원예과학기술지 (Horticultural Science & Technology)

  • 제33권4호
  • /
  • Pages.550-558
  • /
  • 2015
  • /
  • 1226-8763(pISSN)
  • /
  • 2465-8588(eISSN)
한국원예학회 (Korean Society of Horticultural Science)
권호 표지
DOI QR코드

DOI QR Code

Application of the Molecular Marker in Linkage Disequilibrium with Ms, a Restorer-of-fertility Locus, for Improvement of Onion Breeding Efficiency

  • Kim, Sujeong (Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University) ;
  • Kim, Sunggil (Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University)
  • 투고 : 2015.01.08
  • 심사 : 2014.04.01
  • 발행 : 2015.08.31
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

To analyze the linkage relationships among molecular markers recently reported to be linked to onion (Allium cepa L.) Ms, a restorer-of-fertility locus, in onion (Allium cepa L.), three single nucleotide polymorphism markers were converted into cleaved amplified polymorphic sequence (CAPS) markers based on onion transcriptome sequences and the rice genome database. Analysis of the recombinants selected from 4,273 segregating plants using CAPS and other linked markers demonstrated the jnurf13 and jnurf610 markers to perfectly co-segregate with the Ms locus. In contrast to jnurf13, the jnurf610 marker was not in perfect linkage disequilibrium with the Ms locus in diverse breeding lines. Thus, the jnurf13 marker and the marker for identification of cytoplasm types were utilized to enhance the efficiency of onion breeding through four applications. First, 89 maintainer lines containing the normal cytoplasm and homozygous recessive Ms genotypes were successfully identified from 100 breeding lines. Second, these two molecular markers were used to analyze the main sources of male-fertile contaminants frequently found in the male-sterile parental lines during F1 hybrid seed production. The majority of the contaminants contained heterozygous Ms genotypes, indicating that pollen grains harboring the dominant Ms genotype may have been introduced during propagation of the maintainer lines. Therefore, the genetic purity of the two maintainer lines was analyzed in the third application, and the results showed that both maintainer lines contained 13-21% off-types. Finally, the two markers were used to increase the seed yield potentials of two open-pollinated varieties containing sterile cytoplasms by removing the plants harboring homozygous recessive and heterozygous Ms genotypes.

키워드

참고문헌

  1. Arumuganathan, K. and E.D. Earle. 1991. Nuclear DNA content of some important plant species. Plant Mol. Rep. 9:208-218. https://doi.org/10.1007/BF02672069
  2. Bang, H., S. Kim, S.O. Park, K. Yoo, and B.S. Patil. 2013. Development of a codominant CAPS marker linked to the Ms locus controlling fertility restoration in onion (Allium cepa L.). Sci. Hortic. 153:42-49. https://doi.org/10.1016/j.scienta.2013.01.020
  3. Bentolila, S., A.A. Alfonso, and M.R. Hanson. 2002. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc. Natl. Acad. Sci. USA 99:10887-10892. https://doi.org/10.1073/pnas.102301599
  4. Berninger, E. 1965. Contribution a l'etude de la sterilite male de l'oignon (Allium cepa L.). Ann Amelior. Plant 15:183-199.
  5. Brewster, J.L. 2008. Onions and other vegetable alliums, 2nd edn. CAB International: Wallingford, UK.
  6. Brown, G.G., N. Formanova, H. Jin, R. Wargachuk, C. Dendy, P. Patil, M. Laforest, J. Zhang, W.Y. Cheung, and B.S. Landry. 2003. The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. Plant J. 35:262-272. https://doi.org/10.1046/j.1365-313X.2003.01799.x
  7. Budar, F., P. Touzet, and R. De Paepe. 2003. The nucleomitochondrial conflict in cytoplasmic male sterilities revised. Genetica 117:3-16. https://doi.org/10.1023/A:1022381016145
  8. Cho, Y., Y. Lee, B. Park, T. Han, and S. Kim. 2012. Construction of a high-resolution linkage map of Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility conferred by DCGMS cytoplasm in radish (Raphanus sativus L.). Theor. Appl. Genet. 125:467-477. https://doi.org/10.1007/s00122-012-1846-2
  9. Cui, X., R.P. Wise, and P.S. Schnable. 1996. The rf2 nuclear restorer gene of male-sterile T-cytoplasm maize. Science 272:1334-1336. https://doi.org/10.1126/science.272.5266.1334
  10. Desloire, S., H. Gherbi, W. Laloui, S. Marhadour, V. Clouet, L. Cattolico, C. Falentin, S. Giancola, M. Renard, F. Budar, I. Small, M. Caboche, R. Delourme, and A. Bendahmane. 2003. Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family. EMBO Rep. 4:588-594. https://doi.org/10.1038/sj.embor.embor848
  11. Doyle, J.J. and J.L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15.
  12. Duangjit, J., B. Bohanec, A.P. Chan, C.D. Town, and M.J. Havey. 2013. Transcriptome sequencing to produce SNP-based genetic maps of onion. Theor. Appl. Genet. 126:3093-2101.
  13. Engelke, T., D. Terefe, and T. Tatlioglu. 2003. A PCR-based marker system monitoring CMS-(S), CMS-(T) and (N)-cytoplasm in the onion (Allium cepa L.). Theor. Appl. Genet. 107:162-167.
  14. Fossen, T., O.M. Andersen, D.O. Ovstedal, A.T. Pedersen, and A. Raknes. 1996. Characteristic anthocyanin pattern from onions and other Allium spp. J. Food Sci. 61:703-706. https://doi.org/10.1111/j.1365-2621.1996.tb12185.x
  15. Gokce, A.F. and M.J. Havey. 2002. Linkage equilibrium among tightly linked RFLPs and the Ms locus in open-pollinated onion populations. J. Am. Soc. Hortic. Sci. 127:944-946.
  16. Griffiths, G., L. Trueman, T. Crowther, B. Thomas, and B. Smith. 2002. Onions-A global benefit to health. Phytother. Res. 16:603-615. https://doi.org/10.1002/ptr.1222
  17. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Window 95/98/NT. Nucl. Acids Symp. Ser. 41:95-98.
  18. Hamilton, J.P. and C.R. Buell. 2012. Advances in plant genome sequencing. Plant J. 70:177-190. https://doi.org/10.1111/j.1365-313X.2012.04894.x
  19. Hanson, M.R. 1991. Plant mitochondrial mutations and male sterility. Annu. Rev. Genet. 25:461-486. https://doi.org/10.1146/annurev.ge.25.120191.002333
  20. Hanson, M.R. and S. Bentolila. 2004. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 16:S154-S169. https://doi.org/10.1105/tpc.015966
  21. Havey, M.J. 1995. Identification of cytoplasms using the polymerase chain reaction to aid in the extraction of maintainer lines from open-pollinated populations of onion. Theor. Appl. Genet. 90:263-268.
  22. Havey, M.J. 2013. Single nucleotide polymorphisms in linkage disequilibrium with the male-sterility restoration (Ms) locus in open-pollinated and inbred populations of onion. J. Am. Soc. Hortic. Sci. 138:306-309.
  23. Hu, J., W. Huang, Q. Huang, X. Qin, C. Yu, L. Wang, S. Li, R. Zhu, and Y. Zhu. 2014. Mitochondria and cytoplasmic male sterility in plants. Mitochondrion 19:166-171. https://doi.org/10.1016/j.mito.2014.04.009
  24. Jakse, J., J.D.F. Meyer, G. Suzuki, J. McCallum, F. Cheung, C.D. Town, and M.J. Havey. 2008. Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration. Mol. Genet. Genomics 280:287-292. https://doi.org/10.1007/s00438-008-0364-z
  25. Jakse, J., A. Telgmann, C. Jung, A. Khar, S. Melgar, F. Cheung, C.D. Town, and M.J. Havey. 2006. Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice. Theor. Appl. Genet. 114:31-39. https://doi.org/10.1007/s00122-006-0407-y
  26. Jones, H.A. and A. Clarke. 1943. Inheritance of male sterility in the onion and the production of hybrid seed. Proc. Am. Soc. Hortic. Sci. 43:189-194.
  27. Jones, H.A. and S.L. Emsweller. 1936. A male-sterile onion. Proc. Am. Soc. Hortic. Sci. 34:582-585.
  28. Kawahara, Y., M. de la Bastide, J.P. Hamilton, H. Kanamori, W.R. McCombie, S. Ouyang, D.C. Schwartz, T. Tanaka, J. Wu, S. Zhou, K.L. Childs, R.M. Davidson, H. Lin, L. Quesada-Ocampo, B. Vaillancourt, H. Sakai, S.S. Lee, J. Kim, H. Numa, T. Itoh, C.R. Buell, and T. Matsumoto T. 2013. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4. https://doi.org/10.1186/1939-8433-6-4
  29. Kim, S. 2014. A codominant molecular marker in linkage disequilibrium with a restorer-of-fertility gene (Ms) and its application in reevaluation of inheritance of fertility restoration in onions. Mol. Breed. 34:769-778. https://doi.org/10.1007/s11032-014-0073-8
  30. Kim, S., E. Lee, D.Y. Cho, T. Han, H. Bang, B.S. Patil, Y.K. Ahn, and M. Yoon. 2009a. Identification of a novel chimeric gene, orf725, and its use in development of a molecular marker for distinguishing three cytoplasm types in onion (Allium cepa L.). Theor. Appl. Genet. 118:433-441. https://doi.org/10.1007/s00122-008-0909-x
  31. Kim, S., E. Lee, C. Kim, and M. Yoon. 2009b. Distribution of three cytoplasm types in onion (Allium cepa L.) cultivars bred in Korea and Japan. Kor. J. Hort. Sci. Technol. 27:275-279.
  32. Klein, R.R., P.E. Klein, J.E. Mullet, P. Minx, W.L. Rooney, and K.F. Schertz. 2005. Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the collinear region of rice chromosome 12. Theor. Appl. Genet. 111:994-1012. https://doi.org/10.1007/s00122-005-2011-y
  33. Kmiec, B., M. Woloszynska, and H. Janska. 2006. Heteroplasmy as a common state of mitochondrial genetic information in plants and animals. Curr. Genet. 50:149-159. https://doi.org/10.1007/s00294-006-0082-1
  34. Knoop, V. 2004. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr. Genet. 46:123-139.
  35. Koizuka, N., R. Imai, H. Fujimoto, T. Hayakawa, Y. Kimura, J. Kohno-Murase, T. Sakai, S. Kawasaki, and J. Imamura. 2003. Genetic characterization of a pentatricopeptide repeat protein gene, orf687, that restores fertility in the cytoplasmic male-sterile Kosena radish. Plant J. 34:407-415. https://doi.org/10.1046/j.1365-313X.2003.01735.x
  36. Komori, T., S. Ohta, N. Murai, Y. Takakura, Y. Kuraya, S. Suzuki, Y. Hiei, H. Imaseki, and N. Nitta. 2004. Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). Plant J. 37:315-325. https://doi.org/10.1046/j.1365-313X.2003.01961.x
  37. Kubo, T. and K.J. Newton. 2008. Angiosperm mitochondrial genomes and mutations. Mitochondrion 8:5-14. https://doi.org/10.1016/j.mito.2007.10.006
  38. Laser, K.D. and N.R. Lersten. 1972. Anatomy and cytology of microsporogenesis in cytoplasmic male sterile angiosperms. Bot. Rev. 38:425-454. https://doi.org/10.1007/BF02860010
  39. Martin, W.J., J. McCallum, M. Shigyo, J. Jakse, J.C. Kuhl, N. Yamane, M. Pither-Joyce, A.F. Gokce, K.C. Sink, C.D. Town, and M.J. Havey. 2005. Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol. Gen. Genomics 274:197-204. https://doi.org/10.1007/s00438-005-0007-6
  40. Mutz, K., A. Heilkenbrinker, M. Lonne, J. Walter, and F. Stahl. 2013. Transcriptome analysis using next-generation sequencing. Curr. Opin. Biotech. 24:22-30. https://doi.org/10.1016/j.copbio.2012.09.004
  41. Park, J., H. Bang, D.Y. Cho, M. Yoon, B.S. Patil, and S. Kim. 2013. Construction of high-resolution linkage map of the Ms locus, a restorer-of-fertility gene in onion (Allium cepa L.). Euphytica 192:267-278. https://doi.org/10.1007/s10681-012-0851-5
  42. Rhodes, M.J.C. and K.R. Price. 1996. Analytical problems in the study of flavonoid compounds in onions. Food Chem. 57:113-117. https://doi.org/10.1016/0308-8146(96)00147-1
  43. Sato, Y. 1998. PCR amplification of CMS-specific mitochondrial nucleotide sequences to identify cytoplasmic genotypes of onion (Allium cepa L.). Theor. Appl. Genet. 96:367-370. https://doi.org/10.1007/s001220050750
  44. Schweisguth, B. 1973. etude d'un nouveau type de sterilite male chez l'oignon, Allium cepa L. Ann. Amelior. Plant 23:221-233.
  45. Slimestad, R., T. Fossen, and I.M. Vagen. 2007. Onions: a source of unique dietary flavonoids. J. Agric. Food Chem. 55:10067-10080. https://doi.org/10.1021/jf0712503
  46. Small, I., R. Suffolk, and C.J. Leaver. 1989. Evolution of plant mitochondrial genomes via substoichiometric intermediates. Cell 58:69-76. https://doi.org/10.1016/0092-8674(89)90403-0
  47. Vitte, C., M.C. Estep, J. Leebens-Mack, and J.L. Bennetzen. 2013. Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Ann. Bot. 112:881-889. https://doi.org/10.1093/aob/mct155
  48. Wolf, J.B.W. 2013. Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Mol. Ecol. Resour. 13:559-572. https://doi.org/10.1111/1755-0998.12109

피인용 문헌

  1. Perspective and application of molecular markers linked to the cytoplasm types and male‐fertility restorer locus in onion (Allium cepa) vol.140, pp.5, 2015, https://doi.org/10.1111/pbr.12948