Skip to main content
SpringerLink
Log in

Assessment of genetic diversity of pumpkins (Cucurbita spp.) from western Kenya using SSR molecular markers

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Pumpkins (Cucurbita spp.) are among most neglected and underutilized crops cultivated for food and medicine. The major constraint to pumpkin production is lack of genetically improved seeds. The current study was aimed at evaluating the genetic diversity of pumpkins from eight counties in western Kenya using five SSR markers. Seeds were extracted from pumpkin fruits, dried and planted on plastic trays for 4 weeks. DNA was isolated from young leaves using CTAB method and amplified. The samples were genotyped using an ABI 3730 genetic analyzer and the allelic data analyzed using Power Marker V 3.25, DARwin V 6.0.12 and GenAIEx V 6.41software. The five SSR loci were polymorphic with a total of 33 alleles and a mean PIC value of 0.534. The gene diversity and observed heterozygosity was 0.796–0.329 and 0.967–0.164, respectively. Most of genetic variations were found within and among individual samples rather than among counties, with samples of some counties having private alleles. Based on the inbreeding coefficient (F), there was outbreeding in pumpkins from Kakamega county (F = − 0.282) and inbreeding in pumpkins from Kisii, Bungoma and Nyamira counties (F = 0.500, 0.409 and 0.286 respectively). The findings of this study suggest that genetic variation and distribution of pumpkins in western Kenya was due to monocropping and intercropping farming systems, trading of pumpkins in markets and exchange of seeds among local farmers rather than geographical and climatic differences.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Liu C, Ge Y, Wang DJ, Li X, Yang XX, Cui CS, Qu SP (2013) Morphological and molecular diversity in a germplasm collection of seed pumpkin. Sci Hortic 154:8–16. https://doi.org/10.1016/j.scienta.2013.02.015

    Article  CAS  Google Scholar 

  2. Paris HS (2010) History of the Cultivar-Groups Of Cucurbita pepo. Hortic Rev. https://doi.org/10.1002/9780470650783.ch2

    Article  Google Scholar 

  3. Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12(1):104. https://doi.org/10.1186/1471-2164-12-104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Greenway PJ (1945) Origins of some East African food plants: part III. East Afr Agric J 10(1):34–39. https://doi.org/10.1080/03670074.1945.11664438

    Article  Google Scholar 

  5. Kim MY, Kim EJ, Kim YN, Choi C, Lee BH (2012) Comparison of the chemical compositions and nutritive values of various pumpkin (Cucurbitaceae) species and parts. Nutr Res Pract 6(1):21–27

    Article  CAS  Google Scholar 

  6. Rozy M, Evans C, Nicholas K, Joseph P (2016) Characterization and documentation of factors contributing to production and consumption of African leafy vegetables (ALVs) in Kiambu and Kirinyaga Counties in Kenya. Asian Res J Agric. https://doi.org/10.9734/arja/2016/28734

    Article  Google Scholar 

  7. Gwanama C, Labuschagne MT, Botha AM (2000) Analysis of genetic variation in Cucurbita moschata by random amplified polymorphic DNA (RAPD) markers. Euphytica 113(1):34–39. https://doi.org/10.1023/A:1003936019095

    Article  Google Scholar 

  8. Ndinya CA (2019) The genetic diversity of popular African leafy vegetables in western Kenya. Genetic diversity in horticultural plants. Springer, Cham, pp 127–159

    Chapter  Google Scholar 

  9. Gotor E, Irungu C (2010) The impact of Bioversity International’s African leafy vegetables programme in Kenya. Impact Assess Proj Apprais 28(1):41–55. https://doi.org/10.3152/146155110X488817

    Article  Google Scholar 

  10. Chelang’a PK, Obare GA, Kimenju SC (2013) Analysis of urban consumers’ willingness to pay a premium for African Leafy Vegetables (ALVs) in Kenya: a case of Eldoret Town. Food Secur 5(4):591–595. https://doi.org/10.1007/s12571-013-0273-9

    Article  Google Scholar 

  11. Barzegar R, Peyvast G, Ahadi AM, Rabiei B, Ebadi AA, Babagolzadeh A (2013) Biochemical systematic, population structure and genetic variability studies among Iranian Cucurbita (Cucurbita pepo L.) accessions, using genomic SSRs and implications for their breeding potential. Biochem Syst Ecol 50:187–198. https://doi.org/10.1016/j.bse.2013.03.048

    Article  CAS  Google Scholar 

  12. Soltani F, Karimi R, Kashi A (2017) Estimation of genetic diversity in Cucurbita species using morphological and phytochemical analysis. Int J Vege Sci 23(1):42–53. https://doi.org/10.1080/19315260.2016.1174968

    Article  Google Scholar 

  13. Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P (2017) Application of molecular markers in plant genome analysis: a review. Nucleus 60(3):283–297. https://doi.org/10.1007/s13237-017-0214-7

    Article  Google Scholar 

  14. Vieira MLC, Santini L, Diniz AL, Munhoz CD (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39(3):312–328. https://doi.org/10.1590/1678-4685-GMB-2016-0027

    Article  PubMed  PubMed Central  Google Scholar 

  15. Doyle J (1991) DNA protocols for plants. In: Hewitt G, Johnston AB, Young JP (eds) Molecular techniques in taxonomy, vol 57. Springer, Berlin, pp 283–293

    Chapter  Google Scholar 

  16. Watcharawongpaiboon N, Chunwongse J (2007) Development and characterization of microsatellite markers from an enriched genomic library of pumpkin (Cucurbita moschata L.) Songklanakarin. J Sci Technol 29(5):1217–1223

    Google Scholar 

  17. Nei M (2013) Genetic distance. Brenner’s encyclopedia of genetics, 2nd edn. Elsevier, Amstterdam, pp 248–250

    Chapter  Google Scholar 

  18. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x

    Article  Google Scholar 

  19. Peakall R, Smouse PE (2012) GenAlEx tutorials-part 2: genetic distance and analysis of molecular variance (AMOVA). Bioinfo 28(19):2537–2539

    Article  CAS  Google Scholar 

  20. Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int. https://doi.org/10.1155/2015/431487

    Article  PubMed  PubMed Central  Google Scholar 

  21. Kaźmińska K, Sobieszek K, Targońska-Karasek M, Korzeniewska A, Niemirowicz-Szczytt K, Bartoszewski G (2017) Genetic diversity assessment of a winter squash and pumpkin (Cucurbita maxima Duchesne.) germplasm collection based on genomic Cucurbita-conserved SSR markers. Sci Hortic 219:37–44. https://doi.org/10.1016/j.scienta.2017.02.035

    Article  Google Scholar 

  22. Enríquez E, Landaverde-González P, Lima-Cordón R, Solórzano-Ortíz E, Tapia-López R, Nuñez-Farfán J (2018) Population genetics of traditional landraces of Cucurbita pepo L., 1753 in the cloud forest in Baja Verapaz, Guatemala. Genet Resour Crop Evol 65(3):979–991. https://doi.org/10.1007/s10722-017-0589-y

    Article  Google Scholar 

  23. Sánchez-de La Vega G, Castellanos-Morales G, Gámez N, Hernández-Rosales HS, Vázquez-Lobo A, Aguirre-Planter E et al (2018) Genetic resources in the “calabaza pipiana” squash (Cucurbita argyrosperma) in mexico: genetic diversity, genetic differentiation and distribution models. Front Plant Sci 9:400. https://doi.org/10.3389/fpls.2018.00400

    Article  PubMed  PubMed Central  Google Scholar 

  24. Frankham R (2005) Genetics and extinction. Biol Conserv 126(2):131–140. https://doi.org/10.1016/j.biocon.2005.05.002

    Article  Google Scholar 

  25. González-Jara P, Moreno-Letelier A, Fraile A, Piñero D, García-Arenal F (2011) Impact of human management on the genetic variation of wild pepper, Capsicum annuum var. glabriusculum. PLoS ONE. https://doi.org/10.1371/journal.pone.0028715

    Article  PubMed  PubMed Central  Google Scholar 

  26. Kiramana JK, Isutsa DK, Nyende AB (2017) Fluorescent SSR markers and capillary electrophoresis reveal significant genetic diversity in naturalized pumpkin accessions in Kenya. Glob J Biosci Biotechnol 6(1):34–45

    Google Scholar 

  27. Barboza N, Albertazzi FJ, Sibaja-Cordero JA, Mora-Umaña F, Astorga C, Ramírez P (2012) Analysis of genetic diversity of Cucurbita moschata (D.) germplasm accessions from Mesoamerica revealed by PCR SSCP and chloroplast sequence data. Sci Hortic 134:60–71. https://doi.org/10.1016/j.scienta.2011.10.028

    Article  CAS  Google Scholar 

  28. Kitavi MN, Kiambi DK, Haussman B, Semagn K, Muluvi G, Kairichi M, Machuka J (2014) Assessment of the genetic diversity and pattern of relationship of West African sorghum accessions using microsatellite markers. Afr J Biotechnol. https://doi.org/10.5897/AJB08.1030

    Article  Google Scholar 

  29. Titus OM, Eliud KN, Silas DO, Eunice M, Solomon IS (2015) The population structure of wild sorghum species in agro-ecological zones of Western Kenya. Afr J Biotechnol 14(17):1475–1492. https://doi.org/10.5897/ajb2015.14514

    Article  Google Scholar 

  30. Ekhuya NA, Wesonga JM, Abukutsa-Onyango MO (2018) Production, processing and storage techniques of African nightshade (solanum spp.) seeds and their correlations with farmers’ characteristics in western Kenya. Afr J Food Agric Nutr Dev 18(2):13338–13351

    Google Scholar 

Download references

Acknowledgements

The authors thank the Department of Biochemistry and Biotechnology, Technical University of Kenya for facilitating the study.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya

    Lameck A. Nyabera & Steven M. Runo

  2. Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya

    Peris W. Amwayi

  3. Africa Biosystems Limited, Nairobi, Kenya

    Inosters W. Nzuki

Authors
  1. Lameck A. Nyabera
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Inosters W. Nzuki
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Steven M. Runo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Peris W. Amwayi
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed to the study conception and design. The performance of the experiments, Contribution of reagents/material, data collection and analysis were performed by LAN, PWA and IWN. The first draft of the manuscript was written by LAN and all authors reviewed draft manuscript and approved the final manuscript.

Corresponding author

Correspondence to Peris W. Amwayi.

Ethics declarations

Conflict of interest

The authors declare that there is no conflict of interest arising from this work.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

11033_2021_6245_MOESM1_ESM.docx

Supplementary file 1 (DOCX 48 KB) Morphological characteristics of the 80 pumpkin fruit samples collected from 8 counties of Western Kenya

11033_2021_6245_MOESM2_ESM.docx

Supplementary file 2 (DOCX 12 KB) SSR primers and their respective fluorescent dye colour labels. 6-FAM = Blue, VIC = Green, PET = Red, and NED = Yellow

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nyabera, L.A., Nzuki, I.W., Runo, S.M. et al. Assessment of genetic diversity of pumpkins (Cucurbita spp.) from western Kenya using SSR molecular markers. Mol Biol Rep 48, 2253–2260 (2021). https://doi.org/10.1007/s11033-021-06245-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-021-06245-9

Keywords

Search

Navigation