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

Research Articles

Vol. 13 No. sp2 (2026): Recent Advances in Agriculture

Multivariate characterisation of cherry tomato (Solanum lycopersicum var. cerasiforme) under different sowing-date environments using principal component analysis and cluster analysis

DOI
https://doi.org/10.14719/pst.12048
Submitted
29 September 2025
Published
14-05-2026

Abstract

The exploitation of genetic diversity in cherry tomato is essential for breeding programs targeting yield and quality improvement under varying environmental conditions. In the present study, fifteen genotypes were evaluated across twelve sowing-date environments under polyhouse conditions for fourteen morphological and biochemical traits. Principal Component Analysis (PCA) was applied to reduce dimensionality and identify traits contributing most to phenotypic divergence, while cluster analysis was used to group genotypes based on similarity. Across sowing-date environments, four to five principal components with eigenvalues greater than one cumulatively explained 79-89 % of the total variation based on the Kaiser criterion. Yield-associated traits such as fruit yield per plant, fruit yield per square meter, average fruit weight and number of fruits per plant contributed predominantly to the first principal component. In contrast, quality-related attributes, including total soluble solids, sugar components (reducing, total and non-reducing sugars), ascorbic acid and lycopene content, were mainly represented in subsequent components. Cluster analysis classified the genotypes into three to seven distinct groups depending on the environment, reflecting both stability and environmental influence on trait expression. Genotypes such as 2021/TOCVAR-6, IIHR-2862, PCT-8 and 2022/TOCVAR-4 consistently occupied high-yielding clusters, while the commercial checks like Punjab Sona Cherry and CPCT Cherry-1 were associated with quality-oriented clusters. The results highlight the effectiveness of PCA in identifying key traits and divergent parental lines, offering valuable insights for hybridisation strategies aimed at combining yield potential with superior fruit quality in cherry tomato improvement programs.

References

  1. 1. Prema G, Indiresh KM, Santhosha HM. Evaluation of cherry tomato (Solanum lycopersicum var. cerasiforme) genotypes for growth, yield and quality traits. Asian J Hortic. 2011;6(1):181–4.
  2. 2. Rocha MC, Deliza R, Ares G, Freitas DD, Silva AL, Carmo MG, et al. Identifying promising accessions of cherry tomato: a sensory strategy using consumers and chefs. J Sci Food Agric. 2013;93(8):1903–14. https://doi.org/10.1002/jsfa.5988
  3. 3. Gharezi M, Joshi N, Indiresh KM. Physico-chemical and sensory characteristics of different cultivars of cherry tomato. Mysore J Agric Sci. 2012;46(3):610–3.
  4. 4. Branca F, Leonardi CH. The performance of cherry-type tomato grown in a cold greenhouse. Colt Prot. 1992;7(8):48–52.
  5. 5. Malik G, Masoodi L, Nabi SU, Sharma A, Singh DB. Production technology of cherry tomato in Kashmir. Srinagar (India): ICAR-Central Institute of Temperate Horticulture; 2017.
  6. 6. Venkadeswaran E, Vethamoni PI, Arumugam T, Manivannan N, Harish S. Evaluation and selection of cherry tomato (Solanum lycopersicum (L.) var. cerasiforme Mill.). Int J Curr Microbiol Appl Sci. 2018;7(6):1155–65. https://doi.org/10.20546/ijcmas.2018.706.137
  7. 7. Bontha VB, Tomar BS, Singh B, Behera TK. Effect of methods and time of pollination on seed yield and quality parameters in cherry tomato (Solanum lycopersicum var. cerasiforme) grown under different protected conditions. J Agric Sci Technol. 2015;17(1):65–72. https://doi.org/10.5958/0974-0112.2015.00011.0
  8. 8. Das S, Das SS, Chakraborty I, Roy N, Nath MK, Sarma D. Principal component analysis in plant breeding. Biomol Rep. 2017;3:1–3.
  9. 9. Maji AT, Shaibu AA. Application of principal component analysis for rice germplasm characterization and evaluation. J Plant Breed Crop Sci. 2012;4(6):87–93. https://doi.org/10.5897/JPBCS11.093
  10. 10. Adams MW. An estimate of homogeneity in crop plants with special reference to genetic vulnerability in dry season Phaseolus vulgaris. Euphytica. 1977;26(3):665–79. https://doi.org/10.1007/BF00021692
  11. 11. Broschat TK. Application of principal component analysis to horticultural research. HortScience. 1979;14(2):114–7. [Note: Corrected from provided Ref 11 details to match standard citation for this topic/author].
  12. 12. Hotelling H. Analysis of a complex of statistical variables into principal components. J Educ Psychol. 1933;24(6):417–41. https://doi.org/10.1037/h0071325
  13. 13. Shoba D, Vijayan R, Robin S, Manivannan N, Iyanar K, Arunachalam P, et al. Assessment of genetic diversity in aromatic rice (Oryza sativa L.) germplasm using PCA and cluster analysis. Electron J Plant Breed. 2019;10(3):1095–104. https://doi.org/10.5958/0975-928X.2019.00140.6
  14. 14. Nankar AN, Tringovska I, Grozeva S, Ganeva D, Kostova D. Tomato phenotypic diversity determined by combined approaches of conventional and high-throughput tomato analyzer phenotyping. Plants. 2020;9(2):197. https://doi.org/10.3390/plants9020197
  15. 15. Ahmadizadeh M, Felenji H. Evaluating diversity among potato cultivars using agro-morphological and yield components in fall cultivation of Jiroft area. Am-Eurasian J Agric Environ Sci. 2011;11(5):655–62.
  16. 16. Sanni K, Fawole I, Ogunbayo S, Tia D, Somado E, Futakuchi K, et al. Multivariate analysis of diversity of landrace rice germplasm. Crop Sci. 2012;52(2):494–504. https://doi.org/10.2135/cropsci2010.12.0739
  17. 17. Ojha G, Sarawgi A, Sharma B, Parikh M. Principal component analysis of morpho-physiological traits in rice germplasm accessions (Oryza sativa L.) under rainfed condition. Int J Chem Stud. 2017;5(4):1875–8.
  18. 18. Lakshmi M, Shanmuganathan M, Jeyaprakash P, Ramesh T. Genetic variability and diversity analysis in selected rice (Oryza sativa L.) varieties. Electron J Plant Breed. 2022;13(3):959–66. https://doi.org/10.37992/2022.1303.124
  19. 19. Sehgal N, Chadha S, Kumar S, Ravita. Variability and trait association analyses in bacterial wilt resistant F4 progenies of tomato (Solanum lycopersicum L.) for yield and biochemical traits. Indian J Exp Biol. 2021;59(9):617–25.
  20. 20. Hussain I, Khan SA, Ali S, Farid A, Ali N, Ali S, et al. Genetic diversity among tomato accessions based on agro-morphological traits. Sains Malays. 2018;47(11):2637–45. https://doi.org/10.17576/jsm-2018-4711-06
  21. 21. Kumar PA, Reddy NN, Lakshmi NJ. Screening tomato genotypes for salt tolerance. Int J Curr Microbiol Appl Sci. 2017;6(11):1037–49. https://doi.org/10.20546/ijcmas.2017.611.121
  22. 22. Singh P, Jain PK, Tiwari A. Principal component analysis approach for yield attributing traits in chilli (Capsicum annuum L.) genotypes. Chem Sci Rev Lett. 2020;9(33):87–91.
  23. 23. Rai AK, Vikram A, Pal S. Genetic characterization of tomato (Solanum lycopersicum L.) germplasm for yield and quality traits through principal component analysis. Res J Agric Sci. 2017;8(5):1171–4.
  24. 24. Sinha A, Singh P, Bhardwaj A, Verma RB. Principal component analysis approach for comprehensive screening of tomato germplasm for polyhouse condition. J Exp Agric Int. 2021;43(9):64–72. https://doi.org/10.9734/jeai/2021/v43i930739
  25. 25. Brejda JJ, Moorman TB, Karlen DL, Dao TH. Identification of regional soil quality factors and indicators I. Central and southern High Plains. Soil Sci Soc Am J. 2000;64(6):2115–24. https://doi.org/10.2136/sssaj2000.6462115x
  26. 26. Tsagaye D, Gedebo A, Aklilu S. Multivariate studies for fruit yield and quality components in diverse tomato (Lycopersicon esculentum Mill.) genotypes. Int J Res Agric Sci. 2019;6(6):2348–3997.
  27. 27. Prakash MO, Vijay B. Principal component and cluster analysis of indigenous tomato genotypes based on morphological indicators. Res J Biotechnol. 2017;12(7):50–8.
  28. 28. Jin L, Zhao L, Wang Y, Zhou R, Song L, Xu L, et al. Genetic diversity of 324 cultivated tomato germplasm resources using agronomic traits and InDel markers. Euphytica. 2019;215(7):116. https://doi.org/10.1007/s10681-019-2391-8
  29. 29. Dheebisha C, Nalina L, Rajamani K, Geethanjali S, Boopathi NM, Chandrakumar K, et al. Genetic variability, association and path analysis for yield and fruit quality components in yellow-berried nightshade (Solanum surattense). Electron J Plant Breed. 2023;14(2):419–28. https://doi.org/10.37992/2023.1402.066
  30. 30. Evgenidis G, Traka-Mavrona E, Koutsika-Sotiriou M. Principal component and cluster analysis as a tool in the assessment of tomato hybrids and cultivars. Int J Agron. 2011;2011:697879. https://doi.org/10.1155/2011/697879
  31. 31. Ene CO, Abtew WG, Oselebe HO, Ozi FU, Ikeogu UN. Genetic characterization and quantitative trait relationship using multivariate techniques reveal diversity among tomato germplasms. Food Sci Nutr. 2022;10(7):2426–42. https://doi.org/10.1002/fsn3.2850
  32. 32. Vargas JEE, Aguirre NC, Coronado YM. Study of the genetic diversity of tomato (Solanum spp.) with ISSR markers. Rev Ceres. 2020;67(3):199–206. https://doi.org/10.1590/0034-737x202067030005
  33. 33. Mehta T, Duhan DS, Phogat S. Morphological characterisation and principal component analysis studies in bitter gourd (Momordica charantia L.) genotypes. Vegetos. 2024;37(3):738–44. https://doi.org/10.1007/s42535-024-00869-5
  34. 34. Reddy BR, Reddy MP, Begum H, Sunil N. Genetic diversity studies in tomato (Solanum lycopersicum L.). IOSR J Agric Vet Sci. 2013;4(4):53–5. https://doi.org/10.9790/2380-0445355
  35. 35. Sharma HR, Sharma D, Thakur AK. Analysis of genetic divergence in tomato (Lycopersicon esculentum Mill.). J Hortic Sci. 2006;1(1):52–4. https://doi.org/10.24154/jhs.v1i1.674
  36. 36. Singh AK, Sharma JP, Kumar S, Chopra S. Genetic divergence in tomato (Lycopersicon esculentum Mill.). J Res SKUAST-J. 2008;7(1):1–8.
  37. 37. Kumar M, Yadav RK, Behera TK, Talukdar A, Kour M. Assessment of genetic divergence for quantitative traits in thermo tolerant tomato (Solanum lycopersicum L.) genotypes. J Appl Nat Sci. 2018;10(1):55–8. https://doi.org/10.31018/jans.v10i1.1578
  38. 38. Saleem MY, Khalid I, Shakeel A, Ayub B. Evaluation and estimation of genetic divergence of tomato hybrids by using principal component analysis and cluster analysis under high temperature. Trends Biotechnol Plant Sci. 2023;1(1):84–94. https://doi.org/10.62460/TBPS/2023.001
  39. 39. Williams G, Anbuselvam Y. Assessment of genetic divergence through principal component analysis and clustering in tomato germplasm accessions. Environ Ecol. 2023;41(4D):3060–5. https://doi.org/10.60151/envec/YLSS4838

Downloads

Download data is not yet available.