Abstract
Cucurbita pepo is one of the main crops of the Cucurbitaceae family. Despite its agricultural and biological importance, genomic research on this species has started later and progresses slowerthan in other cucurbits. Here we review the latest genetic and genomic tools developed for C. pepo. A whole-genome shotgun strategy based on pair-end and mate-pair Illumina sequencing,has generated a whole genome draft of 263 Mb into 26,005 scaffolds and 32,754 contigs (contig N50:110 kb and scaffold N50:1.8 Mb). The genome sequence has been annotated using the transcriptome (73,239 unigene clusters, with an average length of 1050 bp) and anchored using a high density genetic map based on a recombinant inbred line (RIL) population (with 6763 SNPs distributed across 21 linkage groups, with a total length of 2635 cM). Further RNA-seq resequencing and GBS genotyping efforts in C.pepohave been conducted to better represent the whole species variation, including the three subspecies (pepo, ovifera and fraterna). Similar information has been generated in related cultivated (C. moschata, C. maxima, C. argyrosperma, C. ficifolia) and wild species of the Cucurbita genus, to provide a valuable insight into the Cucurbita genetic variation. These studies have generated large SNPs collections usefulfor different breeding purposes. All this sequence information along with high throughput reverse genetic tools, such as the first C.pepo TILLING population, and with new mapping populations suitable for complex trait genetic dissection, are allowing the identification of candidate genes underlying the variation of key traits for C. pepo breeding.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Andres TC. Cucurbita fraterna, the closest wild relative and progenitor of C. pepo. Cucurbit Genet Coop Rep. 1987;10:69–71.
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. 2011a;12:104.
Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J. Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence. BMC Genomics. 2011b;12:285.
Blanca J, Montero J, Esteras C, Ziarsolo P, Bombarely A, Muller K, et al. The genome of Cucurbita pepo, a tool for breeders. Book of abstracts of the ISHS international symposium on cucurbits; 2015 June 22–26, Cartagena, Spain. ISHS; 2015. p. 20.
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27(4):578–9.
Broman KW, Wu H, Sen Ś, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003;19:889–90.
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.
Conesa A, Götz S, Garcia-Gomez JM, Tero J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–6.
Decker-Walters DS. Evidence for multiple domestications of Cucurbita pepo. In: Bates DM, Robinson RW, Jeffrey C, editors. Biology and utilization of the Cucurbitaceae. New York: Cornell University Press; 1990. p. 96–101.
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.
Esteras C, Nuez F, Picó B. Genetic diversity studies in Cucurbits using molecular tools. In: Behera TK, Wang Y, Kole C, editors. Genetics, genomics and breeding of cucurbits. New Hampshire: Science Publishers Inc; 2012a. p. 140–98.
Esteras C, Gómez P, Monforte A, 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. 2012b;13:80.
FAOSTAT. Food and Agriculture Organization of the United Nations. Statistics Division [cited 2016 Feb]. Available from http://faostat3.fao.org/.
Ferriol M, Pico B, Nuez F. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor Appl Genet. 2003a;107:271–82.
Ferriol M, Picó B, Nuez F. Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SRAP markers. Genet Resour Crop Evol. 2003b;50:227–38.
Ferriol M, Picó B, Fernández de Córdov P, Nuez F. Molecular diversity of a germplasm collection of squash (Cucurbita moschata) determined by SRAP and AFLP markers. Crop Sci. 2004;44:653–64.
Ferriol M, Pico B, Nuez F. Genetic diversity of Cucurbita spp. in the Canary Islands: a bridge between America and Europe. Plant genetic resources of geographical and other islands (Conservation, evaluation and use for plant breeding). In: Proceedings of the XVII Eucarpia genetic resources section meeting, 2005 March 30 April 2, Castelsardo, Italy. CNR-ISPAAM, Sassari. p. 25–32; 2007.
Ferriol M, Picó B. Pumpkin and winter squash. In: Prohens J, Nuez F, editors. Handbook of plant breeding vegetables I Part 4. vol 1. New York: Springer; 2008. p. 317–49.
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, et al. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A. 2012;109:11872–7.
Gong L, Stift G, Kofler R, Pachner M, Lelley T. Microsatellites for the genus Cucurbitaand an SSR-based genetic linkage map of Cucurbita pepo L. Theor Appl Genet. 2008a;117:37–48.
Gong L, Pachner M, Kalai K, Lelley T. SSR-based genetic linkage map of Cucurbitamoschata and its synteny with Cucurbita pepo. Genome. 2008b;51:878–87.
Gong L, Paris HS, Nee MH, Stift G, Pachner M, Vollmann J, et al. Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms. Theor Appl Genet. 2012;124(5):875–91.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seqdata without a reference genome. Nat Biotechnol. 2011;29:644–52.
Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, et al. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet. 2013;45:51–8.
Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9:868–77.
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.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 2013;14:R47.
Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 99:138–48.
Jagadeeswaran G, Nimmakayala P, Zheng Y, Gowdu K, Reddy UK, Sunkar R. Characterization of the small RNA component of leaves and fruits from four different cucurbit species. BMC Genomics. 2012;13:329.
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 Korean Soc Hortic Sci. 1995;36:323–30.
Lee JM, Kubota C, Tsao SJ, Bie Z, Hoyos Echevarria P, Morra L, et al. Current status of vegetable grafting: diffusion, grafting techniques, automation. Sci Hortic. 2010;127:93–105.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009;25:1754–60.
Li R, Fan W, Tian G, Zhu H, He L, Cai J, et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010;463:311–7.
Li C, Li Y, Bai L, Zhang T, He C, Yan Y. Grafting-responsive miRNAs in cucumber and pumpkin seedlings identified by high-throughput sequencing at whole genome level. Physiol Plantarum. 2014;151(4):406–22.
Lira R, Tellez O, Davila P. The effects of climate change on the geographic distribution of Mexican wild relatives of domesticated Cucurbitaceae. Genet Resour Crop Evol. 2009;56(5):691–703.
Martínez C, Manzano S, Megías Z, Garrido D, Picó B, Jamilena M. Involvement of ethylene biosynthesis and signalling in fruit set and early fruit development in zucchini squash (Cucurbita pepo L.). BMC Plant Biol. 2013;13:139.
Martínez C, Manzano S, Megías Z, Barrera A, Boualem A, Garrido D, Bendahmane A, Jamilena M. 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(6):1201–15.
Paris HS. History of the cultivar-groups of Cucurbita pepo. Hortic Rev. 2000;25:71–170.
Paris HS. Germplasm enhancement of Cucurbita pepo (pumpkin, squash, gourd: Cucurbitaceae): progress and challenges. Euphytica. 2015;2015:1–24.
Paris HS, Brown RN. The genes of pumpkin and squash. HortScience. 2005;40:1620–30.
Paris HS, Kabelka E. Gene list for Cucurbita species. Cucurbit Genet Coop Rep. 2009;31–32:44–69.
Paris HS, Padley LD. Gene list for Cucurbita species. Cucurbit Genet Coop Rep. 2014;37:1–14.
Paris HS, Yonash N, Portnoy V, Mozes-Daube N, Tzuri G, Katzir N. Assessment of genetic relationships in Cucurbita pepo (Cucurbitaceae) using DNA markers. Theor Appl Genet. 2003;106:971–8.
Robinson RW, Decker-Walters DS. Cucurbits. New York: CAB International; 1997.
Sanjur OI, Piperno DR, Andres TC, Wessel-Beaver L. Phylogenetic relationships among domesticated and wild species of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene: implications for crop plant evolution and areas of origin. Proc Natl Acad Sci USA. 2002;99:535–40.
Schaefer H, Heibl C, Renner SS. Gourds afloat: a dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events. Proc R Soc Lond. 2009;276:843–51.
Smith BD. The initial domestication of Cucurbita pepo in the Americas 10,000 years ago. Science. 1997;276:932–4.
Smith BD. Seed size as a marker of domestication in C. pepo. In: Zeder MA, Bradley DG, Emshwiller E, Smith BD, editors. Documenting domestication: new genetic and archaeological paradigm. Los Angeles: University of California Press; 2006. p. 25–31.
Taylor J, Butler D. ASMap: linkage map construction using the MSTmap algorithm. R package version 0.4-1. 2015. Available from: http://cran.rproject.org/web/packages/ASMap.
Vicente-Dólera N, Troadec C, Moya M, del Río-Celestino M, Pomares-Viciana T, Bendahmane A, et al. First TILLING platform in Cucurbita pepo: a new mutant resource for gene function and crop improvement. PLoS One. 2014;119(11):e112743.
Wu T, Luo S, Wang R, Zhong Y, Xu X, Lin Y, et al. The first Illumina-based de novo transcriptome sequencing and analysis of pumpkin (Cucurbitamoschata Duch.) and SSR marker development. Mol Breed. 2014;34:1437–47.
Wyatt LE, Strickler SR, Mueller LA, Mazourek M. An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. Hortic Res. 2015;2:14070.
Xie J, Lei B, Niu M, Huang Y, Kong Q, Bie Z. High throughput sequencing of small RNAs in the two Cucurbita germplasm with different sodium accumulation patterns identifies novel microRNAs involved in salt stress response. PLoS One. 2015;10(5):e0127412.
Zraidi A, Stift G, Pachner M, Shojaeiyan A, Gong L, Lelley T. A consensus map for Cucurbita pepo. Mol Breed. 2007;20:375–88.
Acknowledgements
Authors thank to the INIA projects RTA2011-00044-C02-1/2 and E-RTA2013-00020-C04-03 of the Spanish Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and with FEDER funds (EU).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Montero-Pau, J., Esteras, C., Blanca, J., Ziarsolo, P., Cañizares, J., Picó, B. (2016). Genetics and Genomics of Cucurbita spp.. In: Grumet, R., Katzir, N., Garcia-Mas, J. (eds) Genetics and Genomics of Cucurbitaceae. Plant Genetics and Genomics: Crops and Models, vol 20. Springer, Cham. https://doi.org/10.1007/7397_2016_7
Download citation
DOI: https://doi.org/10.1007/7397_2016_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-49330-5
Online ISBN: 978-3-319-49332-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)