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http://dx.doi.org/10.7732/kjpr.2021.34.5.443

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

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)
Publication Information
Korean Journal of Plant Resources / v.34, no.5, 2021 , pp. 443-450 More about this Journal
Abstract
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
Carotenoid; Gene expression; High resolution melting; Varieties;
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1 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.   DOI
2 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.   DOI
3 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.
4 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.
5 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.   DOI
6 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.   DOI
7 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.   DOI
8 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.   DOI
9 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.   DOI
10 Connors, C.H. 1920. Some notes on the inheritance of unit characters in the peach. Proc. Am. Soc. Hortic. Sci. 16:24-36.
11 Shumskaya, M. and E.T. Wurtzel. 2013. The carotenoid biosynthetic pathway: Thinking in all dimensions. Plant Sci. 208:58-63.   DOI
12 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.   DOI
13 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.   DOI
14 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.
15 Forkmann, G. and S. Martens. 2001. Metabolic engineering and applications of flavonoids. Curr. Opin. in Biotech. 12:155-160.   DOI
16 Hui-Hsien, C. and H.H. Michael. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17(12):1093-1104.   DOI
17 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.   DOI
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.   DOI
19 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.   DOI
20 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.   DOI
21 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.   DOI
22 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.   DOI