Genomic and biotechnological interventions for crop improvement in cucurbitaceous crops: A review

Authors

  • Chet Ram
  • MK Berwal
  • JS Gora
  • R Kumar
  • SM Haldhar
  • K Gurjar
  • D Singh

Keywords:

Cucurbitaceous crops, molecular markers, genetic transformation, CRISPR/CAS9

Abstract

The cucurbitaceous family has comprised with diverse economically important cucurbits. It primarily comprised of 118 genera and 825 species which being consumed as food worldwide since the domestication of the plants. In India, cucurbits are being grown throughout regions of the country including hot semi-arid and arid zones. With the advent of genomic breakthrough, a large number of genomic and biotechnological interventions have been developed in cucurbitaceous crops. The plenty of molecular markers are available in cucurbits and these markers were deployed to assess the genetic diversity and mapping of the QTLS/genes of interest. The success in development of genomic tools may happens by genome sequencing of mostly important cucurbitaceous crops such as watermelon, cucumber, muskmelon, bottle gourd, pumpkins. Transgenic and non-transgenic plants were developed in various cucurbitaceous crops by employing of Agrobacterium-mediated transformation and CRISPR/CAS9 approach, respectively. Thus cucurbitaceous crops have been considerably exploited at molecular level and biotechnological interventions were developed for crop improvement. However, a comprehensive report in cucurbitaceous crops regarding genomic and biotechnological developments is not available in public domain. Therefore, in the present review, we have collected the information related to genomics and biotechnology in cucurbits and emphasized on some successful interventions.

Downloads

Download data is not yet available.

References

Ando K & Grumet R. 2010. Transcriptional profiling of rapidly growing cucumber fruit by 454-pyrosequencing analysis. Journal of the American Society for Horticultural Science, 135:291-302.
Bae KM, Kwon YS, Cho IH & Yi SI. 2006. Use of cDNA-AFLP for transcript profiling in narrow genetic pools; for example, cucumber (Cucumis sativus L.). Plant Breeding, 125: 488-492.
Bhawna, Abdin MZ, Arya L, Chet Ram, Sureja AK & Verma M. 2015. Development of novel gene-based microsatellite markers for robust genotyping purposes in Lagenaria siceraria. Scientia Horticulturae, 191:15-24.
Bhawna, Abdin MZ, Arya L, Dipnarayan S, Sureja AK, Chitra P & Verma M. 2014. Population structure and genetic diversity in bottle gourd [Lagenaria siceraria (Mol.) Standl.] accession from India assessed by ISSR markers. Plant Systematics and Evolution, 300:767-773.
Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F & Pico B. 2011. Transcriptome characterization & high throughput SSRs & SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics, 12:104.
Clepet C, Joobeur T, Zheng Y, Jublot D, Huang M, Truniger V, Boualem A, Hernandez-Gonzalez ME, Dolcet-Sanjuan R, Portnoy V, Mascarell-Creus A, Caño-Delgado A, Katzir N, Bendahmane A, Giovannoni JJ, Aranda MA, Garcia-Mas J & Fei Z. 2011. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics, 12:252.
Cucurbit genomic database available at http://cucurbitgenomics.org.
Danin-Poleg Y, Tzuri G, Reis N, Karchi Z & Katzir N. 2000. Search for molecular markers associated with resistance to viruses in melon. Acta Horticulturae, 510:399-404.
Decker-Walters D, Staub J, Lopez-Sese A & Nakata E. 2001. Diversity in landraces & cultivars of bottle gourd (Lagenaria siceraria; Cucurbitaceae) as assessed by random amplified polymorphic DNA. Genetic Resources and Crop Evolution, 48:369-380.
Deleu W, Esteras C, Roig C, González-To M, Fernández-Silva I, Gonzalez-Ibeas D, Blanca J, Aranda MA, Arús P, Nuez F, Monforte MJ, Belén Picó M & Garcia-Mas J. 2009. A set of EST-SNPs for map saturation and cultivar identification in melon. BMC Plant Biology, 9:90.
Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, Staub JE, Zalapa JE, Cuevas HE, Dace G, Oliver M, Boissot N, Dogimont C, Pitrat M, Hofstede R, van Koert P, Harel-Beja R, Tzuri G, Portnoy V, Cohen S, Schaffer A, Katzir N, Xu Y, Zhang H, Fukino N, Matsumoto S, Garcia-Mas J & Monforte AJ. 2011. A consensus linkage map for molecular markers & Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biology, 11:111.
Esteras C, Gómez P, Monforte AJ, Blanca J, Vicente-Dólera N, Roig C, Nuez F & Pico B. 2012. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics, 13:8.
FAOSTAT 2015: www.fao.org/faostat.
Fernandez-silva I, Eduardo I, Blanca J, Esteras C, Pico B, Nuez F, Arus P, Garcia-Mas J & Monforte AJ. 2008. Bin mapping of genomic & EST-derived SSRs in melon (Cucumis melo L.). Theoretical and Applied Genetics, 118:139–150.
Fukino N, Yoshioka Y, Kubo N, Hirai M, Sugiyama M, Sakata Y & Matsumoto S. 2008. Development of 101 novel SSR markers & construction of an SSR-based genetic linkage map in cucumber (Cucumis sativus L.). Breed Science, 58:475–483.
Fanourakis, N.E. & P.W.Simon, 1987. Inheritance and linkage studies of the fruit epidermal structure in the cucumber. J. Hered. 78: 369–371.
Guo S, Liu J, Zheng Y, Huang M, Zhang M, Gong G, He H, Ren Y, Zhong S, Fei Z & Xu Y. 2011. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation & gene expression profiles. BMC Genomics, 12:454.
Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z, Min J, Guo X, Murat F, Ham BK, Zhang Z, Gao S, Huang M, Xu Y, Zhong S, Bombarely A, Mueller LA, Zhao H, He H, Zhang Y, Zhang Z, Huang S, Tan T, Pang E, Lin K, Hu Q, Kuang H, Ni P, Wang B, Liu J, Kou Q, Hou W, Zou X, Jiang J, Gong G, Klee K, Schoof H, Huang Y, Hu X, Dong S, Liang D, Wang J, Wu K, Xia Y, Zhao X, Zheng Z, Xing M, Liang X, Huang B, Lv T, Wang J, Yin Y, Yi H, Li R, Wu M, Levi A, Zhang X, Giovannoni JJ, Wang J, Li Y, Fei Z & Xu Y. 2013. The draft genome of watermelon (Citrullus lanatus) & resequencing of 20 diverse accessions. Nature Genetics, 45:51-58.
Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S & Fei Z. 2010. Transcriptome sequencing & comparative analysis of cucumber flowers with different sex types. BMC Genomics, 11:384.
Gwanama C, Labuschagne MT & Botha AM. 2000. Analysis of genetic variation in Cucurbita moschata by random amplified polymorphic DNA (RAPD) markers. Euphytica, 113:19-24.
Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S, Cohen S, Dai N, Yeselson L, Meir A, Libhaber SE, Avisar E, Melame T, van Koert P, Verbakel H, Hofstede R, Volpin H, Oliver M, Fougedoire A, Stalh C, Fauve J, Copes B, Fei Z, Giovannoni J, Ori N, Lewinsohn E, Sherman A, Burger J, Tadmor Y, Schaffer AA & Katzir N. 2010. A genetic map of melon highly enriched with fruit quality QTLs & EST markers, including sugar & carotenoid metabolism genes. Theoretical and Applied Genetics, 121:511–33.
Hu J, Li J, Liang F, Liu L & Si S. 2010. Genetic relationship of a cucumber germplasm collection revealed by newly developed EST-SSR markers. Journal of Genetics, 3089: 28-32.
Hu JB, Zhou XY & Li JW. 2010. Development of novel EST-SSR markers for cucumber (Cucumis sativus) and their transferability to related species. Scientia Horticulturae, 125: 534-538.
Karsies T, Dean R & Thomas C. 2000. Toward the development of molecular markers linked to race 2 fusarium wilt resistance in melon (cucumis melo l.). Acta Horticulturae, 510:415-420.
Koltun A, Corte LED, Mertz-Henning LM & Gonçalves LSA. 2018. Genetic improvement of horticultural crops mediated by CRISPR/Cas: a new horizon of possibilities. Horticultura Brasileira, 36: 290-298.
Kwon YS. 2013. Use of EST-SSR markers for genetic characterization of commercial watermelon varieties and hybrid seed purity testing. Seed Science and Technology, 41: 245-256.
Lee HS, Kwon EJ, Kwon SY, Jeong YJ, Lee EM, Jo MH, Kim HS, Woo IS, Shinmyo A, Yoshida K, Kwak SS. 2003. Transgenic cucumber fruits that produce elevated level of an anti-aging superoxide dismutase. Molecular Breeding, 11: 213.
LEE GP, KIM CS, RYU KH & RARK KW 2002. Agrobacterium-mediated transformation of Cucumis sativus expressing the coat protein gene of zucchini green mottle mosaic virus (ZGMMV). XXVIth International Horticultural Congress, Metro Toronto Convention Centre, Symposium 11, Asian plants with unique horticulture potential, genetic resources, cultural practices and utilization, S11-P-11: 300.
Li Z, Zhang Z, Yan P, Huang S, Fei Z & Lin K. 2011. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 12: 540.
Lin Y, Chen KS, Liou TD, Huang JW & Chang PFL. 2009. Development of a molecular method for rapid differentiation of watermelon lines resistant to Fusarium oxysporum f. sp. Niveum. Botanical Studies, 50:273-280.
Liu S, Gao P, Zhu Q, Luan F, Davis AR & Wang X. 2016. Development of cleaved amplified polymorphic sequence markers & a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. & Nakai) constructed using whole-genome re-sequencing data. Breeding Science, 66: 244-259.
Lu X, Adedze YMN, Chofong GN, Gandeka M, Deng Z, Teng L, Zhang X & Sun G. 2018. Identification of high-efficiency SSR markers for assessing watermelon genetic purity. Journal of Genetics, 97:1295–1306.
Meng H, Chen S, Cheng Z, Chai D & Li Y. 2012. SRAP markers for fruit shape in cucumber. Pakistan Journal of Botany, 44:1381-1384.
Oumouloud A, Arnedo-Andres MS, Gonzalez-Torres R & Alvarez JM. 2008. Development of molecular markers linked to the Fom-1locus for resistance to Fusarium race 2 in melon. Euphytica, 164: 347.
Park G, Kim N & Park Y. 2015. Genomics and molecular markers for major cucurbitaceae crops. Journal of Life Science, 25:1059-1071.
Patricia SR, Tulio CDLL, Rodrigo LT, Glaucia SCB, Jose AB & Marcio EF. 2004. Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.). BMC Plant Biology, 18: 4-9.
Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X, Du Y, Li Y, Lin T, Yuan J, Yang X, Chen J, Chen H, Xiong X, Huang K, Fei Z, Mao L, Tian L, Städler T, Renner SS, Kamoun S, Lucas WJ, Zhang Z & Huang S. 2013. A genomic variation map provides insights into the genetic basis of cucumber domestication & diversity. Nature Genetics, 45:1510–1515.
Reem NT & Van Eck J. 2019. Application of CRISPR/Cas9-mediated gene editing in tomato. In: Qi Y. (eds) Plant genome editing with CRISPR systems. Methods in molecular biology, vol. 1917. Humana Press, New York, NY.
Ren Y, McGregor C, Zhang Y, Gong G, Zhang H, Guo S. Sun H, Cai W, Zhang J & Xu Y. 2014. An integrated genetic map based on four mapping populations & quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus). BMC Plant Biology, 14: 33.
Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM & Garcia-Mas J. 2018. An improved assembly & annotation of the melon (Cucumis melo L.) reference genome. Scientific Reports, 8: 8088
Sarao NK, Pathak M, Kaur N & Kaur K. 2014. Microsatellite-based DNA fingerprinting & genetic diversity of bottle gourd genotypes. Plant Genetic Resources: Characterization and Utilization, 12: 156-159.
Şigva HO, Firat AF, Hazarhun G & Ipek A. 2015. Development of AFLP markers associated with zucchini yellow mosaic virus resistance in cucumber (Cucumis sativus L.). Turkish Journal of Botany, 39: 982-987.
Srivastava D, Khan NA, Shamim M, Yadav P, Pandey P & Singh KN. 2014. Assessment of the genetic diversity in bottle gourd (Lagenaria siceraria [Molina] Standl.) genotypes using SDS-PAGE & RAPD markers. National Academy Science Letters, 37: 155-161.
Sun H, Wu S, Zhang G, Jiao C, Guo S, Ren Y, Zhang J, Zhang H, Gong G, Jia Z, Zhang F, Tian J, Lucas WJ, Doyle JJ, Li H, Fei Z & Xu Y. 2017. Karyotype stability & unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Molecular Plant, 10:1293–1306.
Szwacka M, Krzymowska M, Osuch A, Kowalczyk ME & Malepszy S. 2002. Variable properties of transgenic cucumber plants containing the thaumatin II gene from Thaumatococcus daniellii. Acta Physiologiae Plantarum, 24:173–185.
Tian S, Jiang L, Gao Q, Zhang J, Zong M, Zhang H, Ren Y, Guo S, Gong G, Liu F & Xu Y. 2017. Efficient CRISPR/Cas9-based gene knockout in watermelon. Plant Cell Reports, 36:399–406.
Verma M & Arya L. 2015. Development of EST-SSRs in watermelon (Citrullus lanatus var. lanatus) and their transferability to Cucumis spp. Journal of Horticultural Science and Biotechnology, 83: 732-736.
Watcharawongpaiboon N & Chunwongse J. 2008. Development & characterization of microsatellite markers from an enriched genomic library of cucumber (Cucumis sativus L). Plant Breeding, 127: 74-81.
Wechter WP, Levi A, Harris KR, Davis AR, Fei Z, Katzir N, Giovannoni JJ, Salman-Minkov A, Hernandez A, Thimmapuram J, Tadmor Y, Portnoy V & Trebitsh T. 2008. Gene expression in developing watermelon fruit. BMC Genomics, 9: 275.
Wu S, Shamimuzzaman M, Sun H, Salse J, Sui X, Wilder A, Wu Z, Levi A, Xu Y, Ling KS & Fei Z. 2017. The bottle gourd genome provides insights into Cucurbitaceae evolution & facilitates mapping of a papaya ringspot virus resistance locus. The Plant Journal, 92: 963-975.
Xu P, Wu X, Luo J, Wang B, Liu Y, Ehlers JD, Wang S, Lu Z & Li G. 2011. Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding. BMC genomics, 12: 467.
Yu C, Dong W, Zhan Y, Huang ZA, Li Z, Kim IS & Zhang C. 2017. Genome-wide identification & expression analysis of CLLAX, CLPIN & CLABCB genes families in Citrullus lanatus under various abiotic stresses & grafting. BMC Genetics, 18: 33.
Zhang N, Huang X, Bao Y, Wang B, Zeng H, Cheng W, Tang M, Li Y, Ren J & Sun Y. 2017. Genome-wide identification of SAUR genes in watermelon (Citrullus lanatus). Physiology & Molecular Biology of Plants, 23: 619-628.
Zhang S, Liu S, Miao H, Wang M, Liu P, Wehner TC & Gu X. 2016. Molecular Mapping & Candidate Gene Analysis for Numerous Spines on the Fruit of Cucumber. Journal of Heredity, 107: 471–477.
Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, Reddy UK, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling K, Wechter WP, Levi A, Garcia-Mas J, Grumet R & Fei Z. 2018. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research, doi: 10.1093/nar/gky944.
Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, Yao DQ, Guo CL, Lian HL, He HL, Pan JS & Cai R. 2016. A high-density genetic linkage map for cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing & QTL analysis of fruit traits in cucumber. Frontiers in Plant Science, 7: 437.
Mujaju C, Sehic J, Werlemark G, Garkava-Gustavsson L, Fatih M & Nybom H. 2010. Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers. Hereditas, 147: 142–153.
Bradeen JM, Staub IE, Wye C, Antonise R, & Peleman J. 2001. Towards an expanded and integrated linkage map of cucumber (C. sativus L.). Genome, 44:111-119.
Fazio G, Staub JE, & Stevens MR. 2003. Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucunus sativus L.) using recombinant inbred lines. Theoretical & AppIied Genetics, 107:864-874.
Sun Z, Staub JE, Chung SM & Lower RL. 2006. Identification and comparative analysis of quantitative trait loci associated with parthenocarpy in processing cucumber. Plant Breeding, 125:281–287.
Yuan XJ, Li XZ, Pan JS, Wang G, Jiang S, Li X H, et al. 2008. Genetic linkage map construction and location of QTLs for fruit-related traits in cucumber. Plant Breeding, 127:180–188.
Pan JS, Wang G, Li XZ, He HL, Wu AZ & Cai R. 2005. Construction of a genetic map with SRAP markers and localization of the gene responsible for the first-flower-node trait in cucumber (Cucumis sativus L.). Progress in Natural Science, 15:407–413.
Sakata Y, Kubo N, Morishita M, Kitadani E, Sugiyama M & Hirai M. 2005. QTL analysis of powdery mildew resistance in cucumber (Cucumis sativus L.). Theoretical & AppIied Genetics, 112:243–250.
Li Z, Huang S, Liu S, Pan J, Zhang Z, Tao Q, et al. 2009. Molecular isolation of the M gene suggests that a conserved-residue onversion induces the formation of bisexual flowers in cucumber plants. Genetics, 182:1381–1385.
Yang XQ, Zhang WW, He HL & Nie JT. (2014). Tuberculate fruit gene Tu encodes a C2H2 zinc finger protein that is required for the warty fruit phenotype in cucumber (Cucumis sativus L.). Plant Journal, 78:1034–1046.
Xu X, Xu R, Zhu B, Yu T, Qu W, Lu L, et al. 2015. A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq). Frontiers in Plant Science, 5:768.
Bezirganoglu I, Hwang SY, Hwang SY, Shaw JF & Fang TJ. 2014. Efficient production of transgenic melon via Agrobacterium-mediated transformation. Genetics and Molecular Research, 13:3218-27.
Wang S, Ku SS, Ye X, He C, Kwon SY & Choi PS. 2015. Current status of genetic transformation technology developed in cucumber (Cucumis sativus L.). Journal of Integrative Agriculture, 14:469–482.
Vinoth A & Ravindhran R. 2015. Reduced hyperhydricity in watermelon shoot cultures using silver ions. In Vitro Cellular & Developmental Biology – Plant, 51: 258–264.
Nadolska-Orczyk, A & Malepszy S. 1989. In vitro culture of Cucumis sativus L. Theoretical & Applied Genetics, 78: 836.
Zhang N, Huang X, Bao Y, Wang B, Liu L, Dai L, Chen J, An X, Sun Y & Peng D. 2015. Genome-wide identification and expression profiling of WUSCHEL-related homeobox (WOX) genes during adventitious shoot regeneration of watermelon (Citrullus lanatus). Acta Physiologiae Plantarum, 37:224.
Nishibayashi S, Kaneko H & Hayakawa T. 1996. Transformation of cucumber (Cucumis sativus L.) plants using Agrobacterium tumefaciens and regeneration from hypocotyl explants. Plant Cell Reports, 15: 809-814.
Trulson AJ, Simpson RB & Shahin EA. 1986. Transformation of cucumber (Cucumis sativus L.) plants with Agrobacterium rhizogenes. Theoretical and Applied Genetics, 73: 11-15.
Tabei Y, Kitade S, Nishizawa Y, Kikuchi N, Kayano T, Hibi T & Akutsu K. 1998. Transgenic cucumber plants harboring a rice chitinase gene exhibit enhanced resistance to gray mold (Botrytis cinerea). Plant Cell Reports, 17: 159.
Salyaev RK, Rekoslavskaya NI & Mapelli S. 2002. Increase of productivity in transgenic plants with introduced genes UGT, ACB and ACP. 13th Congr. of the Federation of European Societies of Plant Physiology, Crete, Greece. Abstract, Section 8, Biological Applications: 49.
Yin Z, Malinowski R, Ziokowska A, Sommer H, Plider W & Malepszy S. 2006. The DefH9- iaaM containing construct efficiently induces parthenocarpy in cucumber. Cell Molecular Biology Letter, 11:279-90.
Yin Z, Pląder W, Wiśniewska A, Szwacka M & Malepszy S. 2005. Transgenic cucumber–a current state. Folia Horticulturae, 17:73-90.
Chen H, Sun J, Li S, Cui Q, Zhang H, Xin F, Wang H, Lin T, Gao D, Wang S, Li X, Wang D, Zhang Z, Xu Z & Huang S. 2016. An ACC oxidase gene essential for cucumber carpel development. Molecular Plant, 9:1315–1327.

Downloads

Published

2019-06-15

How to Cite

Ram, C., Berwal, M., Gora, J., Kumar, R., Haldhar, S., Gurjar, K., & Singh, D. (2019). Genomic and biotechnological interventions for crop improvement in cucurbitaceous crops: A review. Journal of Agriculture and Ecology, 7(7), 1–15. Retrieved from https://saaer.org.in/journals/index.php/jae/article/view/198

Most read articles by the same author(s)

1 2 3 4 > >>