Skip to main navigation menu Skip to main content Skip to site footer
Plant Science Today (PST)

Research Articles

Early Access

Morpho-nutritional characterization and molecular diversity assessment of pumpkin using SSR and SRAP markers

DOI
https://doi.org/10.14719/pst.9076
Submitted
25 April 2025
Published
09-02-2026

Abstract

Pumpkin (Cucurbita moschata Duch. Ex Poir.) is incredibly useful and nutritionally rich vegetable crop having numerous industrial uses regarding seed, flesh and flesh flour, but it is still underutilized in India. Hence, it is necessary to introduce some potential selections with high yield and nutrition content. The present investigation was elucidated the morpho-nutritional potential of pumpkin for 28 morpho-biochemical characters estimated and assessment of molecular diversity using Simple Sequence Repeats (SSR) and Sequence-Related Amplified Polymorphism (SRAP) marker in 34 diverse genotypes of pumpkin collected from different regions of India. The study was conducted at the Main Vegetable Research Station, Anand Agricultural University (AAU), Anand, during the kharif season of 2018. PCA explained 82.72 % total variation across traits, while multi-trait genotype-ideotype distance index (MGIDI) identified three high-performing genotypes; Anand Pumpkin 1, GPPK 95 and GPPK 59. A set of five SSR and SRAP polymorphic primers were used to estimate genetic diversity among the genotypes. The similarity matrix generates dendrogram with UPGM based on Jaccard’s coefficient implemented in NTYSIS. The clustering grouped 34 genotypes into six main clusters viz. I, II, III, IV, V and VI with 25, 4, 1, 1, 2 and 1 genotypes, respectively. The maximum genetic distance (0.75) was recorded between the genotype pairs GPPK 59 and Arka Chandan, as well as GPPK 90 and Arka Chandan. These findings highlight the potential of specific genotypes for breeding programs aimed at enhancing yield and nutritional value in pumpkin.

References

  1. 1. Andres TC. Diversity in tropical pumpkin (Cucurbita moschata): A review of intraspecific classifications. In: Progress in Cucurbit Genetics and Breeding Research. Proceedings of Cucurbitaceae; 2020. p. 107–12.
  2. 2. Tindall HD. Vegetables in the tropics. London: Macmillan Education; 1987.
  3. 3. Bailey LH. The domesticated cucurbits. J Genet Herb. 1929;2:62.
  4. 4. Sharma S, Rao TR. Nutritional quality characteristics of pumpkin fruit as revealed by its biochemical analysis. Int Food Res J. 2013;20(5):2309-16.
  5. 5. Xinyu MX. Study on GTF pumpkin milk powder. China Dairy Ind. 1988;6:6.
  6. 6. Bose TK, Som MG. Vegetable crops in India. Calcutta: Naya Prakash; 1988. p. 92-5.
  7. 7. Singh JK, Kumar JC, Sharma JR. Genetic variability and heritability of some economic traits in pumpkin in different seasons. Punjab Hortic J. 1988;28(3-4):238-42.
  8. 8. Satkar KP, Kulthe AA, Chalke PR. Preparation of bitter gourd ready-to-serve beverage and effect of storage temperature on its keeping quality. Bioscan. 2013;8(1):115-7.
  9. 9. Fisher RA. The correlation between relatives on the supposition of Mendelian inheritance. Philos Trans R Soc. 1918;52:399-433. https://doi.org/10.1017/S0080456800012163
  10. 10. Al-Ashkar I, Alderfasi A, El-Hendawy S, Al-Suhaibani N, El-Kafafi S, Seleiman MF. Detecting salt tolerance in doubled haploid wheat lines. Agronomy. 2019;9(4):211. https://doi.org/10.3390/agronomy9040211
  11. 11. El-Hendawy S, Al-Suhaibani N, Al-Ashkar I, Alotaibi M, Tahir MU, Solieman T, et al. Combining genetic analysis and multivariate modeling to evaluate spectral reflectance indices as indirect selection tools in wheat breeding under water deficit stress conditions. Remote Sens. 2020;12(9):1480. https://doi.org/10.3390/rs12091480
  12. 12. Olivoto T, Nardino M. MGIDI: Toward an effective multivariate selection in biological experiments. Bioinformatics. 2021;37(10):1383-9. https://doi.org/10.1093/bioinformatics/btaa981
  13. 13. Weising K, Atkinson RG, Gardner RC. Genomic fingerprinting by microsatellite-primed PCR: A critical evaluation. Genome Res. 1995;4(5):249-55. https://doi.org/10.1101/gr.4.5.249
  14. 14. Akkaya MS, Shoemaker RC, Specht JE, Bhagwat AA, Cregan PB. Integration of simple sequence repeat DNA markers into a soybean linkage map. Crop Sci. 1995;35:1439-45. https://doi.org/10.2135/cropsci1995.0011183X003500050030x
  15. 15. Robarts DW, Wolfe AD. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology. Appl Plant Sci. 2014;2(7):1400017. https://doi.org/10.3732/apps.1400017
  16. 16. Malik CP, Singh MB. Extraction and estimation of amino acids and keto acids. In: Plant enzymology and histo-enzymology. New Delhi: Kalyani Publishers; 1980.
  17. 17. Sadasivam S. Biochemical methods. New Delhi: New Age International Publishers; 1970.
  18. 18. Cox HE, Pearson D. The chemical analysis of foods. New York: Publishing Campus Inc.; 1962. p. 420.
  19. 19. Sadasivam S, Manickam A. Biochemical methods. New Delhi: New Age International Publishers; 1996.
  20. 20. Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus. 1990;12:13-5. https://doi.org/10.2307/2419362
  21. 21. Goldman D, Merril CR. Silver staining of DNA in polyacrylamide gels: Linearity and effect of fragment size. Electrophoresis. 1982;3:24-6. https://doi.org/10.1002/elps.1150030105
  22. 22. Gopinath PP, Parsad R, Joseph B, Adarsh VS. GRAPES: General RShiny Based Analysis Platform Empowered by Statistics; 2020.
  23. 23. Olivoto T, Lúcio AD. Metan: An R package for multi-environment trial analysis. Methods Ecol Evol. 2020;11:783-9. https://doi.org/10.1111/2041-210X.13384
  24. 24. Akter S, Rasul MG, Islam AA, Rahman MM. Genetic variability, correlation and path coefficient analysis of yield and quality traits in pumpkin (Cucurbita moschata Duch. ex Poir.). Bangladesh J Plant Breed Genet. 2013;26:25-33. https://doi.org/10.3329/bjpbg.v26i1.19981
  25. 25. Chaudhari DJ, Acharya RR, Gohil SB, Patel NA. Genetic divergence study in pumpkin (Cucurbita moschata Duch. ex Poir.). J Pharmacogn Phytochem. 2017;6:744-7.
  26. 26. Kumar V, Mishra DP, Yadav GC, Dwivedi DK. Genetic diversity assessment for morphological, yield and biochemical traits in genotypes of pumpkin. J Pharmacogn Phytochem. 2017;6:14-8. https://doi.org/10.20546/ijcmas.2017.605.108
  27. 27. Kumar R, Rajasree V, Praneetha S, Rajeswari S, Tripura U. Correlation and path coefficient analysis studies in pumpkin (Cucurbita moschata Duch. ex Poir.) for yield and quality traits. Int J Curr Microbiol Appl Sci. 2018;7:3067-75. https://doi.org/10.20546/ijcmas.2018.705.358
  28. 28. Mahmud E, Karim MR, Talukder MMR, Hasan GN, Islam MN. Phenotypic variability among pumpkin germplasm (Cucurbita moschata Duch. ex Poir.) in the southern part of Bangladesh. Int J Agric Pap. 2016;1:22-6.
  29. 29. Rasul MG, Akter S, Animul IAKM. Genetic variability, correlation and path coefficient analysis of yield and quality traits in pumpkin (Cucurbita moschata Duch. ex Poir.). Bangladesh J Plant Breed Genet. 2013;26:25-33. https://doi.org/10.3329/bjpbg.v26i1.19981
  30. 30. Srikanth M, Bharad SG, Thulasiram LB, Potdukhe NR. Studies on genetic variability, heritability and genetic advance in pumpkin (Cucurbita moschata Duch. ex Poir.). Int J Curr Microbiol Appl Sci. 2017;6:1416-22. https://doi.org/10.20546/ijcmas.2017.606.166
  31. 31. Sultana S, Kawochar MA, Naznin S, Siddika A, Mahmud F. Variability, correlation and path analysis in pumpkin (Cucurbita moschata). Bangladesh J Agric Res. 2015;40:479-89. https://doi.org/10.3329/bjar.v40i3.25421
  32. 32. Muralidhara MS, Narasegowda NC, Narayanaswamy P. Genetic divergence in pumpkin (Cucurbita moschata Duch. ex Poir.). Indian J Hortic. 2014;4(3):144-7.
  33. 33. Cyril NC, Ayinde DL, Olatunji O. Genetic variability and heritability of vegetative, fruit and seed yield traits in fluted pumpkin (Telfairia occidentalis Hook. f.). Afr J Biotechnol. 2014;13:3262-70. https://doi.org/10.5897/AJB2013.13088
  34. 34. Zinash A, Workneh TS, Woldetsadik K. Effect of accessions on the chemical quality of fresh pumpkin. Afr J Biotechnol. 2013;12(51):7092-8.
  35. 35. Pandey S, Singh J, Upadhyay AK, Ram D. Genetic variability for antioxidant and yield components in pumpkin (Cucurbita moschata Duch. ex Poir.). J Veg Sci. 2002;29(2):123-26.
  36. 36. Tarek AE, Khaled MT. Characteristics and composition of watermelon, pumpkin and paprika seed oils and flours. J Agric Food Chem. 2001;49(3):1253-9. https://doi.org/10.1021/jf001117+
  37. 37. Pandya JB, Rao RTV. Analysis of certain biochemical changes associated with growth and ripening of pumpkin fruit in relation to its seed development. J Pure Appl Sci. 2010;18:34-9.
  38. 38. Habib A, Biswas S, Siddique AH, Manirujjaman M, Uddin B, Hasan S, et al. Nutritional and lipid composition analysis of pumpkin seed (Cucurbita maxima Linn.). J Nutr Food Sci. 2015;5:374-80.
  39. 39. Kulaitiene J, Jariene E, Danilcenko H, Cerniauskiene J, Wawrzyniak A, Hamulka J, et al. Chemical composition of pumpkin (Cucurbita maxima Duch.) flesh flours used for food. J Agric Food Environ. 2014;12:61-4.
  40. 40. Montesano D, Blasi F, Simonetti M, Santini A, Cossignani L. Chemical and nutritional characterization of seed oil from Cucurbita maxima L. var. Berrettina pumpkin. Foods. 2018;7(3):30. https://doi.org/10.3390/foods7030030
  41. 41. Rupji M, Dwivedi B, Kowalski J. NOJAH: Not Just Another Heatmap for genome-wide cluster analysis. PLoS One. 2019;14:42-5. https://doi.org/10.1371/journal.pone.0204542
  42. 42. Meier C, Marchioro V, Meira D, Olivoto T, Klein L. Genetic parameters and multiple-trait selection in wheat genotypes. Pesq Agropecu Trop. 2021;51:79-86. https://doi.org/10.1590/1983-40632021v5167996
  43. 43. Uddin S, Billah M, Afroz R, Rahman S, Jahan N, Hossain M, et al. Evaluation of 130 eggplant (Solanum melongena L.) genotypes for future breeding program based on qualitative and quantitative traits and genetic parameters. Horticulturae. 2021;7:376. https://doi.org/10.3390/horticulturae7100376
  44. 44. Benakanahalli NK. A framework for identification of stable genotypes based on MTSI and MGIDI indexes: An example in guar (Cyamopsis tetragonoloba L.). Agronomy. 2021;11:1221. https://doi.org/10.3390/agronomy11061221
  45. 45. Singamsetti A, Zaidi PH, Seetharam K, Vinayan MT, Olivoto T, Mahato A, et al. Genetic gains in tropical maize hybrids across moisture regimes with multi-trait-based index selection. Front Plant Sci. 2023;14:1147424. https://doi.org/10.3389/fpls.2023.1147424
  46. 46. Ahmed SR, Ali Z, Ijaz I. Multi-trait selection of quinoa ideotypes at different levels of cutting and spacing. Sustainability. 2023;15:11446. https://doi.org/10.3390/su151411446
  47. 47. Smith JSC, Smith OS. Fingerprinting crop varieties. Adv Agron. 2000;47(1):85-140. https://doi.org/10.1016/S0065-2113(08)60489-7
  48. 48. Zraidi A, Stift G, Pachner M, Shojaeiyan A, Gong L, Lelley T. A consensus map for Cucurbita pepo. Mol Breed. 2007;20(4):375-88. https://doi.org/10.1007/s11032-007-9098-6
  49. 49. Ferriol M, Pico B, Nuez F. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor Appl Genet. 2003;107:271-82. https://doi.org/10.1007/s00122-003-1242-z
  50. 50. Paris HS, Yonash N, Portnoy V, Mozes-Daube N, Tzuri G, Katzir N. Assessment of genetic relationships in Cucurbita pepo using DNA markers. Theor Appl Genet. 2002;106(6):971-8. https://doi.org/10.1007/s00122-002-1157-0
  51. 51. Ramu P, Senthilvel S, Upadhyaya HD, Hash CT. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor Appl Genet. 2013;126(8):2051-64. https://doi.org/10.1007/s00122-013-2117-6

Downloads

Download data is not yet available.