한국자원식물학회지 (Korean Journal of Plant Resources)

  • 제34권5호
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  • Pages.443-450
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  • 2021
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  • 1226-3591(pISSN)
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  • 2287-8203(eISSN)
한국자원식물학회 (The Plant Resources Society of Korea)
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황육계 복숭아 품종 선발용 SNP 마커

SNP Markers Useful for the Selection of Yellow-fleshed Peach Cultivar

  • 김세희 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 권정현 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 조강희 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 신일섭 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 전지혜 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 조상윤 (농촌진흥청 국립원예특작과학원 과수과)
  • Kim, Se Hee (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Kwon, Jung-hyun (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Cho, Kang Hee (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Shin, Il Sheob (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Jun, Ji Hae (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Cho, Sang-Yun (Fruit Research Division, National Institute of Horticultural & Herbal Science)
  • Received : 2021.06.22
  • Accepted : 2021.09.16
  • Published : 2021.10.01
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Abstract

복숭아 과육색은 상업적으로 중요한 분류 기준이며 영양 품질에 영향을 미친다. 카로티노이드가 다량 함유된 새로운 황색 과육 품종을 육성하기 위해서는 많은 교배 조합과 세대가 진전되어야 한다. 따라서 육종 효율을 높이기 위해서는 경제적으로 중요한 형질을 가진 교배 집단과 유전자원에 적용할 조기 선발마커를 개발할 필요가 있다. 과육색이 다르게 발현되는 복숭아 품종의 유전자 발현을 비교하기 위해 2개의 cDNA library를 제작하였다. 황색 과육 품종인 '장호원황도'와 백색 과육 품종인 '미백도'의 유전자 발현 차이를 보기 위해 차세대 염기서열 분석 기술을 사용하였고 두 품종으로부터 얻은 EST의 염기서열을 결정하고 기존에 보고된 유전자와의 상동성을 분석하였다. EST 데이터로부터 황색 과육 품종 17개와 백색 과육 품종 22개를 구분할 수 있는 2종의 SNP 마커(SNP ID, ppa002847m:cds와 SNP ID, ppa002540m:cds)를 선발하였고, HRM 방법으로 분석하였다. 본 연구 결과는 복숭아 육종에 유용하게 사용할 수 있으며 복숭아 품종의 다양한 색 변화에 관한 분자 기작 연구에 좋은 참고자료가 될 수 있을 것이다.

Peach flesh color is commercially important criteria for classification and has implications for nutritional quality. To breed new yellow-fleshed peach cultivar many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection molecular markers for screening cross seedlings and germplasm with economically important traits to increase breeding efficiency. For the comparison of transcription profiles in peach varieties with a different flesh color expression, two cDNA libraries were constructed. Differences in gene expression between yellow-fleshed peach cultivar, 'Changhowon Hwangdo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two varieties was selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNPs) were screened from peach EST contigs by high resolution melting (HRM) analysis, SNP ID ppa002847m:cds and ppa002540m:cds displayed specific difference between 17 yellow-fleshed and 21 white-fleshed peach varieties. The SNP markers for distinguishing yellow and white fleshed peach varieties by HRM analysis offers the opportunity to use early selection. This SNP markers could be useful for marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach varieties.

Keywords

Acknowledgement

본 연구는 농촌진흥청 연구과제(세부과제번호:PJ013381012021)의 지원에 의해 이루어진 것임

References

  1. Ahmad, R., D. Potter and S.M. Southwick. 2004. Genotyping of peach and nectarine cultivars with SSR and SRAP molecular markers. J. Amer. Soc. Hort. Sci. 129(2):204-210. https://doi.org/10.21273/jashs.129.2.0204
  2. Ahmad, R., D.E. Parfitt, J. Fass, E. Ogundiwin, A. Dhingra, T.M. Gradziel, D. Lin, N.A. Joshi, P.J. Martinez-Garcia and C.H. Crisosto. 2011. Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics doi:10.1186/1471-2164-12-569.
  3. Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  4. Ashburner, M., C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppiq, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Rinqwald, G.M. Rubin and G. Sherlock. 2000. Gene ontology: tool for the unification of biology. Nature Genet. 25(1):25-29. https://doi.org/10.1038/75556
  5. Bliss, F.A., S. Arulsekar, M.R. Foolad, V. Becerra, A.M. Gillen, M.L. Warburton, A.M. Dandekar, G.M. Kocsisne and K.K. Mydin. 2002. An expanded genetic linkage map of Prunus based on an interspecific cross between almond and peach. Genome 45:520-529. https://doi.org/10.1139/g02-011
  6. Brandi, F., E. Bar, F. Mourgues, G. Horvath, E. Turcsi, G. Giuliano, A. Liverani, S. Tartarini, E. Lewinsohn and C. Rosati. 2011. Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile meta-bolism. BMC Plant Biol. 11:24. https://doi.org/10.1186/1471-2229-11-24
  7. Cao, X.Q., J.Y. Wang, L. Zhou, B. Chen, Y. Jin and Y.W. He. 2018. Biosynthesis of the yellow xanthomonadin pigments involves an ATP-dependent 3-hydroxybenzoic acid: acyl carrier protein ligase and an unusual type II polyketide synthase pathway. Mol. Microbiol. 110(1):16-32. https://doi.org/10.1111/mmi.14064
  8. Cevallos-Casals, B.A., B. David, R.O. William and L. Cisneros-Zevallos. 2006. Selecting new peach and plum genotypes rich in phenolic compounds and enhanced functional properties. Food Chemistry 96:273-280. https://doi.org/10.1016/j.foodchem.2005.02.032
  9. Connors, C.H. 1920. Some notes on the inheritance of unit characters in the peach. Proc. Am. Soc. Hortic. Sci. 16:24-36.
  10. Dhanapal, A.P. and C.H. Crisosto. 2013. Association genetic of chilling injury susceptibility in peach (Prunus persica (L.) Batsch) across multiply years. 3Biotech 3:481-490.
  11. Falchi, R., E. Vendramin, L. Zanon, S. Scalabrin, G. Cipriani, I. Veerde, G. Vizzotto and M. Morgante. 2013. Three distinct mutational mechanisms actiong on a single gene underpin the origin of yellow flesh in peach. The Plant J. 6:15-187.
  12. Forkmann, G. and S. Martens. 2001. Metabolic engineering and applications of flavonoids. Curr. Opin. in Biotech. 12:155-160. https://doi.org/10.1016/S0958-1669(00)00192-0
  13. Hui-Hsien, C. and H.H. Michael. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17(12):1093-1104. https://doi.org/10.1093/bioinformatics/17.12.1093
  14. Kim, S.H., E.Y. Nam, K.H. Cho, J.H. Jun and K.H. Chung. 2019. Development of SNP molecular marker for red-fleshed color identification of peach genetic resources. Korean J. Plant Res. 32(4):303-311.
  15. Margulies, M., M. Egholm, W.E. Altman, S. Attiya, J.S. Bader, L.A. Bemben, J. Berka, M.S. Braverman, Y.J. Chen, Z. Chen, S.B. Dewell, L. Du, J.M. Fierro, X.V. Gomes, B.C. Godwin, W. He, S. Helgesen, C.H. Ho, G.P. Irzyk, S.C. Jando, M.L. Alenquer, T.P. Jarvie, K.B. Jirage, J.B. Kim, J.R. Knight, J.R. Lanza, J.H. Leamon, S.M. Lefkowitz, M. Lei, J. Li, K.L. Lohman, H. Lu, V.B. Makhijani, K.E. McDade, M.P. McKenna, E.W. Myers, E. Nickerson, J.R. Nobile, R. Plant, B.P. Puc, M.T. Ronan, G.T. Roth, G.J. Sarkis, J.F. Simons, J.W. Simpson, M. Srinivasan, K.R. Tartaro, A. Tomasz, K.A. Vogt, G.A. Volkmer, S.H. Wang, Y. Wang, M.P. Weiner, P. Yu, R.F. Begley and J.M. Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380. https://doi.org/10.1038/nature03959
  16. Murayama, S. and H. Handa. 2007. Genes for alkaline/neutral invertase in rice: alkaline/neutral invertases are located in plant mitochondria and also in plastids. Planta 225:1193-1203. https://doi.org/10.1007/s00425-006-0430-x
  17. Prince, J.P., Y. Zhang, E.R. Radwanski and M.M. Kyle. 1997. A versatile and high-yielding protocol for the preparation of genomic DNA from Capsicum spp. (pepper). Hortscience 32:937-939. https://doi.org/10.21273/hortsci.32.5.937
  18. Shujun, C., P. Jeff and C. John. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep.11(2):113-116. https://doi.org/10.1007/BF02670468
  19. Shumskaya, M. and E.T. Wurtzel. 2013. The carotenoid biosynthetic pathway: Thinking in all dimensions. Plant Sci. 208:58-63. https://doi.org/10.1016/j.plantsci.2013.03.012
  20. Verde, I., A.G. Abbott, S. Scalabrin, S. Jung, S. Shu, F. Marroni and F. Salamini. 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat. Genet. 45:487-494. https://doi.org/10.1038/ng.2586
  21. Verde, I., N. Bassil, S. Scalabrin, B. Gilmore, C.T. Lawley, K. Gasic, D. Micheletti, U.R. Rosyara, F. Cattonaro, E. Vendramin, D. Main, V. Aramini, A.L. Blas, T.C. Mockler, D.W. Bryant, L. Wklhelm, M. Troggio, B. Sosinski, M.J. Aranzana, P. Arus, A. Iezzoni, M. Morgante and C. Peace. 2012. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP dection and validation in breeding germplasm. Plos One 7(4):e35668. https://doi.org/10.1371/journal.pone.0035668
  22. Wittwer, C.T., G.H. Reed, C.N. Gundry, J.G. Vandersteen and R.J. Pryor. 2003. High-resolution genotyping by amplicon melting analysis using LCGreen. Clinic Chem. 49:853-860. https://doi.org/10.1373/49.6.853