Melon, Cucumis melo L. is an important vegetable crop worldwide. At present, there are phenomena of homonyms and synonyms present in the melon seed markets of China, which could cause variety authenticity issues influencing the process of melon breeding, production, marketing and other aspects. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for cultivar identification. The aim of this study was to construct a DNA fingerprinting database of major melon cultivars, which could provide a possibility for the establishment of a technical standard system for purity and authenticity identification of melon seeds. In this study, to develop the core set SSR markers, 470 polymorphic SSRs were selected as the candidate markers from 1219 SSRs using 20 representative melon varieties (lines). Eighteen SSR markers, evenly distributed across the genome and with the highest contents of polymorphism information (PIC) were identified as the core marker set for melon DNA fingerprinting analysis. Fingerprint codes for 471 melon varieties (lines) were established. There were 51 materials which were classified into17 groups based on sharing the same fingerprint code, while field traits survey results showed that these plants in the same group were synonyms because of the same or similar field characters. Furthermore, DNA fingerprinting quick response (QR) codes of 471 melon varieties (lines) were constructed. Due to its fast readability and large storage capacity, QR coding melon DNA fingerprinting is in favor of read convenience and commercial applications.
References
[1]
Hector G, Nunez-Palenius, Miguel Gomez-Lim, Neftali Ochoa-Alejo, Rebecca Grumet, et al. (2008) Melon Fruits: Genetic Diversity, Physiology, and Biotechnology Features. Critical Reviews in Biotechnology 28(1): 13–55.
[2]
Krishna GK, Zhang J, Burow M, Pittman R, Delikostadinov S, et al. (2004) Genetic diversity analysis in Valencia peanut (Arachis hypogaea L.) using microsatellite markers. Cellular and Molecular Biology Letters 9: 685–697.
[3]
Naito Y, Suzuki S, Iwata Y, Kuboyama T (2008) Genetic diversity and relationship analysis of peanut germplasm using SSR markers. Breeding Science 58: 293–300.
[4]
Staub JE (2001) Inheritance of RAPD markers in melon (Cucumis melo L.). Cucurbit Genetics Cooperative Report 24: 29–32.
[5]
Garcia-Mas J, Oliver M, Gómez H, de Vicente MC (2000) Comparing AFLP, RAPD and RFLP markers to measure genetic diversity in melon. Theoretical and Applied Genetics 101: 860–864.
[6]
Deleu W, Esteras C, Roig C, González-To M, Fernández-Silva I, et al. (2009) A set of EST-SNPs for map saturation and cultivar identification in melon. BMC Plant Biology 9: 90.
[7]
Monforte AJ, Garcia-Mas J, Arús P (2003) Genetic variability in melon based on microsatellite variation. Plant Breeding 122: 153–157.
[8]
Ding C, Jin S (2009) High-throughput methods for SNP genotyping. Methods in Molecular Biology 578: 245–254.
[9]
Arif IA, Bakir MA, Khan HA, Farhan AH, Homaidan AA, et al. (2010) A brief review of molecular techniques to assess plant diversity. International Journal of Molecular Sciences 11: 2079–2096.
[10]
Mujaju C, Sehic J, Werlemark G, Garkava-Gustavsson L, Fatih M, et al. (2010) Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers. Hereditas 147(4): 142–153.
[11]
Danin-Poleg Y, Reis N, Baudracco-Arnas S, Pitrat M, Staub JE, et al. (2000) Simple sequence repeats in Cucumis mapping and map merging. Genome 43(6): 963–974.
[12]
Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45: 1095–1106.
[13]
Maestri E, Malcevschi A, Massari A, Marmiloni N (2002) Genomic analysis of cultivated barley (Hordeum vulgare) using sequence tags molecular markers. Estimates of divergence based on RFLP and PCR markers derived from stress-responsive genes, and simple sequence repeats (SSRs). Molecular Genetics and Genomics 267: 186–201.
[14]
Baek HJ, Beharav A, Nevo E (2003) Ecological-genomic diversity of microsatellites in wild barley, Hordeum spontaneum, population in Jordan. Theoretical and Applied Genetics 106: 397–410.
[15]
Achtar S, Moualla MY, Kalhout A, R？der MS, MirAli N (2010) Assessment of genetic diversity among Syrian durum (Triticum turgidum subsp. durum) and bread wheat (Triticum aestivum L.) using SSR markers. Genetika 46(11): 1500–1506.
[16]
Ng'uni D, Geleta M, Bryngelsson T (2011) Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR). Hereditas 148(2): 52–62.
[17]
Bornet B, Goraguer F, Joly G, Branchard M (2002) Genetic diversity in european and Argentinian cultivated potatoes (Solanum tuberosum subsp. tuberosum) detected by inter-simple sequence repeats (ISSRs). Genome 45(3): 481–484.
[18]
Zhang P, Li J, Li X, Liu X, Zhao X, et al. (2011) Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One 6(12): e27565.
[19]
Ashfaq M, Khan AS (2012) Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers. Genetika 48(1): 62–71.
[20]
Reif JC, Warburton ML, Xia XC, Hoisington DA, Crossa J, et al. (2006) Grouping of accessions of Mexican races of maize revisited with SSR markers. Theoretical and Applied Genetics 113(2): 177–185.
[21]
Yu RH, Wang YL, Sun Y, Liu B (2012) Analysis of genetic distance by SSR in waxy maize. Genetics and Molecular Research 11(1): 254–260.
[22]
Katzir N, Danin-Poleg T, Tzuri G, Karchi Z, Lavi U, et al. (1996) Length polymorphism and homologies of microsatellites in several Cucurbitaceae species. Theoretical and Applied Genetics 93: 1282–1290.
[23]
Stepansky A, Kovalski I, Perl-Treves R (1999) Intraspecific classification of melon (Cucumis melo L.) in view of their phenotypic and molecular variation. Plant Systematics and Evolution 217: 313–332.
[24]
Staub JE, Danin-Poleg Y, Fazio G, Horejsi T, Reis N, et al. (2000) Comparison analysis of cultivated melon groups (Cucumis melo L.) using random amplified polymorphic DNA and simple sequence repeat markers. Euphytica 115: 225–241.
[25]
Monforte AJ, Garcia-Mas J, Arus P (2003) Genetic variability in melon based on microsatellite variation. Plant Breeding 122: 153–157.
[26]
Danin-Poleg Y, Reis N, Tzuri G, Katzir N (2001) Development and characterization of microsatellite in Cucumis. Theoretical and Applied Genetics 102: 61–72.
[27]
Fazio G, Staub J E, Chung SM (2002) Development and characterization of PCR markers in cucumber. American Society for Horticultural Science 127 (4): 545–557.
[28]
Silberstein L, Kovalski I, Brotman Y, Perin C, Dogimont C, et al. (2003) Linkage map of Cucumis melo including phenotypic traits and sequence-characterized genes. Genome 46 (5): 761–773.
[29]
Gonzalo MJ, Oliver M, Garcia-Mas J, Monfort A, Dolcet-Sanjuan R, et al. (2005) Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theoretical and Applied Genetics 110 (5): 802–811.
[30]
Joobeur T, Gusmini G, Zhang X, Levi A, Xu Y, et al. (2006) Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes. Theoretical and Applied Genetics 112: 1553–1562.
[31]
Zalapa JE, Staub JE, McCreight JD, Chung SM, Cuevas H (2007) Detection of QTL for yield-related traits using recombinant inbred lines derived from exotic and elite US western shipping melon germplasm. Theoretical and Applied Genetics 114 (7): 1185–1201.
[32]
Fernandez-Silva I, Eduardo I, Blanca J, Esteras C, Picó B, et al. (2008) Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.). Theoretical and Applied Genetics 118: 139–150.
[33]
Luan F, Delannay I, Staub JE (2008) Melon (Cucumis melo L.) diversity analyses provide strategies for genetic improvement and evidentiary support of domestication patterns. Euphytica 164: 445–461.
[34]
Luan F, Sheng Y, Wang Y, Staub JE (2010) Performance of melon hybrids derived from parents of diverse geographic origins. Euphytica 137(1): 1–16.
[35]
Kirst M, Cordeiro GD, Rezende SP, Grattapaglia D (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. Journal of Heredity 96: 1–6.
[36]
Nei M (1977) F-statistics and analysis of gene diversity in subdivided populations. Annals of Human Genetics 41: 225–233.
[37]
Pavlicek A, Hrda S, Flegr J (1999) FreeTree-freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of the genus Frenkelia. Folia Biologica (Praha) 45: 97–99.
[38]
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731–2739.
[39]
Wang JY, Chen YY, Huang BZ, Yu F, Wu YT (2009) Establishment of fingerprinting for bananas (Musa nana) by SSR marker. Journal of Fruit Science 26 (5): 733–738 (in Chinese).
[40]
Ma HB, Xu XM, Wei XY, Yang WX, Zou WG (2010) DNA fingerpringing and genetic analysis based on SSR markers for rice cultivars in Fujian. Fujian Journal of Agricultural Science 25(1): 33–38 (in Chinese).
[41]
Zhu Z, Gao M, Gao P, Luan F (2011) QTL Analysis of the First Fertile Flower Node of Cucumis melo L. Acta Horticulturae Sinica. 38(9): 1753–1760.
[42]
Gao M, Zhu Z, Gao P, Luan F (2011) A Microsatellite-based Genetic Map of Melon and Localization of Gene for Gynoecious Sex Expression Using Recombinant Inbred Lines. Acta Horticulturae Sinica 38(7): 1308–1316.
[43]
Diaz A, Fergany M, Ziarsolo P, Blanca J, Fei Z, et al. (2011) A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biology 11: 111.
[44]
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, et al. (2012) The genome of melon (Cucumis melo L.). Proceedings of the National Academy of Sciences USA 109(29): 11872–11877.
