- -

An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing.

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by

Statistics

An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing.

Show simple item record

Files in this item

dc.contributor.author Montero-Pau, Javier es_ES
dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Esteras Gómez, Cristina es_ES
dc.contributor.author Martínez Pérez, Eva María es_ES
dc.contributor.author GOMEZ P es_ES
dc.contributor.author Monforte Gilabert, Antonio José es_ES
dc.contributor.author Cañizares Sales, Joaquín es_ES
dc.contributor.author Picó Sirvent, María Belén es_ES
dc.date.accessioned 2018-06-08T04:22:30Z
dc.date.available 2018-06-08T04:22:30Z
dc.date.issued 2017 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/103607
dc.description.abstract [EN] Background: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. Results: We report the Genotyping-by-sequencing analysis of a RIL population developed from the inter subspecific cross Zucchini x Scallop (ssp. pepo x ssp. ovifera). Several thousands of SNP markers were identified and genotyped, followed by the construction of a high-density linkage map based on 7,718 SNPs (average of 386 markers/linkage group) covering 2,817.6 cM of the whole genome, which is a great improvement with respect to previous maps. A QTL analysis was performed using phenotypic data obtained from the RIL population from three environments. In total, 48 consistent QTLs for vine, flowering and fruit quality traits were detected on the basis of a multiple-environment analysis, distributed in 33 independent positions in 15 LGs, and each QTL explained 1.5 62.9% of the phenotypic variance. Eight major QTLs, which could explain greater than 20% of the phenotypic variation were detected and the underlying candidate genes identified. Conclusions: Here we report the first SNP saturated map in the species, anchored to the physical map. Additionally, several consistent QTLs related to early flowering, fruit shape and length, and rind and flesh color are reported as well as candidate genes for them. This information will enhance molecular breeding in C. pepo and will assist the gene cloning underlying the studied QTLs, helping to reveal the genetic basis of the studied processes in squash. es_ES
dc.description.sponsorship This work has been carried out in the framework of the INIA projects RTA2011-00044-C02-1/2 and E-RTA2013-00020-C04-03 of the Spanish Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) cofunded with FEDER funds (EU). en_EN
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation INST NAC DE INV. Y TECNOL. AGRARIA Y ALIMENT/RTA2011-00044-C02-02 es_ES
dc.relation INST NAC DE INV. Y TECNOL. AGRARIA Y ALIMENT/E_RTA2013-00020-C04-03 es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Cucurbita pepo es_ES
dc.subject RIL es_ES
dc.subject GBS es_ES
dc.subject Cartography es_ES
dc.subject Phenotyping es_ES
dc.subject Candidate genes es_ES
dc.subject.classification GENETICA es_ES
dc.title An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing. es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12864-016-3439-y es_ES
dc.rights.accessRights Abierto 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.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana es_ES
dc.description.bibliographicCitation Montero-Pau, J.; Blanca Postigo, JM.; Esteras Gómez, C.; Martínez Pérez, EM.; GOMEZ P; Monforte Gilabert, AJ.; Cañizares Sales, J.... (2017). An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing. BMC Genomics. 18(94):1-21. doi:10.1186/s12864-016-3439-y es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12864-016-3439-y es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 21 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 18 es_ES
dc.description.issue 94 es_ES
dc.identifier.pmid 28100189 en_EN
dc.identifier.pmcid PMC5241963 en_EN
dc.relation.pasarela 324140 es_ES
dc.contributor.funder INST NAC DE INV. Y TECNOL. AGRARIA Y ALIMENT es_ES
dc.relation.references FAOSTAT 2015. http://www.fao.org/faostat/en/#data/QC . Accessed 1 Apr 2016. es_ES
dc.relation.references Manzano S, Martínez C, Megias Z, Garrido D, Jamilena M. Involvement of ethylene biosynthesis and signalling in the transition from male to female flowering in the monoecious Cucurbita pepo. J Plant Growth Regul. 2013;32(4):789–98. es_ES
dc.relation.references Martínez C, Manzano S, Megias Z, Garrido D, Pico B, Jamilena M. Sources of parthenocarpy for Zucchini breeding: relationship with ethylene production and sensitivity. Euphytica. 2014;200(3):349–62. es_ES
dc.relation.references Decker-Walters DS, Walters TW, Posluszny U, Kevan PG. Genealogy and gene flow among annual domesticated species of Cucurbita. Can J Bot. 1990;68:782–9. es_ES
dc.relation.references Paris HS, Doron-Faigenboim A, Reddy UK, Donahoo R, Levi A. Genetic relationships in Cucurbita pepo (pumpkin, squash, gourd) as viewed with high frequency oligonucleotide-targeting active gene (HFO-TAG) markers. Genet Resour Crop Evol. 2015;62:1095–111. es_ES
dc.relation.references Ferriol M, Picó B, Nuez F. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor Appl Genet. 2003;107:271–82. es_ES
dc.relation.references Formisano G, Roig C, Esteras C, Ercolano MR, Nuez F, Monforte AJ, et al. Genetic diversity of Spanish Cucurbita pepo landraces: an unexploited resource for summer squash breeding. Genet Resour Crop Evol. 2012;59(6):1169–84. es_ES
dc.relation.references Paris HS. Historical records, origins, and development of the edible cultivar groups of Cucurbita pepo (Cucurbitaceae). Econ Bot. 1989;43:423–43. es_ES
dc.relation.references Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet. 2009;41:1275–81. es_ES
dc.relation.references Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, et al. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci. 2012;109:11872–7. es_ES
dc.relation.references Guo SG, Zhang JG, Sun HH, Salse J, Lucas WJ, Zhang HY, et al. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet. 2013;45(1):51–U82. es_ES
dc.relation.references Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 2011;12:104. es_ES
dc.relation.references Cucurbigene. https://cucurbigene.upv.es . Accessed 1 Apr 2016. es_ES
dc.relation.references Martínez C, Manzano S, Megías Z, Barrera A, Boualem A, Garrido D, et al. Molecular and functional characterization of CpACS27A gene reveals its involvement in monoecy instability and other associated traits in squash (Cucurbita pepo L.). Planta. 2014;239:1201–15. es_ES
dc.relation.references Paris HS. History of the cultivar-groups of Cucurbita pepo. In: Janick J, Wiley J, editors. Horticulture Review. New York, USA: John Wiley & Sons; 2000;25:71–170. es_ES
dc.relation.references Vitiello A, Scarano D, D’Agostino N, Digilio MC, Pennacchio F, Corrado G, et al. Unraveling zucchini transcriptome response to aphids. PeerJ PrePrints. 2016; https://peerj.com/preprints/1635.pdf es_ES
dc.relation.references Xanthopoulou A, Psomopoulos F, Ganopoulos I, Manioudaki M, Tsaftaris A, Nianiou-Obeidat I, et al. De novo transcriptome assembly of two contrasting pumpkin cultivars. Genomics Data. 2016;7:200–1. es_ES
dc.relation.references Lee YH, Jeon HJ, Hong KH, Kim BD. Use of random amplified polymorphic DNA for linkage group analysis in an interspecific cross hybrid F2 generation of Cucurbita. J Kor Soc Hortic Sci. 1995;36:323–30. es_ES
dc.relation.references Brown RN, Myers JR. A genetic map of squash (Cucurbita ssp.) with randomly amplified polymorphic DNA markers and morphological markers. J Am Soc Hortic Sci. 2002;127:568–75. es_ES
dc.relation.references Zraidi A, Stift G, Pachner M, Shojaeiyan A, Gong L, Lelley T. A consensus map for Cucurbita pepo. Mol Breed. 2007;20:375–88. es_ES
dc.relation.references Gong L, Pachner M, Kalai K, Lelley T. SSR-based genetic linkage map of Cucurbita moschata and its synteny with Cucurbita pepo. Genome. 2008;51:878–87. es_ES
dc.relation.references Gong L, Stift G, Kofler R, Pachner M, Lelley T. Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Theor Appl Genet. 2008;117:37–48. es_ES
dc.relation.references Esteras C, Gómez P, Monforte AJ, Blanca J, Vicente-Dólera N, Roig C, et al. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics. 2012;13:80. es_ES
dc.relation.references Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011;6(5):e19379. es_ES
dc.relation.references Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome J. 2012;5(3):92–102. es_ES
dc.relation.references Takuno S, Terauchi R, Innan H. The power of QTL mapping with RILs. PLoS ONE. 2012;7(10):e46545. es_ES
dc.relation.references GBS barcode splitter. https://sourceforge.net/projects/gbsbarcode/ . Accessed 1 Apr 2016. es_ES
dc.relation.references Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. es_ES
dc.relation.references Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. ArXiv preprint. 2012; arXiv:1207.3907. es_ES
dc.relation.references da Silva Pereira G, Di Cassia Laperuta L, Nunes ES, Chavarría L, Pastina MM, Gazaffi R, et al. The sweet passion fruit (Passiflora alata) crop: genetic and ghenotypic parameter estimates and QTL mapping for fruit traits. Tropical Plant Biol. 2016; DOI 10.1007/s12042-016-9181-4 . es_ES
dc.relation.references Broman KW, Wu H, Sen S, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003;19(7):889–90. es_ES
dc.relation.references Taylor J, Butler D. ASMap: Linkage Map Construction using the MSTmap Algorithm. R package version 0.4-5. 2015. es_ES
dc.relation.references Wu Y, Bhat PR, Close TJ, Lonardi S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 2008;4(10):e1000212. es_ES
dc.relation.references van Os H, Stam P, Visser RGF, van Eck HJ. SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet. 2005;112:187–94. es_ES
dc.relation.references Kosambi DD. The estimation of map distances from recombination values. Ann Eugenics. 1943;12:172–5. es_ES
dc.relation.references Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 2001;29:1165–88. es_ES
dc.relation.references Voorrips RE. MapChart: Software for the graphical presentation of linkage maps and QTL. J Hered. 2002;93(1):77–8. es_ES
dc.relation.references Zhang G, Ren Y, Sun H, Guo S, Zhang F, Zhang J, et al. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.). BMC Genomics. 2015;16(1):1101. es_ES
dc.relation.references Hepworth SR, Klenz JE, Haughn GW. UFO in the Arabidopsis inflorescence apex is required for floral-meristem identity and bract suppression. Planta. 2006;223(4):769–78. es_ES
dc.relation.references Baurle I, Smith L, Baulcombe DC, Dean C. Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing. Science. 2007;318:109–12. es_ES
dc.relation.references Zhang W, Fan S, Pang C, Wei H, Ma J, Song M, et al. Molecular cloning and function analysis of two SQUAMOSA-Like MADS-box genes from Gossypium hirsutum L. J Integr Plant Biol. 2013;55(7):597–607. es_ES
dc.relation.references Tsuda K, Ito Y, Sato Y, Kurata N. Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice. Plant Cell. 2011;23(12):4368–81. es_ES
dc.relation.references Li S. The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development. Plant Signal Behav. 2015;10(7):e1044192. es_ES
dc.relation.references Wanga Y, Henrikssona E, Södermana E, Henrikssona KN, Sundberga E, Engströma P. The Arabidopsis homeobox gene, ATHB16, regulates leaf development and the sensitivity to photoperiod in Arabidopsis. Dev Biol. 2003;264(1):228–39. es_ES
dc.relation.references Bou-Torrenta J, Salla-Martreta M, Brandtb R, Musielakb T, Palauquic JC, Martínez-García JF, et al. ATHB4 and HAT3, two class II HD-ZIP transcription factors, control leaf development in Arabidopsis. Plant Signal Behav. 2012;7(11):1382–7. es_ES
dc.relation.references Paris HS, Nerson H, Burger Y. Leaf silvering of Cucurbita. Can J Plant Sci. 1987;67:593–8. es_ES
dc.relation.references Shifriss O. Further notes on the silvery-leaf trait in Cucurbita. Cucurbit Genet Coop Rep. 1984;7:81–3. es_ES
dc.relation.references Paris HS, Padley Jr LD. Gene List for Cucurbita species. Cucurbit Genet Coop Rep. 2014;37:1–7. es_ES
dc.relation.references Young K, Kabelka EA. Characterization of resistance to squash silverleaf disorder in summer squash. Hortscience. 2009;44(5):1213–4. es_ES
dc.relation.references Knopf RR, Trebitsh T. The female-specific Cs-ACS1G gene of cucumber. A case of gene duplication and recombination between the non-sex-specific 1-aminocyclopropane-1-carboxylate synthase gene and a branched-chain amino acid transaminase gene. Plant Cell Physiol. 2006;47(9):1217–28. es_ES
dc.relation.references Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H, et al. A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science. 2008;321:836–8. es_ES
dc.relation.references Boualem A, Troadec C, Kovalski I, Sari MA, Perl-Treves R, Bendahmane A. A conserved ethylene biosynthesis enzyme leads to andromonoecy in two Cucumis species. PLoS One. 2009;4:e6144. es_ES
dc.relation.references Li Z, Huang S, Liu S, Pan J, Zhang Z, Tao Q, et al. Molecular isolation of the m gene suggests that a conserved-residue conversion induces the formation of bisexual flowers in cucumber plants. Genetics. 2009;182(4):1381–5. es_ES
dc.relation.references Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, et al. A transposon induced epigenetic change leads to sex determination in melon. Nature. 2009;461:1135–8. es_ES
dc.relation.references Boualem A, Troadec C, Camps C, Lemhemdi A, Morin H, Sari MA, et al. A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges. Science. 2015;350(6261):688–91. es_ES
dc.relation.references Manzano S, Martínez C, Domínguez V, Avalos E, Garrido D, Gómez P, et al. Major gene conferring reduced ethylene sensitivity and maleness in Cucurbita pepo. J Plant Growth Regul. 2010;29:73–80. es_ES
dc.relation.references Wien HC, Stapleton SC, Maynard DN, McClurg C, Riggs D. Flowering, sex expression, and fruiting of pumpkin (Cucurbita sp.) cultivars under various temperatures in greenhouse and distant field trials. Hortscience. 2004;39(2):239–42. es_ES
dc.relation.references Peñaranda A, Payan MC, Garrido D, Gómez P, Jamilena M. Production of fruits with attached flowers in zucchini squash is correlated with the arrest of maturation of female flowers. J Hortic Sci Biotech. 2007;82(4):579–84. es_ES
dc.relation.references Yoo SK, Wu X, Lee JS, Ahn JH. AGAMOUS-LIKE 6 is a floral promoter that negatively regulates the FLC/MAF clade genes and positively regulates FT in Arabidopsis. Plant J. 2011;65(1):62–76. es_ES
dc.relation.references Na X, Jian B, Yao W, Wu C, Hou W, Jiang B, et al. Cloning and functional analysis of the flowering gene GmSOC1-like, a putative SUPPRESSOR OF OVEREXPRESSION CO1/AGAMOUS-LIKE 20 (SOC1/AGL20) ortholog in soybean. Plant Cell Rep. 2013;32:1219–29. es_ES
dc.relation.references Shi P, Guy KM, Wu W, Fang B, Yang J, Zhang M, et al. Genome-wide identification and expression analysis of the ClTCP transcription factors in Citrullus lanatus. BMC Plant Biol. 2016;16:85. es_ES
dc.relation.references Lu H, Lin T, Klein J, Huang S. QTL-seq identifies an early flowering QTL located near flowering locus T in cucumber. Theor Appl Genet. 2014;127(7):1491–9. es_ES
dc.relation.references Lian G, Ding Z, Wang Q, Zhang D, Xu J. Origins and evolution of WUSCHEL-related homeobox protein family in plant kingdom. Sci World J. 2014;2014:534140. es_ES
dc.relation.references Costanzo E, Trehin C, Vandenbussche M. Review: Part of a special issue on flower development. The role of WOX genes in flower development. Ann Bot. 2014;114:1545–53. es_ES
dc.relation.references Chao QM, Rothenberg M, Solano R, Roman G, Terzaghi W, Ecker JR. Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell. 1997;89(7):1133–44. es_ES
dc.relation.references Liu J, Van Eck J, Cong B, Tanksley SD. A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci. 2002;99:13302–6. es_ES
dc.relation.references Monforte AJ, Diaz A, Caño-Delgado A, van der Knaap E. The genetic basis of fruit morphology in horticultural crops: lessons from tomato and melon. J Exp Bot. 2014;65(16):4625–37. es_ES
dc.relation.references Wang S, Chang Y, Ellis B. Overview of OVATE FAMILY PROTEINS, a novel class of plant-specific growth regulators. Front Plant Sci. 2016;7:417. es_ES
dc.relation.references Muños S, Ranc N, Botton E, Bérard A, Rolland S, Duffé P, et al. Increase in tomato locule number is controlled by two SNPs located near WUSCHEL. Plant Physiol. 2011;156(4):2244–54. es_ES
dc.relation.references Pan Y, Bradley G, Pyke K, Ball G, Lu C, Fray R, et al. Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits. Plant Physiol. 2013;161(3):1476–85. es_ES
dc.relation.references Feder A, Burger J, Gao S, Lewinsohn E, Katzir N, Schaffer AA, et al. A Kelch domain-containing F-Box coding gene negatively regulates flavonoid accumulation in muskmelon. Plant Physiol. 2015;169(3):1714–26. es_ES
dc.relation.references Monforte AJ, Oliver M, Gonzalo MJ, Alvarez JM, Dolcet-Sanjuan R, Arús P. Identification of quantitative trait loci involved in fruit quality traits in melon (Cucumis melo L.). Theor Appl Genet. 2004;108:750–8. es_ES
dc.relation.references Eduardo I, Arús P, Monforte AJ, Obando J, Fernández-Trujillo JP, Martínez JA, et al. Estimating the genetic architecture of fruit quality traits in melon using a genomic library of near isogenic lines. J Amer Soc Hort Sci. 2007;132:80–9. es_ES
dc.relation.references Nakkanong K, Yang JH, Zhang MF. Carotenoid accumulation and carotenogenic gene expression during fruit development in novel interspecific inbred squash lines and their parents. J Agric Food Chem. 2012;60(23):5936–44. es_ES
dc.relation.references Hughes MB. The inheritance of two characters of Cucumis melo and their interrelationship. Proc American Soc Horticultural Sci. 1948;52:399–402. es_ES
dc.relation.references Iman MK, Abo-Bakr MA, Hanna HY. Inheritance of some economic characters in crosses between sweet melon and snake cucumber. I. Inheritance of qualitative characters. Assiut J Ag Sco. 1972;3:363–80. es_ES
dc.relation.references Tzuri G, Zhou X, Chayut N, et al. A ‘golden’ SNP in CmOr governs the fruit flesh color of melon (Cucumis melo). Plant J. 2015;82:267–79. es_ES
dc.relation.references Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S, Cohen S, et al. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theor Appl Genet. 2010;121:511–33. es_ES
dc.relation.references Ramamurthy RK, Waters BM. Identification of fruit quality and morphology QTLs in melon (Cucumis melo) using a population derived from flexuosus and cantalupensis botanical groups. Euphytica. 2015;204:163–77. es_ES
dc.relation.references Leida C, Moser C, Esteras C, Sulpice R, Lunn JE, de Langen F, et al. 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


This item appears in the following Collection(s)

Show simple item record