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

Research Articles

Early Access

Genetic diversity analysis in eggplant (Solanum melongena L.) using Mahalanobis D² analysis, Principal Component Analysis (PCA) and Start Codon Targeted (SCoT)

DOI
https://doi.org/10.14719/pst.9286
Submitted
4 May 2025
Published
05-08-2025
Versions

Abstract

This study evaluated morpho-molecular diversity among 34 eggplant (Solanum melongena L.) accessions using 10 morphological descriptors, 16 quantitative traits and 15 SCoT to parent selection and broadening the breeding base effectively. Mahalanobis D² analysis grouped the accessions into five clusters, with the greatest inter-cluster divergence between Clusters V and IV. PCA identified five components (eigenvalues >1) explaining 75.65 % of the total variance, with PC1 contributing 38.3 %. High-performing and genetically diverse accessions such as Kashi Uttam, Kashi Green Round, CHBR-2, BUB-18-12 and BUB-18-27 were identified through PCA biplot. SCoT markers amplified 4-10 loci/primer (mean: 6.13), all polymorphic, with SCoT-20, SCoT-13, SCoT-17 and SCoT-25 being the most informative based on PIC values. UPGMA clustering grouped accessions into three clusters (A:14, B:15, C:5), while population structure analysis identified two sub-populations (A:26, B:10). SCoT analysis revealed significant molecular variability. The lack of unique clustering across morphological and molecular data highlights the importance of integrated approaches. Crosses among divergent clusters are recommended to enhance genetic gain and cultivar development.

References

  1. 1. Bhanushree N, Saha P, Tomar BS, Lyngdoh YA, Gopala KS, Gurung B, et al. Genetic analysis and identification of molecular marker linked to the gene for fruit skin colour in eggplant (Solanum melongena L). Veg Sci. 2018;45:149-53. https://doi.org/10.61180/4em4mk71
  2. 2. Chithra K, Devaraju M, Srinivasa V, Varalakshmi B, Asha AB. Genetic investigation in segregating generation of brinjal (Solanum melongena L). Natl Acad Sci Lett. 2022;45:5-8. https://doi.org/10.1007/s40009-021-01070-x
  3. 3. Verma AK, Mishra AC, Tripathi PK. Evaluation of brinjal genotypes (Solanum melongena L) for growth, yield, and quality characters in the Bundelkhand region of UP, India. Int J Plant Soil Sci. 2023;35:1690-9. https://doi.org/10.9734/ijpss/2023/v35i183444
  4. 4. Salem N, Msaada K, Hammami M, Limam F, Vasapollo G, Marzouk B. Variation in anthocyanin and essential oil composition and their antioxidant potentialities during flower development of borage (Borago officinalis L). Plant Biosyst. 2014;148:444-59. https://doi.org/10.1080/11263504.2013.778349
  5. 5. Taher D, Solberg SØ, Prohens J, Chou Y, Rakha M, Wu T. World Vegetable Centre eggplant collection: Origin, composition, seed dissemination and utilization in breeding. Front Plant Sci. 2017;8:1484. https://doi.org/10.3389/fpls.2017.01484
  6. 6. Docimo T, Francese G, Ruggiero A, Batelli G, De Palma M, Bassolino L. Phenylpropanoids accumulation in eggplant fruit: Characterization of biosynthetic genes and regulation by a MYB transcription factor. Front Plant Sci. 2016;6:1233. https://doi.org/10.3389/fpls.2015.01233
  7. 7. Ullah S, Ijaz U, Shah TI, Najeebullah M, Niaz S. Association and genetic assessment in brinjal. Eur J Biotechnol Biosci. 2014;2:41-5.
  8. 8. Hassan I, Jatoi SA, Arif M, Siddiqui SU. Genetic variability in eggplant for agro-morphological traits. Sci Tech Dev. 2015;34(1):34-40.
  9. 9. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan A. Microsatellite markers: an overview of the recent progress in plants. Euphytica. 2011;177:309-34. https://doi.org/10.1007/s10681-010-0286-9
  10. 10. Collard BCY, Mackill DJ. Start Codon Targeted (SCoT) polymorphism: A simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep. 2008;27:86-93. https://doi.org/10.1007/s11105-008-0060-5
  11. 11. Xiong FQ, Tang RH, Chen ZL, Pan LH, Zhuang WJ. SCoT: A novel gene-targeted marker technique based on the translation start codon. Mol Plant Breed. 2009;7:635-8.
  12. 12. Sultana S, Islam MN, Hoque MdE. DNA fingerprinting and molecular diversity analysis for the improvement of brinjal (Solanum melongena L) cultivars. J Adv Biotechnol Exp Ther. 2018;1:1-6. https://doi.org/10.5455/jabet.d1
  13. 13. Laxman L, Nandi, Saha P, Behera TK, Lyngdoh YA, Munshi AD, et al. Genetic characterisation and population structure analysis of indigenous and exotic eggplant (Solanum spp) accessions using microsatellite markers. J Hortic Sci Biotechnol. 2020;96:73-86. https://doi.org/10.1080/14620316.2020.1763211
  14. 14. Chauhan H, Sirohi U, Aastha V, Sharma R, Mohit, Chaudhary V, et al. Identification of diverse genotypes in brinjal (Solanum melongena L) based on RAPD markers analysis. Ecol Environ Conserv. 2022;28:248-54. http://doi.org/10.53550/EEC.2022.v28i03s.037
  15. 15. Luo C, He XH, Chen H, Ou SJ, Gao MP, Brown JS, et al. Genetic diversity of mango cultivars was estimated using SCoT and ISSR markers. Biochem Syst Ecol. 2011;39:676-84. http://dx.doi.org/10.1016/j.bse.2011.05.023
  16. 16. Xiong FQ, Zhong RC, Han ZQ, Jiang J, He LQ, Zhuang WJ, Tang R. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L) genotypes. Mol Biol Rep. 2011;38:3487-94. https://doi.org/10.1007/s11033-010-0459-6
  17. 17. Protection of Plant Varieties and Farmers’ Rights Authority. Test guidelines applied for all varieties, hybrids, and parental lines of brinjal/eggplant (Solanum melongena L). Plant Var J. 2009;3(11):185-96. https://plantauthority.gov.in/sites/default/files/fbrinjal.pdf
  18. 18. Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980;8(19):4321-5. https://doi.org/10.1093/nar/8.19.4321
  19. 19. Mahalanobis PC. On the generalized distance in statistics. Proc Natl Acad Sci India. 1936;2:49-55. https://www.scirp.org/reference/ReferencesPapers?ReferenceID=1649365
  20. 20. Rao CR. Advanced statistical methods in biometrical research. New York: John Wiley and Sons Inc; 1952. https://www.scirp.org/reference/referencespapers?referenceid=268780
  21. 21. R Software. A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2023. https://www.R-project.org/
  22. 22. Rohlf FJ. NTSYS-PC: Numerical taxonomy and multivariate analysis system, version 2.1. Exeter Publications, New York; 2000. https://wwwresearchgatenet/publication/246982444
  23. 23. Pritchard JK, Stephens P, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945-59. https://doi.org/10.1093/genetics/155.2.945
  24. 24. Singh B, Chaubey T, Pandey S, Singh RK, Upadhyay DK, Jha A, et al. Categorization of diverse and stable extant cultivars of brinjal by using pheno-morphometric DUS characters. Indian J Plant Genet Resour. 2023;36(1):1-18. https://doi.org/10.5958/0976-1926.2023.00036.1.01
  25. 25. Begum F, Islam AA, Rasul MG, Mian MK, Hossain MM. Morphological diversity of eggplant (Solanum melongena) in Bangladesh. Emir J Food Agric. 2013;25:45-51. https://doi.org/10.9755/ejfa.v25i1.4937
  26. 26. Sharma A, Sharma S, Kumar N, Rana RS, Sharma P, Kumar P. Morpho-molecular genetic diversity and population structure analysis in garden pea (Pisum sativum L) genotypes using simple sequence repeat markers. PLOS ONE. 2022;17(9):e0273499. https://doi.org/10.1371/journal.pone.0273499
  27. 27. Kumar S, Rattan P, Sharma JP, Gupta RK. D2 analysis for fruit yield and quality components in tomato (Lycopersicon esculentum Mill). Ind J Plant Gen Res. 2010;23:318-20. https://ispgr.in/index.php/ijpgr/article/download/1678/1514
  28. 28. Mohanty KK, Mishra H, Barik S. Morphological profiling and assessment of genetic divergence of brinjal (Solanum melongena L). J Pharm Phytochem. 2021;10:602-7. http://www.phytojournal.com
  29. 29. Dash SP, Singh J, Sharma D, Thakur P. Genetic divergence study in brinjal (Solanum melongena L). J Ent Zool Stud. 2020;8:1277-81. https://www.entomoljournal.com
  30. 30. Sanga L, Pandey AK, Warade SDL, Hazarika BN, Singh S. Assessment of wild brinjal (Solanum gilo) genotypes of North-Eastern region. Int J Curr Microbiol Appl Sci. 2017;6:1451-8. https://doi.org/10.20546/ijcmas.2017.610.171
  31. 31. Nand N, Adarsh A, Kumar A, Akhtar S, Kumar R, Ray PK. Morphological characterization of different genotypes of brinjal (Solanum melongena L). Int J Curr Microbiol Appl Sci. 2018;7:2218-26. https://doi.org/10.20546/ijcmas.2018.701.267
  32. 32. Quamruzzaman AKM, Rashid MA, Ahmad S, Moniruzzaman M. Genetic divergence analysis in eggplant (Solanum melongena L). Bangladesh J Agric Res. 2009;34(4):705-12. https://doi.org/10.3329/bjar.v34i4.5845
  33. 33. Barik S, Ponnam N, Acharya GC, Singh TH, Dash M, Sahu GS, et al. Genetic variability, character association and diversity studies in brinjal (Solanum melongena L). Electron J Plant Breed. 2021;12(4):1102-10. https://www.ejplantbreeding.org/index.php/EJPB/article/view/3822
  34. 34. Chaudhary AK, Yadav GC, Maurya RK, Anjana CS, Prajapati J. Estimates of genetic variability, yield and quality traits of brinjal (Solanum melongena L). Int J Environ Clim Chang. 2023;13(9):583-9. https://doi.org/10.9734/ijecc/2023/v13i92273
  35. 35. Singh B, Chaubey T, Singh RK, Upadhyay K, Jha A, Pandey S. Genetic variation in phenatic traits of extant varieties of brinjal (Solanum melongena L). J Appl Hort. 2024;26(1):107-11. https://doi.org/10.37855/jah.2024.v26i01.20
  36. 36. Kousalya R, Praneetha S, Irene, Vethamoni P, Ravichandran V, Iyanar K, et al. Unveiling the genetic variability, character association, and principal component analysis for yield and yield contributing traits in brinjal (Solanum melongena) genotypes. Indian J Agric Sci. 2024;94(10):1039-44. https://doi.org/10.56093/ijas.v94i10.152248
  37. 37. Baraki F, Berhe M. Evaluating the performance of sesame (Sesamum indicum L) genotypes in different growing seasons in northern Ethiopia. Int J Agron. 2019;7:1-7. https://doi.org/10.1155/2019/7804621
  38. 38. Mukhthambica K, Bisen R, Ramya KT. Principal component analysis for yield and yield-related traits in sesame (Sesamum indicum L). Biol Forum Int J. 2023;15(3):227-32. https://www.researchtrend.net/bfij/pdf/Principal-Component-Analysis-for-Yield-and-Yield-Related-Traits-in-Sesame-(Sesamum-indicum-L.)-Mukhthambica-K-35.pdf
  39. 39. Dar AA, Mahajan R, Lay P, Sharma S. Genetic diversity and population structure of Cucumis sativus L by using SSR markers. Biotechnology. 2017;7:307. https://doi.org/10.1007/s41207-024-00713-x
  40. 40. Oliveira MM, Sousa LB, Reis MC, Silva Junior ES, Cardoso DBO, Hamawaki OT. Evaluation of genetic diversity among soybean (Glycine max) genotypes using univariate and multivariate analysis. Genet Mol Res. 2017;16:1-10. https://pubmed.ncbi.nlm.nih.gov/28613377/
  41. 41. Raja WH, Yousuf N, Qureshi I, Sharma OC, Singh DB, Kumawat KL. Morpho-molecular characterization and genetic diversity analysis across wild apple (Malus baccata) accessions using simple sequence repeat markers. South Afr J Bot. 2022;145:378-85. https://doi.org/10.1016/j.sajb.2021.08.020
  42. 42. Bhandari HR, Bhanu AN, Srivastava K. Assessment of genetic diversity in crop plants - an overview. Plants Agric Res. 2017;7:279-86. https://doi.org/10.15406/apar.2017.07.00255
  43. 43. Mohamed A, García-Martínez S, Loumerem M, Carbonell P, Ruiz JJ, Boubaker M. Assessment of genetic diversity among local pea (Pisum sativum L) accessions cultivated in the arid regions of Southern Tunisia using agro-morphological and SSR molecular markers. Genet Resour Crop Evol. 2019;66:1189-203. https://doi.org/10.1007/s10722-019-00784-8
  44. 44. Sharma R, Dar AA, Mahajan R, Sharma S. Molecular and biochemical characterization of Indian germplasm of Pisum sativum L. Proc Natl Acad Sci India Sect B Biol Sci. 2020;90:103-11. https://doi.org/10.1007/s40011-018-01069-3
  45. 45. Cericola F, Portis E, Toppino L, Barchi L, Acciarri N, Ciriaci T, et al. The population structure and diversity of eggplant from Asia and the Mediterranean Basin. PLOS ONE. 2013;8:e73702. https://doi.org/10.1371/journal.pone.0073702
  46. 46. Kaur A, Kaur N, Bassi G, Kaur N, Dhatt AS. Morphological and molecular markers-based assessment of genetic diversity in eggplant. Indian J Hort. 2020;77(1):116-24. https://doi.org/10.5958/0974-0112.2020.00012.2
  47. 47. Knapp S, Vorontsova MS, Prohens J. Wild relatives of the eggplant (Solanum melongena L: Solanaceae): New understanding of species names in a complex group. PLOS ONE. 2013;8:12. https://doi.org/10.1371/journal.pone.0057039
  48. 48. Nandi LL, Saha P, Behera TK, Lyngdoh YA, Munshi AD, Saha ND, et al. Genetic characterisation and population structure analysis of indigenous and exotic eggplant (Solanum spp) accessions using microsatellite markers. J Hortic Sci Biotechnol. 2021;96:73-86. https://doi.org/10.1080/14620316.2020.1763211

Downloads

Download data is not yet available.