Abstract
The decreasing costs associated with next generation sequencing and related bioinformatics computing resources have facilitated the large-scale discovery of single nucleotide polymorphisms (SNPs) in crop species. In this study, the genomes of the two melon varieties CM-P01 (orange-fleshed) and MM-P02 (green-fleshed) were resequenced to identify genome-wide SNPs. A total of 2.0 Gb (CM-P01) and 1.5 Gb (MM-P02) quality-filtered sequences were generated that corresponded to 9.6× and 7.2× genome coverage, respectively, relative to the melon reference genome. By comparing these sequences, we detected 534,477 SNPs between the two varieties across the genome. The number of SNPs per chromosome ranged from 30,337 (chromosome 8) to 60,832 (chromosome 1). Of these, 15,674 SNPs were identified in predicted coding sequences, of which 8057 were synonymous and 7617 were non-synonymous. Analysis of Gene Ontology associations demonstrated that the non-synonymous SNPs were present in genes encoding various molecular functions. A subset of 97 non-synonymous SNPs was randomly selected for validation via high-resolution melting analysis. Of these, 84 SNPs (86.6%) were validated using a collection of 18 varieties, including CM-P01 and MM-P02. For these SNPs, the estimates of polymorphic information content (PIC) ranged from 0.18 to 0.38 and 62 SNPs (73.8%) showed more than 0.30 of PIC. The orange-fleshed varieties were separated from the green-fleshed varieties in our collection using the 84 SNPs. These SNPs will be a useful resource for the genetic dissection of loci that are responsible for fruit-related traits, including flesh color in melon.
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References
Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J (2015) Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics 16:4. https://doi.org/10.1186/s12864-014-1196-3
Aubert C, Bourger N (2004) Investigation of volatiles in charentais cantaloupe melons (Cucumis melo Var. cantalupensis). Characterization of aroma constituents in some cultivars. J Agric Food Chem 52:4522–4528. https://doi.org/10.1021/jf049777s
Blanca JM, Cañizares J, Ziarsolo P, Esteras C, Mir G, Nuez F, Garcia-Mas J, Picó MB (2011) Melon transcriptome characterization: simple sequence repeats and single nucleotide polymorphisms discovery for high throughput genotyping across the species. Plant Genome 4:118–131. https://doi.org/10.3835/plantgenome2011.01.0003
Blanca J, Esteras C, Ziarsolo P, Pérez D, Fernández-Pedrosa V, Collado C, RodrÃguez de Pablos R, Ballester A, Roig C et al (2012) Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics 13:280. https://doi.org/10.1186/1471-2164-13-280
Causse M, Desplat N, Pascual L, Le Paslier M-C, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M et al (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14:791. https://doi.org/10.1186/1471-2164-14-791
Chayut N, Yuan H, Ohali S, Meir A, Yeselson Y, Portnoy V, Zheng Y, Fei Z, Lewinsohn E et al (2015) A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with orange allelic variation and fruit β-carotene accumulation in melon fruit. BMC Plant Biol 15:274. https://doi.org/10.1186/s12870-015-0661-8
Dreher K, Morris M, Khairallah M, Ribaut JM, Pandey S, Srinivasan G (2002) Is marker-assisted selection cost-effective compared to conventional plant breeding methods? The case of quality protein maize. In: Proceedings of the 4th annual conference of the international consortium on agricultural biotechnology research (ICABR’00), pp 203–236
Esteras C, Formisano G, Roig C, Díaz A, Blanca J, Garcia-Mas J, Gómez-Guillamón ML, López-Sesé AI, Lázaro A et al (2013) SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theor Appl Genet 126:1285–1303. https://doi.org/10.1007/s00122-013-2053-5
Fukino N, Ohara T, Monforte AJ, Sugiyama M, Sakata Y, Kunihisa M, Matsumoto S (2008) Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.). Theor Appl Genet 118:165–175. https://doi.org/10.1007/s00122-008-0885-1
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci 109:11872–11877. https://doi.org/10.1073/pnas.1205415109
Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58. https://doi.org/10.1038/ng.2470
Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18. https://doi.org/10.1038/hdy.2008.35
Han B, Rhee S, Jang Y, Sim T, Kim J, Park T, Lee G (2016) Identification of a causal pathogen of watermelon powdery mildew in Korea and development of a genetic linkage marker for resistance in watermelon (Citrullus lanatus). Korean J Hortic Sci Technol 34:912–925. https://doi.org/10.12972/kjhst.20160095
Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281. https://doi.org/10.1038/ng.475
Ibrahim SRM, Mohamed GA (2015) Cucumin S, a new phenylethyl chromone from Cucumis melo var. reticulatus seeds. Rev Bras Farmacogn 25:462–464
Jeong IS, Yoon UH, Lee GS, Ji HS, Lee HJ, Han CD, Hahn JH, An G, Kim TH (2013) SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing. Rice 6:6. https://doi.org/10.1186/1939-8433-6-6
Kabelka E, Franchino B, Francis DM (2002) Two Loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. michiganensis. Phytopathology 92:504–510. https://doi.org/10.1094/PHYTO.2002.92.5.504
Kaçar YA, Simsek O, Solmaz I, Sari N, Mendi YY (2012) Genetic diversity among melon accessions (Cucumis melo) from Turkey based on SSR markers. Genet Mol Res 11:4622–4631. https://doi.org/10.4238/2012.November.29.2
Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278. https://doi.org/10.1038/ng.2877
Lester G (1997) Melon (Cucumis melo L.) fruit nutritional quality and health functionality. Horttechnology 7:222–227
Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C, Bendahmane A (2009) A transposon-induced epigenetic change leads to sex determination in melon. Nature 461:1135–1138. https://doi.org/10.1038/nature08498
Morata J, Puigdomènech P (2017) Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes. BMC Genomics 18:138. https://doi.org/10.1186/s12864-017-3529-5
Natarajan S, Kim HT, Thamilarasan SK, Veerappan K, Park JI, Nou IS (2016) Whole genome re-sequencing and characterization of powdery mildew disease-associated allelic variation in melon. PLoS ONE 11:e0157524. https://doi.org/10.1371/journal.pone.0157524
Nuñez-Palenius HG, Gomez-Lim M, Ochoa-Alejo N, Grumet R, Lester G, Cantliffe DJ (2008) Melon fruits: genetic diversity, physiology, and biotechnology features. Crit Rev Biotechnol 28:13–55. https://doi.org/10.1080/07388550801891111
Pavan S, Marcotrigiano AR, Ciani E, Mazzeo R, Zonno V, Ruggieri V, Lotti C, Ricciardi L (2017) Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools. BMC Genomics 18:59. https://doi.org/10.1186/s12864-016-3429-0
Périn C, Gomez-Jimenez M, Hagen L, Dogimont C, Pech JC, Latché A, Pitrat M, Lelièvre JM (2002) Molecular and genetic characterization of a non-climacteric phenotype in melon reveals two loci conferring altered ethylene response in fruit. Plant Physiol 129:300–309. https://doi.org/10.1104/pp.010613
Perpiñá G, Esteras C, Gibon Y, Monforte AJ, Picó B (2016) A new genomic library of melon introgression lines in a cantaloupe genetic background for dissecting desirable agronomical traits. BMC Plant Biol 16:154. https://doi.org/10.1186/s12870-016-0842-0
Phan NT, Sim S (2017) Genomic tools and their implications for vegetable breeding. Hortic Sci Technol 35:149–164. https://doi.org/10.12972/kjhst.20170018
Pitrat M (2013) Phenotypic diversity in wild and cultivated melons (Cucumis melo). Plant Biotechnol 30:273–278
Ramamurthy RK, Waters BM (2015) Identification of fruit quality and morphology QTLs in melon (Cucumis melo) using a population derived from flexuosus and cantalupensis botanical groups. Euphytica 204:163–177. https://doi.org/10.1007/s10681-015-1361-z
Ritschel PS, de Lins TCL, Tristan RL, Buso GSC, Buso JA, Ferreira ME (2004) Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.). BMC Plant Biol 4:9. https://doi.org/10.1186/1471-2229-4-9
Rohlf FJ (2008) NTSYSpc: numerical taxonomy system, version 2.20. Exeter Publishing, Setauket
Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM (2015) Transposon insertions, structural variations, and SNPS contribute to the evolution of the melon genome. Mol Biol Evol 32:2760–2774. https://doi.org/10.1093/molbev/msv152
Serra-Soriano M, Navarro JA, Genoves A, Pallás V (2015) Comparative proteomic analysis of melon phloem exudates in response to viral infection. J Proteomics 124:11–24
Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL (2006) Whole-genome genotyping with the single-base extension assay. Nat Methods 3:31–33. https://doi.org/10.1038/nmeth842
The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. https://doi.org/10.1038/nature11119
Tzuri G, Zhou X, Chayut N, Yuan H, Portnoy V, Meir A, Sa’ar U, Baumkoler F, Mazourek M et al (2015) A ‘golden’ SNP in CmOr governs the fruit flesh color of melon (Cucumis melo). Plant J 82:267–279. https://doi.org/10.1111/tpj.12814
Wolbang CM, Fitos JL, Treeby MT (2008) The effect of high pressure processing on nutritional value and quality attributes of Cucumis melo L. Innov Food Sci Emerg Technol 9:196–200
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This work was supported by the National Agricultural Genome Program (Project No. PJ01043804), Rural Development Administration, Republic of Korea to S. Sim.
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Sim, SC., Nguyen, N.N., Kim, N. et al. Whole-genome resequencing reveals genome-wide single nucleotide polymorphisms between orange-fleshed and green-fleshed melons. Hortic. Environ. Biotechnol. 59, 275–283 (2018). https://doi.org/10.1007/s13580-018-0030-2
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DOI: https://doi.org/10.1007/s13580-018-0030-2