Horticultural Science & Technology (원예과학기술지)

Korean Society of Horticultural Science (한국원예학회)
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Analysis of Seed Hair Formation Related Genes by EST Profiling in Carrot (Daucus carota var. sativa)

EST profiling을 통한 당근(Daucus carota var. sativa)의 종모 형성에 관련된 유전자 분석

  • Hwang, Eun-Mi (Department of Horticultural Biotechnology, Kyung Hee University) ;
  • Oh, Gyu-Dong (Department of Horticultural Biotechnology, Kyung Hee University) ;
  • Shim, Eun-Jo (Department of Horticultural Biotechnology, Kyung Hee University) ;
  • Jeon, Sang-Jin (Breeding Research Institute, Carrotop Seed Co.) ;
  • Park, Young-Doo (Department of Horticultural Biotechnology, Kyung Hee University)
  • 황은미 (경희대학교 원예생명공학과) ;
  • 오규동 (경희대학교 원예생명공학과) ;
  • 심은조 (경희대학교 원예생명공학과) ;
  • 전상진 ((주)캐로톱씨드 육종연구소) ;
  • 박영두 (경희대학교 원예생명공학과)
  • Received : 2010.11.08
  • Accepted : 2010.11.13
  • Published : 2010.12.31
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Abstract

Carrot is one of the useful crops used abundantly in cooking in Western as well as Asia regions such as China and Korea. However, seed coats have hairs which should be removed to increase germination rate. Furthermore, because of seed hairs, farmers face several additional losses, such as time consumption, manpower, capital and so on, for seed handling. To prevent these problems, study of gene related hair formation using short-hair seed lines is required. We analyzed genes related to hair formation from seed through expressed sequenced tag (EST) profiling, based on the fact that the development of carrot seed hair is related to cellulose synthesis pathway in secondary cell wall synthesis stage. To study the gene expression related to hair formation of the carrot seed, a cDNA library was constructed by using the early maturation stage of the short-hair line (659-1) and hairy seed line (677-14). In short-hair (659-1) and hairy seed (677-14) lines, results from of EST profiling through BLASTX search analysis using the NCBI database showed that 172 and 224 unigenes had significant homology with known protein sequences, whereas 233 and 192 unigenes were not, respectively. All ESTs were grouped into 16 categories according to their putative functions. Twenty nine unigenes among all ESTs were considered to be genes regulating seed hair development from cellulose synthesis pathway during secondary cell wall synthesis stage; in results, 14 unigenes related to seed hair development were found only in hairy seed line.

당근은 서양뿐만 아니라 중국 및 한국과 같은 아시아 전역에서 요리로 많이 이용되는 유용한 작물 중 하나이다. 그러나 당근 종자 표면에는 모(毛)가 존재하고 이 종모는 발아율을 증가시키기 위해 제거해야 한다. 더욱이 종모 처리는 시간과 인력 및 자본의 소비와 같은 추가적인 손실을 동반하였다. 이러한 문제점을 방지하기 위해 단모종자를 이용하여 모형성과 관련된 유전자의 연구가 필요하다. 당근 종모의 발달은 2차 세포벽의 합성단계 동안 cellulose의 합성 과정과 연관되어 있음을 바탕으로, EST profiling을 통해 종모와 관련된 유전자를 탐색하고자 하였다. 당근 종모 형성에 관련된 유전자 발현을 조사하기 위해, 성숙 초기 단계의 단모종자 659-1개체와 유모종자 677-14개체를 이용하여 cDNA library를 구축하였다. 단모종자 659-1개체와 유모종자 677-14개체에서 확보된 EST 염기서열의 NCBI database BLASTX 분석을 통한 EST profiling 결과, 172개와 224개의 unigene은 이미 알려진 단백질 염기서열과 상동성을 보였으며 나머지 233개와 192개의 unigene은 확인되지 않는 유전자들이었다. EST는 추정되는 기능에 따라 16개의 category로 그룹화되었다. 전체 EST 중 29개의 unigene이 2차 세포벽 합성 단계 동안 cellulose의 합성 pathway상의 종모 형성을 조절하는 유전자로 추정되며, 실제로 종모 발달과 관련된 14개의 unigene이 유모종자 계통에서만 발견되었다.

Keywords

References

  1. Adams, M.D., A.R. Kerlavage, R.D. Fleischmann, R.A. Fuldner, C.J. Bult, N.H. Lee, E.F. Kirkness, K.G. Weinstock, J.D. Gocayne, O. White, G. Sutton, J.A. Blake, R.C. Brandon, M.W. Chiu, R.A. Clayton, R.T. Cline, M.D. Cotton, J.E. Hughes, L.D. Fine, L.M. Fitzgerald, W.M. FitzHugh, J.L. Fritchman, N.S.M. Geoghagen, A. Glodek, C.L. Gnehm, M.C. Hanna, E. Hedblom, P.S. Hinkle Jr., J.M. Kelley, K.M. Klimek, J.C. Kelley, L.I. Liu, S.M. Marmaros, J.M. Merrick, R.F. Moreno-Palanques, L.A. McDonald, D.T. Nguyen, S.M. Pellegrino, C.A. Phillips, S.E. Ryder, J.L. Scott, D.M. Saudek, R. Shirley, K.V. Small, T.A. Spriggs, T.R. Utterback, J.F. Weidman, Y. Li, R. Barthlow, D.P. Bednarik, L. Cao, M.A. Cepeda, T.A. Coleman, E.J. Collins, D. Dimke, P. Feng, A. Ferrie, C. Fischer, G.A. Hastings, W.W. He, J.S. Hu, K.A. Huddleston, J.M. Greene, J. Gruber, P. Hudson, A. Kim, D.L. Kozak, C. Kunsch, H.J. Ji, H.D. Li, P.S. Meissner, H. Olsen, L. Raymond, Y.F. Wei, J. Wing, C. Xu, G.L. Yu, S.M. Ruben, P.J. Dillon, M.R. Fannon, C.A. Rosen, W.A. Haseltine, C. Fields, C.M. Fraser, and J.C. Venter. 1995. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377:173-174. https://doi.org/10.1038/377173a0
  2. Amor, Y., C.H. Haigler, S. Johnson, M. Wainscott, and D.P. Delmer. 1995. A membrane-associated form of sucrose synthase and its potential role in synthesis of cellulose and callose in plants. Proc. Natl. Acad. Sci. USA. 92:9353-9357. https://doi.org/10.1073/pnas.92.20.9353
  3. Applequist, W.L., R. Cronn, and J.F. Wendel. 2001. Comparative development of fiber in wild and cultivated cotton. Evol. Dev. 3:3-17. https://doi.org/10.1046/j.1525-142x.2001.00079.x
  4. Arioli, T., L. Peng, A.S. Betzner, J. Burn, W. Wittke, W. Herth, C. Camilleri, H. Hofte, J. Plazinski, R. Birch, A. Cork, J. Glover, J. Redmond, and R.E. Williamson. 1998. Molecular analysis of cellulose biosynthesis in Arabidopsis. Science 279:717-720. https://doi.org/10.1126/science.279.5351.717
  5. Arpat, A.B., M. Waugh, J.P. Sullivan, M. Gonzales, D. Frisch, D. Main, T. Wood, A. Leslie, R.A. Wing, and T.A. Wilkins. 2004. Functional genomics of cell elongation in developing cotton fibers. Plant Mol. Biol. 54:911-929. https://doi.org/10.1007/s11103-004-0392-y
  6. Basra, A.S. and C.P. Malik. 1984. Development of the cotton fiber. Int. Rev. Cytol. 89:65-113. https://doi.org/10.1016/S0074-7696(08)61300-5
  7. Betancur, L., B. Singh, R.A. Rapp, J.F. Wendel, M.D. Marks, A.W. Roberts, and C.H. Haigler. 2010. Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber. J. Integr. Plant Biol. 52:205-220. https://doi.org/10.1111/j.1744-7909.2010.00934.x
  8. Boguski, M.S. and G.D. Schuler. 1995. EST ablishing a human transcript map. Nat. Genet. 10:369-371. https://doi.org/10.1038/ng0895-369
  9. Brett, C.T. and K.W. Waldron. 1996. Physiology and Biochemistry of Plant Cell Walls, 2nd ed. Chapman and Hall. London.
  10. Brown, D.M., L.A. Zeef, J. Ellis, R. Goodacre, and S.R. Turner. 2005. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17:2281-2295. https://doi.org/10.1105/tpc.105.031542
  11. Chourey, P.S. and O.E. Nelson. 1976. The enzymatic deficiency conditioned by the shrunken 1 mutation in maize. Biochem. Genet. 14:1041-1055. https://doi.org/10.1007/BF00485135
  12. Ewing, R.M., A.B. Kahla, O. Poirot, F. Lopez, S. Audic, and J.M. Claverie. 1999. Large-scale statistics analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9:950-959. https://doi.org/10.1101/gr.9.10.950
  13. Gou, J.Y., L.J. Wang, S.P. Chen, W.L. Hu, and X.Y. Chen. 2007. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis. Cell Res. 17:422-434.
  14. Lee, P.S. and K.H. Lee. 2000. Genomic analysis. Curr. Opin. Biotechnol. 11:171-175. https://doi.org/10.1016/S0958-1669(00)00077-X
  15. Menon, A.R.S. and Y. Dave. 1989. Micromorphology of hairs and spines on ovary and fruit of Daucus carota L. var. sativa (The cultivated carrot). Bot. Mat. Tokyo 102:503-509. https://doi.org/10.1007/BF02488432
  16. Nolte, K.D., D.L. Hendrix, J.W. Radin, and K.E. Koch. 1995. Sucrose synthase localization during initiation of seed development and trichome differentiation in cotton ovules. Plant Physiol. 109:1285-1293.
  17. Ogihara, Y., K. Mochida, Y. Nemoto, K. Murai, Y. Yamazaki, I.T. Shin, and Y. Kohara. 2003. Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. Plant J. 33:1001-1011. https://doi.org/10.1046/j.1365-313X.2003.01687.x
  18. Park, Y., M.S. Cho, Y.S. Kim, and S.G. Park. 2002. A promising carrot mutant, spineless seeds. J. Kor. Soc. Hort. Sci. 43: 707-709.
  19. Pavy, N., C. Paule, L. Parsons, J.A. Crow, M.J. Morency, J. Cooke, J.E. Johnson, E. Noumen, C. Guillet-Claude, Y. Butterfield, S. Barber, G. Yang, J. Liu, J. Stott, R. Kirkpatrick, A. Siddiqui, R. Holt, M. Marra, A. Seguin, E. Retzel, J. Bousquet, and J. MacKay. 2005. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6:144. https://doi.org/10.1186/1471-2164-6-144
  20. Pear, J.R., Y. Kawagoe, W.E. Schreckengost, D.P. Delmer, and D.M. Stalker. 1996. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Proc. Natl. Acad. Sci. USA. 93:12637-12642. https://doi.org/10.1073/pnas.93.22.12637
  21. Ronning, C.M., S.S. Stegalkina, R.A. Ascenzi, O. Bougri, A.L. Hart, T.R. Utterbach, S.E. Vanaken, S.B. Riedmuller, J.A. White, J. Cho, G.M. Pertea, Y. Lee, S. Karamycheva, R. Sultana, J. Tsai, J. Quackenbush, H.M. Griffiths, S. Restrepo, C.D. Smart, W.E. Fry, R. Van Der Hoeven, S. Tanksley, P. Zhang, H. Jin, M.L. Yamamoto, B.J. Baker, and C.R. Buell. 2003. Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 131:419-429. https://doi.org/10.1104/pp.013581
  22. Ruan, Y.L. and P.S. Chourey. 1998. A fiberless seed mutation in cotton is associated with lack of fiber cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds. Plant Physiol. 118: 399-406. https://doi.org/10.1104/pp.118.2.399
  23. Ruan, Y.L., P.S. Chourey, D.P. Delmer, and L. Perez-Grau. 1997. The differential expression of sucrose synthase in relation to diverse patterns of carbon partitioning in developing cotton seed. Plant Physiol. 115:375-385.
  24. Somerville, C. 2006. Cellulose synthesis in higher plants. Ann.Rev. Cell Dev. Biol. 22:53-78. https://doi.org/10.1146/annurev.cellbio.22.022206.160206
  25. Uchimiya, H., S. Kiou, T. Shimazaki, S. Aotsuka, S. Takamatsu, R. Nishi, H. Hashimoto, Y. Matsubayashi, N. Kidou, M. Umeda, and A. Kato. 1992. Random sequencing of cDNA libraries reveals a variety of expressed genes in cultured cells of rice. Plant J. 2:1005-1009. https://doi.org/10.1111/j.1365-313X.1992.01005.x
  26. Wanjie, S.W., R. Welti, R.A. Moreau, and K.D. Chapman. 2005. Identification and quantification of glycerolipids in cotton fibers: reconciliation with metabolic pathway predictions from DNA databases. Lipids 40:773-785. https://doi.org/10.1007/s11745-005-1439-4
  27. Yves, A.G., S. Bourot, T. Arioli, E.S. Dennis, and J.L. Danny. 2009. Transcript profiling during fiber development identifies pathways in secondary metabolism and cell wall structure that may contribute to cotton fiber quality. Plant Cell Physiol. 50:1364-1381. https://doi.org/10.1093/pcp/pcp084
  28. Zhang, L., X.L. Ma, Q. Zhang, C.L. Ma, P.P. Wang, Y.F. Sun, Y.X. Zhao, and H. Zhang. 2001. Expressed sequence tags from a NaCl-treated Suaeda salsa cDNA library. Gene 267:193-200. https://doi.org/10.1016/S0378-1119(01)00403-6
  29. Zrenner, R., M. Salanoubat, L. Willimitzer, and U. Sonnewald. 1995. Evidence of the crucial role of sucrose synthase for sink strength using transgenic potato plants (Solanum tuberosum L.). Plant J. 7:97-107. https://doi.org/10.1046/j.1365-313X.1995.07010097.x