, J. L., Wang, W., Kudrna, D., et al. (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res. 16, 140-147
  4. Brar, D. S. (2004) Crop scientists use wide crosses to breed into cultivated rice varieties. Rice Today, 1-2
  5. Brar, D. S. and Khush, G. S. (1997) Alien introgression in rice. Plant Mol. Biol. 35, 35-47 https://doi.org/10.1023/A:1005825519998
  6. Brondani, C., Rangel, P. H. N., Brondani, R. P. V., and Ferreira, M. E. (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor. Appl. Genet. 104, 1192-1203 https://doi.org/10.1007/s00122-002-0869-5
  7. Cai, H. W. and Morishima, H. (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor. Appl. Genet. 104, 1217-1228 https://doi.org/10.1007/s00122-001-0819-7
  8. Chen, X., Temnykh, S., Xu, Y., Cho, Y. G., and McCouch, S. R. (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor. Appl. Genet. 95, 553-567 https://doi.org/10.1007/s001220050596
  9. Cho, Y. C., Suh, J. P., Choi, I. S., Hong, H. C., Baek, M. K., et al. (2003) QTLs analysis of yield and its related traits in wild rice relative Oryza rufipogon. Treat. Crop. Res. 4, 19-29
  10. Doi, K., Yoshimura, A., and Iwata, N. (1998) RFLP mapping and QTL analysis of heading date and pollen sterility using back cross population between Oryza sativa L and Oryza glaberrima Steud. Breed. Sci. 48, 395-399
  11. Ge, X. J., Xing, Y. Z., Xu, C. G., and He, Y. Q. (2005) QTL analysis of cooked garmene rice grain elongation, volume expansion, and water absorption using a recombinant inbred population. Plant Breeding 124, 121-126 https://doi.org/10.1111/j.1439-0523.2004.01055.x
  12. Gu, X. Y., Kianian, S. F., Hareland, G. A., Hoffer, B. L., and Floley, M. E. (2005) Genetic analysis of adaptive syndromes interrelated with seed dormacy in weedy rice (Oryza sativa). Theor. Appl. Genet. 110, 1108-1118 https://doi.org/10.1007/s00122-005-1939-2
  13. Harushima, Y., Yano, M., Shomura, A., Sato, M., Shimano, T., et al. (1998) A high-density rice genetic map with 2275 markers using a single F2 population. Genetics 148, 479-494
  14. Hittalmani, S., Huang, N., Courtois, B., Venuprasad, R., Shashidhar, H. E., et al. (2003) Identification of QTL for growth and grain yield-related traits in rice across nine locations of Asia. Theor. Appl. Genet. 107, 679-690 https://doi.org/10.1007/s00122-003-1269-1
  15. Hua, J. P., Xing, Y. Z., Xu, C. G., Sun, X. L., Yu, S. B., et al. (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics 162, 1885-1895
  16. Ishii, T., Brar, D. S., Multani, D. S., and Khush, G. S. (1994) Molecular tagging of genes of brown plant hopper resistance and earliness introduced from Oryza australiensis into cultivar rice, O. sativa. Genome 37, 217-221 https://doi.org/10.1139/g94-030
  17. Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., et al. (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor. Appl. Genet. 102, 793-800 https://doi.org/10.1007/s001220000467
  18. Jena, K. K. and Kochert, G. S. (1991) Restriction fragment polymorphism analysis of CCDD genome species of the genus Oryza. Plant. Mol. Biol. 5, 109-118 https://doi.org/10.1007/BF00020093
  19. Jena, K. K., Khush, G. S., and Kochert, G. (1992) RFLP analysis of rice (Oryza sativa L) introgression lines. Theor. Appl. Genet. 84, 608-616
  20. Jena, K. K., Pasula, I. C., Rao, Y. K., Varalaxmi, Y., Krishnaiah, K., et al. (2003) Molecular tagging of a gene fro resistance to brown plant hopper in rice (Oryza sativa L.). Euphytica 129, 81-88 https://doi.org/10.1023/A:1021590025240
  21. Jin, F. X., Ling, L., Kang, K. H., and Ahn, S. N. (2005) Mapping Quantitative Trait Loci for grain traits using near isogenic line from a cross between Oryza minuta and O. sativa. Korean J. Breed. 37, 221-228
  22. Kobayashi, S., Fukata, Y., Sato, T., Osaki, M., and Khush, G. S. (2003) Molecular marker dissection of rice (Oryza sativa L.) plant architecture under temperate and tropical climates. Theor. Appl. Genet. 107, 1350-1356 https://doi.org/10.1007/s00122-003-1388-8
  23. Lander, E. S., Green, P., Abrahamson, J., Barlow, M. J., Daly, M. J., et al. (1996) RFLP mapping of QTLs for yield and related characters in rice (Oryza sativa L.). Theor. Appl. Genet. 92, 920-927 https://doi.org/10.1007/BF00224031
  24. Lee, S. Y., Ahn, J. H., Cha, Y. S., Yun, D. W., Lee, M. C., et al. (2006) Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol. Cells 22, 192-196
  25. Li, J. Z., Zheng, X. W., Zhu, L. H., He, P., and Lu, R. L. (1999) Identification and interaction analysis of six agronomic trait loci of rice based on a recombinant inbred population. Acta Bot. Sinica. 41, 1199-1203
  26. Liao, C. Y., Wu, P., Hu, B., and Yi, K. K. (2001) Effects of genetic background and environment on QTLs and epistasis for rice (Oryza sativa L.) panicle number. Theor. Appl. Genet. 103, 104-111 https://doi.org/10.1007/s001220000528
  27. Lin, S. Y., Sasaki, T., and Yano, M. (1998) Mapping of quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using back cross inbred lines. Theor. Appl. Genet. 96, 997-1003 https://doi.org/10.1007/s001220050831
  28. Linh, L. H., Jin, F. X., Kang, K. H., Lee, Y. T., Kwon, S. J., et al. (2006) Mapping quantitative trait loci for heading date and awn length using an advanced backcross line from a cross between Oryza sativa and O. minuta. Breed. Sci. 56, 341-349 https://doi.org/10.1270/jsbbs.56.341
  29. Liu, G., Lu, G., Zeng, L., and Wang, G. L. (2002) Two broadspectrum blast resistance genes, Pi9(t) and Pi2(t), are physically linked on rice chromosome 6. Mol. Genet. Genomics 267, 472-480 https://doi.org/10.1007/s00438-002-0677-2
  30. Lu, C. F., Slen, L. H., Tan, Z. B., Xu, Z. B., He, P., et al. (1997) Comparative mapping of QTLs for agronomic traits of rice across environments by using a double haploid population. Theor. Appl. Genet. 94, 145-150 https://doi.org/10.1007/s001220050393
  31. Mei, H. W., Luo, L. J., Ying, C. S., Wang, Y. P., Yu, X. Q., et al. (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two test cross populations. Theor. Appl. Genet. 107, 89-101 https://doi.org/10.1007/s00122-003-1192-5
  32. Mei, H. W., Li, Z. K., Shu, Q. Y., Guo, L. B., Wang, Y. P., et al. (2005) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two back cross populations. Theor. Appl. Genet. 110, 649-659 https://doi.org/10.1007/s00122-004-1890-7
  33. Moncada, P., Martinez, C. P., Borrero, J., Chatel, M., Gauch, J. H., et al. (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, 41-52 https://doi.org/10.1007/s001220051616
  34. Multani, D. S., Khush, G. S., Delosreys, B. G., and Brar, D. S. (2003) Alien genes introgression and development of monosomic alien addition lines from Oryza latifolia Desv to rice, Oryza sativa L. Theor. Appl. Genet. 107, 339-405
  35. Nelson, J. C. (1997) QGENE: software for marker-based genomic analysis and breeding. Mol. Breed. 3, 239-245 https://doi.org/10.1023/A:1009604312050
  36. Suh, J., Ahn, S. N., Cho, Y. C., Kang, K. H., Choi, I. M., et al. (2005) Mapping for QTLs for yield traits using an advanced backcross population from a cross between Oryza sativa and O. glaberrima. Korean J. Breed. 37, 214-220
  37. Tan, Z. B., Shen, L. S., Yuan, Z. L., Lu, C. F., and Chen, Y. (1997) Identification of QTLs for ratooning ability and grain yield traits of rice and analysis of their genetic effects. Acta Agronomica Sinica. 23, 289-295
  38. Tanksley, S. D. (1993) Mapping polygenes. Ann. Rev. Genet. 27, 205-233 https://doi.org/10.1146/annurev.ge.27.120193.001225
  39. Temnykh, S., Park, W. D., Ayres, N., Catinhour, S., Hauck, N., et al. (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 697-712 https://doi.org/10.1007/s001220051342
  40. Thomson, M. J., Tai, T., McClung, A. M., Lai, X. H., Hinga, M. E., et al. (2003) Mapping quantitative trait loc for yield components and morphological traits in an advanced backcross population between O. rufipogon and the Oryza sativa cultivar Jefferson. Theor. Appl. Genet. 107, 479-493 https://doi.org/10.1007/s00122-003-1270-8
  41. Tian, F., Li, D. J., Qiang, F., Zu, Z. F., Fu, Y. C., et al. (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of Introgressed segments associated with yield-related traits. Theor. Appl. Genet. 112, 570-580 https://doi.org/10.1007/s00122-005-0165-2
  42. Wan, X. Y., Wan, J. M., Weng, J. F., Jiang, L., Bi, J. C., et al. (2005) Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor. Appl. Genet. 110,1334-1346 https://doi.org/10.1007/s00122-005-1976-x
  43. Wang, D. L., Zhu, J., Li, Z. K., and Paterson, A. H. (2001) A computer software for mapping quatitative trait loci QTLs with main effects and QTL x environment interactions. Copyright by Zhejiang University, Hangzhou, China
  44. Xiao, J., Li, J., Yuan, L., and Tanksley, S. D. (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor. Appl. Genet. 92, 230-244 https://doi.org/10.1007/BF00223380
  45. Xiao, J., Li, J., Grandillo, S., Ahn, S. N., Yuan, L., et al. (1998) Identification of trait improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150, 899-909
  46. Xing, Y. Z., Xu, C. G., Hua, J. P., Tan, Y. F., and Sun, X. L. (2001) Mapping and isolation of quantitative trait loci controlling plant height and heading date in rice. Acta Bot. Sincia. 43, 721-726
  47. Xiong, L. Z., Liu, K. D., Dai, X. K., Xu, C. G., and Zhang, Q. (1999) Identification of genetic factors controlling domestication- related traits of rice using an F2 population of a cross between Oryza sativa and O rufipogon. Theor. Appl. Genet. 98, 243-251 https://doi.org/10.1007/s001220051064
  48. Xu, Y., Shen, Z., Xu, J., Zhu, H., Chen, Y., et al. (1995) Interval mapping of quantitative trait loci by molecular markers in rice (Oryza sativa L). Sci. China 38, 422-428
  49. Xu, C. G., Yu, S. B., Zhang, Q., Li, J. X., Xing, Y. Z., et al. (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor. Appl. Genet. 101, 823-829 https://doi.org/10.1007/s001220051549
  50. Yamagishi, M., Takeuchi, Y., Kono, I., and Yano, M. (2002) QTL analysis for panicle characteristics in temperate japonica rice. Euphytica 128, 219-224 https://doi.org/10.1023/A:1020893731249
  51. Yamamoto, T., Taguch, S. F., Ukai, Y., Sasaki, T., and Yano, M. (2001) Mapping quantitative trait loci for days to heading, and culm, panicle and internode lengths in a BC1F3 population using an elite rice variety, Koshikari, as the recurrent parent. Breed. Sci. 51, 63-71 https://doi.org/10.1270/jsbbs.51.63
  52. Yan, J. Q., Zhu, J., He, C. X., Benmoussa, M., and Wu, P. (1998) Quantitative trait loci analysis for the developmental behavior of tiller number in rice (Oryza sativa L.). Theor. Appl. Genet. 97, 267-274 https://doi.org/10.1007/s001220050895
  53. Yoon, D. B., Kang, K. H., Kim, H. J., Ju, H. G., Kwon, S. J., et al. (2006) Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseoungbyeo. Theor. Appl. Genet. 112, 1052-1062 https://doi.org/10.1007/s00122-006-0207-4
  54. Yu, S. B., Li, J. X., Xu, C. G., Tan, Y. F., Gao, Y. J., et al. (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc. Natl. Acad. Sci. USA 94, 9226-92331
  55. Zhuang, J. Y., Lin, H. X., Lu, J., Qian, H. R., Hittalmani, S., et al. (1997) Analysis of QTL x environment interaction for yield components and plant height in rice. Theor. Appl. Genet. 95, 799-808 https://doi.org/10.1007/s001220050628