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dc.contributor.author | Gonzalo, M.J. | es_ES |
dc.contributor.author | Díaz Bermúdez, Aurora | es_ES |
dc.contributor.author | Dhillon, Narinder P. S. | es_ES |
dc.contributor.author | Reddy, Umesh K. | es_ES |
dc.contributor.author | Picó Sirvent, María Belén | es_ES |
dc.contributor.author | Monforte Gilabert, Antonio José | es_ES |
dc.date.accessioned | 2020-11-10T04:33:08Z | |
dc.date.available | 2020-11-10T04:33:08Z | |
dc.date.issued | 2019-06-03 | es_ES |
dc.identifier.issn | 1471-2164 | es_ES |
dc.identifier.uri | http://hdl.handle.net/10251/154506 | |
dc.description.abstract | [EN] BackgroundThe importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. In this study, a sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data.ResultsA set of 6158 informative Single Nucleotide Polymorphism (SNP) in 175 melon accessions was generated. Melon germplasm could be classified into six major groups, in concordance with horticultural groups. Indian group was in the center of the diversity plot, with the highest genetic diversity. No strict genetic differentiation between wild and cultivated accessions was appreciated in this group. Genomic regions likely involved in the process of diversification were also found. Interestingly, some SNPs differentiating inodorus and cantalupensis groups are linked to Quantitiative Trait Loci involved in ripening behavior (a major characteristic that differentiate those groups). Linkage disequilibrium was found to be low (17kb), with more rapid decay in euchromatic (8kb) than heterochromatic (30kb) regions, demonstrating that recombination events do occur within heterochromatn, although at lower frequency than in euchromatin. Concomitantly, haplotype blocks were relatively small (59kb). Some of those haplotype blocks were found fixed in different melon groups, being therefore candidate regions that are involved in the diversification of melon cultivars.ConclusionsThe results support the hypothesis that India is the primary center of diversity of melon, Occidental and Far-East cultivars have been developed by divergent selection. Indian germplasm is genetically distinct from African germplasm, supporting independent domestication events. The current set of traditional Indian accessions may be considered as a population rather than a standard collection of fixed landraces with high intercrossing between cultivated and wild melons. | es_ES |
dc.description.sponsorship | This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO)-FEDER grant AGL2015-64625-C2-R to AJM (project conception, experiments, data acquisition and analysis, manuscript writing, publication costs), AGL2017-85563-C2-1-R and the PROMETEO/2017/078 grant funded by Generalitat Valenciana (Conselleria d'Educacio, Investigacio, Cultura i Esport) to BP (project conception, provide samples and manuscript drafting). AD was supported by a Jae-Doc contract from CSIC (experiments and manuscript drafting). | es_ES |
dc.language | Inglés | es_ES |
dc.publisher | Springer (Biomed Central Ltd.) | es_ES |
dc.relation.ispartof | BMC Genomics | es_ES |
dc.rights | Reconocimiento (by) | es_ES |
dc.subject | Cucumis melo | es_ES |
dc.subject | SNP | es_ES |
dc.subject | Haplotype | es_ES |
dc.subject | Genetic structure | es_ES |
dc.subject | Diversity | es_ES |
dc.subject | Linkage disequilibrium | es_ES |
dc.subject.classification | GENETICA | es_ES |
dc.title | Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis | es_ES |
dc.type | Artículo | es_ES |
dc.identifier.doi | 10.1186/s12864-019-5784-0 | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/MINECO//AGL2015-64625-C2-2-R/ES/EVOLUCION Y DIVERSIFICACION EN CUCUMIS. GENETICA DE LA DOMESTICACION, MORFOLOGIA DE FRUTO Y BARRERAS REPRODUCTIVAS/ | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/GVA//PROMETEO%2F2017%2F078/ES/Selección de variedades tradicionales y desarrollo de nuevas variedades de cucurbitáceas adaptadas a la producción ecológica/ | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2017-85563-C2-1-R/ES/CONTROL MULTIDISCIPLINAR DE ENFERMEDADES FUNGICAS Y VIROSIS EN MELON Y SANDIA: UN NUEVO RETO/ | es_ES |
dc.rights.accessRights | Abierto | es_ES |
dc.contributor.affiliation | Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia | es_ES |
dc.contributor.affiliation | Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes | es_ES |
dc.description.bibliographicCitation | Gonzalo, M.; Díaz Bermúdez, A.; Dhillon, NPS.; Reddy, UK.; Picó Sirvent, MB.; Monforte Gilabert, AJ. (2019). Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis. BMC Genomics. 20:1-13. https://doi.org/10.1186/s12864-019-5784-0 | es_ES |
dc.description.accrualMethod | S | es_ES |
dc.relation.publisherversion | https://doi.org/10.1186/s12864-019-5784-0 | es_ES |
dc.description.upvformatpinicio | 1 | es_ES |
dc.description.upvformatpfin | 13 | es_ES |
dc.type.version | info:eu-repo/semantics/publishedVersion | es_ES |
dc.description.volume | 20 | es_ES |
dc.identifier.pmid | 31159730 | es_ES |
dc.identifier.pmcid | PMC6547464 | es_ES |
dc.relation.pasarela | S\406591 | es_ES |
dc.contributor.funder | Generalitat Valenciana | es_ES |
dc.contributor.funder | Agencia Estatal de Investigación | es_ES |
dc.contributor.funder | European Regional Development Fund | es_ES |
dc.contributor.funder | Ministerio de Economía y Competitividad | es_ES |
dc.description.references | Munger HM, Robinson RW. Nomenclature of Cucumis melo L. Cucurbit Genet Coop Rep. 1991;14:43–4. | es_ES |
dc.description.references | Pitrat M, Hanelt P, Hammer K. Some comments on infraspecific classification of cultivars of melon. Proc Cucurbitaceae. 2000;2000(510):29–36. | es_ES |
dc.description.references | Pitrat M. Melon genetic resources: phenotypic diversity and horticultural taxonomy. In: Grumet R, Katzir N, editors. Genetics and genomics of the Cucurbitaceae. New York: J Garcia-Mas Springer; 2017. p. 25–60. | es_ES |
dc.description.references | Stepansky A, Kovalski I, Perl-Treves R. Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation. Plant Syst Evol. 1999;217(3–4):313–32. | es_ES |
dc.description.references | Monforte AJ, Garcia-Mas J, Arus P, Minch E. Genetic variability in melon based on microsatellite variation. Plant Breed. 2003;122(2):153–7. | es_ES |
dc.description.references | Esteras C, Formisano G, Roig C, Diaz A, Blanca J, Garcia-Mas J, Gomez-Guillamon ML, Lopez-Sese AI, Lazaro A, Monforte AJ, et al. SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theor Appl Genet. 2013;126(5):1285–303. | es_ES |
dc.description.references | Sebastian P, Schaefer H, Telford IRH, Renner SS. Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci U S A. 2010;107(32):14269–73. | es_ES |
dc.description.references | Newton C. Growing, gathering and offering: predynastic plant economy at Adaïma (upper Egypt). In: R. Cappers Groningen Institute of Archaeology, editor. Fields of change: progress in African archaeobotany; 2007. p. 139–55. | es_ES |
dc.description.references | Paris HS. Overview of the origins and history of the five major cucurbit crops: issues for ancient DNA analysis of archaeological specimens. Veg Hist Archaeobotany. 2016;25(4):405–14. | es_ES |
dc.description.references | Sabato D, Esteras C, Oscar G, Peña-Chocarro L, Leida C, Ucchesu M, Usai A, Bacchetta G, Pico B. Molecular and morphological characterisation of the oldest Cucumis melo L. seeds found in the Western Mediterranean Basin. Archaeol. Anthropol. Sci. 2017;11(3):789–810. | es_ES |
dc.description.references | Serres-Giardi L, Dogimont C. How microsatellite diversity helps to understand the domestication history of melon. In: Cucurbitaceae 2012: proceedings of the Xth Eucarpia meeting on genetics and breeding of Cucurbitaceae; 2012. p. 254–63. | es_ES |
dc.description.references | Endl J, Achigan-Dako EG, Pandey AK, Monforte AJ, Pico B, Schaefer H. Repeated domestication of melon (Cucumis melo) in Africa and Asia and a new close relative from India. Am J Bot. 2018;105(10):1662–71. | es_ES |
dc.description.references | Dhillon NPS, Ranjana R, Singh K, Eduardo I, Monforte AJ, Pitrat M, Dhillon NK, Singh PP. Diversity among landraces of Indian snapmelon (Cucumis melo var. momordica). Genet Resour Crop Evol. 2007;54(6):1267–83. | es_ES |
dc.description.references | Dhillon NPS, Singh J, Fergany M, Monforte AJ, Sureja K. Phenotypic and molecular diversity among landraces of snapmelon (Cucumis melo var. momordica) adapted to the hot and humid tropics of eastern India. Plant Genet Resour. 2009;7(3):291–300. | es_ES |
dc.description.references | Fergany M, Kaur B, Monforte AJ, Pitrat M, Rys C, Lecoq H, Dhillon NPS, Dhaliwal SS. Variation in melon (Cucumis melo) landraces adapted to the humid tropics of southern India. Genet Resour Crop Evol. 2011;58(2):225–43. | es_ES |
dc.description.references | Roy A, Bal SS, Fergany M, Kaur S, Singh H, Malik AA, Singh J, Monforte AJ, Dhillon NPS. Wild melon diversity in India (Punjab state). Genet Resour Crop Evol. 2012;59(5):755–67. | es_ES |
dc.description.references | Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379. | es_ES |
dc.description.references | Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011;12(7):499–510. | es_ES |
dc.description.references | Nimmakayala P, Tomason YR, Abburi VL, Alvarado A, Saminathan T, Vajja VG, Salazar G, Panicker GK, Levi A, Wechter WP, et al. Genome-wide differentiation of various melon horticultural groups for use in GWAS for fruit firmness and construction of a high resolution genetic map. Front Plant Sci. 2016;7:1437. | es_ES |
dc.description.references | Gur A, Tzuri G, Meir A, Sa'ar U, Portnoy V, Katzir N, Schaffer AA, Li L, Burger J, Tadmor Y. Genome-wide linkage-disequilibrium mapping to the candidate gene level in melon (Cucumis melo). Sci Rep. 2017;7:9770. | es_ES |
dc.description.references | Pavan S, Marcotrigiano AR, Ciani E, Mazzeo R, Zonno V, Ruggieri V, Lotti C, Ricciardi L. 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. 2017;18:59. | es_ES |
dc.description.references | Deleu W, Esteras C, Roig C, González-To M, Fernández-Silva I, Gonzalez-Ibeas D, Blanca J, Aranda MA, Arús P, Nuez F, Monforte AJ, Picó M, Garcia-Mas J. A set of EST-SNPs for map saturation and cultivar identification in melon. BMC Plant Biology. 2009;9(1):90. | es_ES |
dc.description.references | Leida C, Moser C, Esteras C, Sulpice R, Lunn JE, de Langen F, Monforte AJ, Pico B. Variability of candidate genes, genetic structure and association with sugar accumulation and climacteric behavior in a broad germplasm collection of melon (Cucumis melo L.). BMC Genet. 2015;16:28. | es_ES |
dc.description.references | Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X, et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet. 2013;45(12):1510–U1149. | es_ES |
dc.description.references | Wang Y-L, Gao L-Y, Yang S-Y, Xu Y-B, Zhu H-Y, Yang L-M, Li Q, Hu J-B, Sun S-R, Ma C-S. Molecular diversity and population structure of oriental thin-skinned melons, Cucumis melo subsp agrestis, revealed by a set of core SSR markers. Sci Hortic. 2018;229:59–64. | es_ES |
dc.description.references | Zhang Y, Fan X, Aierken Y, Ma X, Yi H, Wu M. Genetic diversity of melon landraces (Cucumis melo L.) in the Xinjiang Uygur autonomous region on the basis of simple sequence repeat markers. Genet Resour Crop Evol. 2017;64(5):1023–35. | es_ES |
dc.description.references | Omari S, Kamenir Y, Benichou JIC, Pariente S, Sela H, Perl-Treves R. Landraces of snake melon, an ancient middle eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement. BMC Genet. 2018;19:34. | es_ES |
dc.description.references | Tomason Y, Nimmakayala P, Levi A, Reddy UK. Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon. Mol Breed. 2013;31(4):829–41. | es_ES |
dc.description.references | Vegas J, Garcia-Mas J, Monforte AJ. Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening. Theor Appl Genet. 2013;126(6):1531–44. | es_ES |
dc.description.references | Rios P, Argyris J, Vegas J, Leida C, Kenigswald M, Tzuri G, Troadec C, Bendahmane A, Katzir N, Pico B, et al. ETHQV6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor. Plant J. 2017;91(4):671–83. | es_ES |
dc.description.references | Moreno E, Obando JM, Dos-Santos N, Fernandez-Trujillo JP, Monforte AJ, Garcia-Mas J. Candidate genes and QTLs for fruit ripening and softening in melon. Theor Appl Genet. 2008;116(4):589–602. | es_ES |
dc.description.references | Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J. Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics. 2015;16:4. | es_ES |
dc.description.references | Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R. Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor Appl Genet. 2011;122(3):523–31. | es_ES |
dc.description.references | Vos PG, Paulo MJ, Voorrips RE, Visser RGF, van Eck HJ, van Eeuwijk FA. Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato. Theor Appl Genet. 2017;130(1):123–35. | es_ES |
dc.description.references | Ruggieri V, Francese G, Sacco A, D'Alessandro A, Rigano MM, Parisi M, Milone M, Cardi T, Mennella G, Barone A. An association mapping approach to identify favourable alleles for tomato fruit quality breeding. BMC Plant Biol. 2014;14:337. | es_ES |
dc.description.references | Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M. Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by genome wide association study. Theor Appl Genet. 2017;130(5):875–89. | es_ES |
dc.description.references | Dhillon NPS, Monforte AJ, Pitrat M, Pandey S, Singh PK, et al. Melon landraces of India: contributions and importance. Plant Breeding Rev. 2012;35:85–150. | es_ES |
dc.description.references | Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, Henaff E, Camara F, Cozzuto L, Lowy E, et al. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A. 2012;109(29):11872–7. | es_ES |
dc.description.references | Yoo J, Lee Y, Kim Y, Rha SY, Kim Y. SNP analyzer 2.0: a web-based integrated workbench for linkage disequilibrium analysis and association analysis. BMC Bioinf. 2008;9:290. | es_ES |
dc.description.references | Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23(19):2633–5. | es_ES |
dc.description.references | Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–59. | es_ES |
dc.description.references | Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14(8):2611–20. | es_ES |
dc.description.references | Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinforma. 2005;1:47–50. | es_ES |
dc.description.references | Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population-structure. Evolution. 1984;38(6):1358–70. | es_ES |
dc.description.references | Peltier J. LOESS utility for excel. Peltier Tech Blog. http://peltiertech.com/WordPress/loess-smoothing-in-excel . 2009. | es_ES |