Horticulture, Environment, and Biotechnology

, Volume 59, Issue 2, pp 275–283 | Cite as

Whole-genome resequencing reveals genome-wide single nucleotide polymorphisms between orange-fleshed and green-fleshed melons

  • Sung-Chur Sim
  • Nam Ngoc Nguyen
  • Nahui Kim
  • Joohnyup Kim
  • Younghoon Park
Research Report Genetics and Breeding
  • 73 Downloads

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.

Keywords

Vegetable Flesh color NGS-based SNP discovery Molecular marker 

Notes

Acknowledgements

This work was supported by the National Agricultural Genome Program (Project No. PJ01043804), Rural Development Administration, Republic of Korea to S. Sim.

Supplementary material

13580_2018_30_MOESM1_ESM.xlsx (16 kb)
Supplementary material 1 (XLSX 15 kb)
13580_2018_30_MOESM2_ESM.xlsx (15 kb)
Supplementary material 2 (XLSX 14 kb)
13580_2018_30_MOESM3_ESM.pptx (678 kb)
Supplementary material 3 (PPTX 678 kb)

References

  1. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 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 CrossRefPubMedGoogle Scholar
  3. 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 CrossRefGoogle Scholar
  4. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 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 203–236Google Scholar
  8. 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 CrossRefPubMedGoogle Scholar
  9. 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 CrossRefPubMedGoogle Scholar
  10. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 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 CrossRefPubMedGoogle Scholar
  12. 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 CrossRefPubMedGoogle Scholar
  13. 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 Google Scholar
  14. 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 CrossRefPubMedGoogle Scholar
  15. Ibrahim SRM, Mohamed GA (2015) Cucumin S, a new phenylethyl chromone from Cucumis melo var. reticulatus seeds. Rev Bras Farmacogn 25:462–464CrossRefGoogle Scholar
  16. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 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 CrossRefPubMedGoogle Scholar
  18. 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 CrossRefPubMedGoogle Scholar
  19. 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 CrossRefPubMedGoogle Scholar
  20. Lester G (1997) Melon (Cucumis melo L.) fruit nutritional quality and health functionality. Horttechnology 7:222–227Google Scholar
  21. 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 CrossRefPubMedGoogle Scholar
  22. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  24. 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 CrossRefPubMedGoogle Scholar
  25. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  27. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  28. 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 Google Scholar
  29. Pitrat M (2013) Phenotypic diversity in wild and cultivated melons (Cucumis melo). Plant Biotechnol 30:273–278CrossRefGoogle Scholar
  30. 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 CrossRefGoogle Scholar
  31. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Rohlf FJ (2008) NTSYSpc: numerical taxonomy system, version 2.20. Exeter Publishing, SetauketGoogle Scholar
  33. 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 CrossRefPubMedGoogle Scholar
  34. Serra-Soriano M, Navarro JA, Genoves A, Pallás V (2015) Comparative proteomic analysis of melon phloem exudates in response to viral infection. J Proteomics 124:11–24CrossRefPubMedGoogle Scholar
  35. 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 CrossRefPubMedGoogle Scholar
  36. 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 CrossRefGoogle Scholar
  37. 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 CrossRefPubMedGoogle Scholar
  38. 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 9:196–200CrossRefGoogle Scholar

Copyright information

© Korean Society for Horticultural Science and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Sung-Chur Sim
    • 1
    • 2
  • Nam Ngoc Nguyen
    • 1
  • Nahui Kim
    • 3
  • Joohnyup Kim
    • 3
  • Younghoon Park
    • 3
    • 4
  1. 1.Department of Bioresources EngineeringSejong UniversitySeoulRepublic of Korea
  2. 2.Plant Engineering Research InstituteSejong UniversitySeoulRepublic of Korea
  3. 3.Department of Horticultural BiosciencePusan National UniversityMiryangRepublic of Korea
  4. 4.Life and Industry Convergence Research InstitutePusan National UniversityMiryangRepublic of Korea

Personalised recommendations