Assessment of Genetic Variability Using Morphological Markers and DNA Quality Using Conventional and Kit-Based Extraction Protocols in Tomato Genotypes, Lycopersicon Esculentum (L.)
Abstract
Genetic improvement in tomato requires a deep understanding of agronomic diversity and the reliability of DNA extraction methods for downstream molecular analysis. This study evaluated and assessed the genetic variability of tomato genotypes using morphological traits and genomic DNA concentration and quality using three extraction protocols: Cetyltrimethylammonium bromide , Sodium dodecyl sulfate , and a commercial Zymo kit. Fifteen tomato genotypes were evaluated in a randomized complete block design, and data were collected on thirteen traits. The analysis of variance revealed highly significant (p < 0.01) differences among genotypes for all measured characters, indicating that the genotypes were from divers’ origins and of substantial genetic variability. The genotypic and phenotypic coefficients of variation (PCV and GCV) ranged widely fro 10.79% to 64.82% and 11.07% to 65.7% for the genotypic coefficients of variation and the phenotypic coefficients of variation respectively, confirming the presence of exploitable variability. The Heritability values were generally high (62.00% – 98.00%), suggesting strong additive genetic control for all the traits. DNA yield differed significantly among the three extraction methods, with SDS producing the highest concentration, followed by CTAB and Zymo kit. However, Zymo kit produced DNA with the highest purity (A260/A280 ≈ 1.810 - 2.000), suitable for PCR and other downstream applications. The combined morphological and DNA quality assessment demonstrates the genetic diversity among tomato genotypes and the suitability of SDS for yield-intensive extraction and Zymo kit for high DNA purity-dependent molecular assays.it can be concluded from this study that the tomato genotypes were from diverse origin and Genotypes; NGB0075, NGB00714, NGB00724 and NGB00737 are identified and selected as promising genotypes for use in tomato breeding programs aimed at yield improvement.
Keywords
Genetic variabilityMorphological markersDna qualityConventionalkit-basedExtraction protocolsTomatoGenotypes
References
Alemán-Duarte, M. I., et al. (2023). Improvement and validation of a genomic DNA extraction method: comparison with commercial kits. Scientific Reports / PMC (2023). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10144544/. Alemu, B., Tesfaye, K., & Dagne, K. (2022). Genetic diversity and variability assessment of tomato (Solanum lycopersicum L.) genotypes using morphological markers. Journal of Horticultural Science, 58(3), 450–462. Bunjkar, A., Walia, P., & Sandal, S. S. (2024). Unlocking genetic diversity and germplasm characterization with molecular markers: strategies for crop improvement. Journal of Advances in Biology & Biotechnology, 27(6), 160-173. Burton, G. W., & DeVane, E. H. (1953). Estimating heritability in tall fescue from replicated clonal material. Agronomy Journal, 45(10), 478–481. Chioma, I. C. (2024). The yield and purity of DNA extracts from seeds of Treculia africana accessions using the Zymo Research mini plant/seed DNA extraction kit. Journal of Biological Research & Biotechnology, 2024. https://bio- research.com.ng/index.php/home/article/view/1. (bio-research.com.ng) Collins, E. J., Bowyer, C., Tsouza, A., & Chopra, M. (2022). Tomatoes: An extensive review of the associated health impacts of tomatoes and factors that can affect their cultivation. Biology, 11(2), 239. Doyle, J. J., & Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13–15. Haraira, A., Ahmad, A., Khalid, M. N., Tariq, M., Nazir, S., & Habib, I. (2022). Enhancing health benefits of tomato by increasing its antioxidant contents through different techniques: A review. Advancements in Life Sciences, 9(2), 131-142. Johnson, H. W., Robinson, H. F., & Comstock, R. E. (1955). Estimates of genetic and environmental variability in soybeans. Agronomy Journal, 47(7), 314–318. Krawczak, M., & Schmidtke, J. (2020). Principles of DNA purification and quality assessment in molecular genetics. Journal of Molecular Diagnostics, 22(2), 100–118. Mallick, P. K. (2021). Medicinal values of tomato (Lycopersicon esculentum Mill.–Solanaceae). International Journal of Applied Sciences and Biotechnology, 9(3), 166-168. Mallick, S. (2021). Advances in tomato crop production and improvement strategies: A review. Plant Science Today, 8(4), 321–330. https://doi.org/10.14719/pst.2021.8.4.1104 Panda, S., Mohanty, A., & Pradhan, K. (2019). Assessment of genetic variability, heritability and genetic advance in tomato (Solanum lycopersicum L.). Scientia Horticulturae, 256, 108– 118. https://doi.org/10.1016/j.scienta.2019.108518 Pathak, R. K., Singh, S., Meghna, Kumar, S., Kumar, S., Narayan, A., & Chaudhary, S. (2024). Genetic variability, heritability and genetic advance in tomato (Solanum lycopersicum L.). Biochem & Physiology Journal (2024). https://doi.org/10.33545/26174693.2024.v8.i8Sc.1762. (Biochemistry Journal) Rasheed, A., Ilyas, M., Khan, T. N., Mahmood, A., Riaz, U., Chattha, M. B., & Qari, S. H. (2023). Study of genetic variability, heritability, and genetic advance for yield-related traits in tomato (Solanum lycopersicum Mill.). Frontiers in Genetics, 13, Article 1030309. https://doi.org/10.3389/fgene.2022.1030309. Saleem, S., Arif, M., & Tariq, M. (2020). Phenotypic diversity and genetic variability in tomato germplasm for yield and related traits. Genetic Resources and Crop Evolution, 67(5), 1205–1214. https://doi.org/10.1007/s10722-020-00907-3 P-ISSN 2695-222X Tiwari, J. K., Yerasu, S. R., Rai, N., Singh, D. P., Singh, A. K., Karkute, S. G., & Behera, T. K. (2022). Progress in marker-assisted selection to genomics-assisted breeding in tomato. Critical Reviews in Plant Sciences, 41(5), 321-350. Table 1: Analysis of Variance of the Agronomic Characters studied in Tomato genotypes *, ** indicate significance at 1% and 5% level of probability. DF= Degree of freedom; DTF= Days to flowering ; DTFFA= Days to first flower appearance ; DTM= Days to maturity; PHTF= Plant height at flowering (cm); PHTM= Plant height at maturity (cm); PHTH= Plant height at harvest (cm); NLPF= Number of leaves per plant at flowering; NBP= Number of branches per plant; NFP = Number of fruits per plant; NCP= Number of clusters per plant; IFWT= Individual fruit weight (g); YD/P= Yield per plant (g) and YD/HA= Yield per hectare . TABLE 2: Mean performance of the Agronomic characters studied in Tomato genotypes. S/ N Ge no ty pe co de DT F (da ys) DTF FA (days ) DT M (day s) PH TF (cm ) PH TM (cm ) PHT H (cm) NLP F NB P NFP NCP IF WT (g) YD/P (g) YD/ HA 1 G1 35.3 0a 46.30 a 88.3 0a 33.6 0a 123. 10b 147.1 0b 27.8 0a 8.8 0a 43.9 0ab 6.60ab c 4.2 8e 188.1 0defg 6.97d efg 2 G2 35.6 0a 46.60 a 88.6 0a 30.1 0a 126. 60b 152.6 0b 18.4 0d 6.6 0a 20.0 0d 3.50e 4.2 3e 84.45h 3.13h 3 G3 29.6 0b 38.60 c 73.6 0b 43.7 0a 176. 30a 200.7 0ab 25.7 0a 5.9 0a 23.0 0cd 4.40de 5.4 9cde 126.8 3fgh 4.69f gh 4 G4 35.4 0a 45.90 ab 89.4 0a 35.2 0a 147. 70ab 170.2 0a 19.7 0bcd 8.5 0a 40.9 0b 6.30ab cd 6.4 5abc 266.7 3bcd 9.88b cd 5 G5 35.3 0b 38.80 c 74.3 0b 46.5 0a 178. 50a 207.0 0a 19.4 0cd 6.5 0a 23.4 0cd 4.20de 5.0 4de 117.50 fgh 4.36f gh SO V D f DT F (Da ys) DTF FA (Da ys) DT M (Da ys) PH TF (cm ) PH TM (cm) PH TH (cm ) NL PF NB P NF P N C P IFW T (g) YD/ P (g) YD/H A (Tons ) Re p 1 2.58 * 0.26 6.72 131 .46 * 274. 82 186. 5 3.8 9 0.1 3 6.7 2 0.6 5 0.01 130. 20 0.18 GE N 1 4 15.6 0** 21.2 5** 86.4 7** 79. 34* 109 9.72 ** 133 4.4* * 33. 86* * 3.5 2 24 8.9 8* * 4.0 6* * 1.98 ** 1672 0.30 ** 22.94 ** Er ror 1 4 0.32 1.10 2.15 26. 36 76.5 6 110. 50 1.5 6 1.4 1 3.7 9 0.. 28 0.11 503. 50 0.69 P-ISSN 2695-222X 6 G6 35.9 0a 44.90 ab 84.9 0a 38.7 0a 135. 20b 155.2 0b 17.2 0d 7.3 0a 44.8 0ab 7.40a 7.1 0bcd 318.3 4ab 11.79 ab 7 G8 36.6 0a 46.60 a 89.1 0a 32.3 0a 128. 80b 151.8 0b 17.2 0d 6.0 0a 21.8 0cd 4.30de 5.8 9bcd 128.3 6fgh 4.75f gh 8 G9 30.6 0b 39.60 c 74.6 0b 47.5 0a 176. 50a 205.0 0a 27.1 0a 8.6 0a 44.1 0ab 6.80ab 6.9 0ab 304.8 8ab 11.29 ab 9 G1 0 34.9 0a 44.40 ab 86.4 0a 35.3 0a 126. 80b 150.8 0b 24.3 0abc 8.2 0a 24.0c d 4.70bc de 5.9 8abc d 143.6 8efgh 5.32ef gh 10 G1 1 34.8 0a 42.80 abc 84.8 0a 31.8 0a 126. 80b 148.3 0b 16.7 0d 8.8 0a 40.1 0b 7.50a 5.7 9bcd 232.9 4bcde 8.63b cde 11 G1 2 30.5 0b 39.50 c 75.0 0b 30.2 0a 125. 20b 146.7 0b 25.4 0a 5.4 0a 21.6 0d 4.60cd e 5.4 6cde 118.92 fgh 4.40f gh 12 G1 3 35.7 0a 46.20 a 87.2 0a 37.3 0a 129. 80b 152.8 0b 18.5 0d 6.5 0a 29.5 0c 5.00b cde 6.7 8abc 201.0 3cdef 7.45c def 13 G1 5 29.8 0b 38.80 c 74.3 0b 34.8 0a 131. 30b 151.3 0b 18.5 0d 5.6 0a 21.8 0cd 4.00e 4.8 2de 105.0 8gh 3.89g h 14 G1 6 30.0 0b 40.00 c 75.5 0b 41.6 0a 171. 60a 199.1 0a 26.2 0a 7.8 0a 41.9 0b 6.70ab c 6.7 2abc 281.0 0bn 10.41 bc 15 G1 9 30.5 0b 41.80 b 77.3 0b 48.4 0a 180. 90a 209.4 0a 24.5 0ab 9.3 0a 52.3 0a 7.40a 7.3 0a 374.4 8a 13.87 a Values with the same superscript letter(s) along the same column are not significantly different DTF= Days to flowering ; DTFFA= Days to first flower appearance ; DTM= Days to maturity; PHTF= Plant height at flowering (cm); PHTM= Plant height at maturity (cm); PHTH= Plant height at harvest (cm); NLPF= Number of leaves per plant at flowering; NBP= Number of branches per plant; NFP = Number of fruits per plant; NCP= Number of clusters per plant; IFWT= Individual fruit weight (g); YD/P= Yield per plant (g) and YD/HA= Yield per hectare . G1= NGB 00695; G2= NGB 00696; G3=NGB 00708; G5=NGB 00713; G6= NGB 00714; G8= NGB 0072; G9= NGB 00724; G10= NGB 00725; G11=NGB 00726; G12= NGB 00727; G13= NGB 00729; G15= NGB 00735; G16= NGB 00737; G19= NGB 0075 P-ISSN 2695-222X Table 3: Component of genetic parameters of characters considered in tomato genotypes Character s Mean Rang e Genotypi c Variance Phenotypi c Variance GCV % PCV % HB % GA GAM % DTF 33.05 32.60 - 36.60 15.60 15.98 11.95 12.07 98.00 8.05 24.36 DTFFA 42.72 38.60 - 46.20 21.25 22.35 10.79 11.07 95.00 9.26 21.67 DTM 81.55 74.30 -89.40 86.47 88.62 11.40 11.54 98.00 18.9 2 23.20 PHTF (cm) 37.80 30.10 - 48.40 79.34 105.70 23.56 27.19 67.00 15.9 0 42.05 PHTM (cm) 145.7 3 123.1 0 - 180.9 0 1099.72 1176.29 22.76 23.53 93.00 66.0 5 45.32 PHTH (cm) 169.8 7 147.1 0 - 209.4 0 1334.4 1444.9 21.50 22.38 92.00 72.3 2 42.57 NLPF 21.77 17.20 - 27.80 33.86 35.45 26.73 27.35 95.00 11.71 53.81 NBP 7.32 5.40 - 9.30 3.51 4.92 25.59 30.30 62.00 3.25 44.53 NFP 32.81 20.00 - 51.30 248.98 252.77 48.09 48.46 98.00 32.2 6 98.35 NCP 5.56 3.50 - 7.50 4.06 4.34 36.24 32.47 94.00 4.01 72.23 IFWT(g) 5.88 4.23 – 7.30 1.98 2.09 23.93 24.59 94.00 2.82 47.98 YD/P (g) 199.5 0 84.45- 374.4 8 16720.30 17223.80 64.82 65.78 97.00 26.2 5 131.55 YD/HA 7.39 3.13 - 13.87 22.94 23.63 64.81 65.78 97.00 9.72 131.54 DTF= Days to flowering ; DTFFA= Days to first flower appearance ; DTM= Days to maturity; PHTF= Plant height at flowering (cm); PHTM= Plant height at maturity (cm); P-ISSN 2695-222X PHTH= Plant height at harvest (cm); NLPF= Number of leaves per plant at flowering; NBP= Number of branches per plant; NFP = Number of fruits per plant; NCP= Number of clusters per plant; IFWT= Individual fruit weight (g); and YD/HA= Yield per hectare . GV= Genotypic variance; PV= Phenotypic variance; GCV= Genotypic coefficient of variation; PCV= Phenotypic coefficient of variation; HB= Heritability; GA= Genetic advance; GAM= Genetic advance as percent of mean P-ISSN 2695-222X TABLE 4:Comparison of genomic DNA concentration and purity level using 3 different extraction protocol in tomato genotypes CTAB ZY MO KIT SD S Genot ype code Nucleic acid concentrat ion (ng/μL) A26 0 A28 0 DNA PURIT Y A260/ 280 Nucleic acid concentrat ion (ng/μL) A26 0 A28 0 DNA PURIT Y A260/2 80 Nucleic acid concentr ation (ng/μL) A2 60 A2 80 DNA PURIT Y A260/2 80 G1 250.800 0.23 0 0.14 0 1.643 271.200 0.22 0 0.11 0 2.000 999.600 0.8 30 0.4 50 1.844 G2 85.200 0.27 0 0.14 0 1.929 157.200 0.11 0 0.06 0 1.833 649.200 0.5 40 0.3 10 1.742 G3 190.800 0.21 0 0.12 0 1.750 475.200 0.34 0 0.18 0 1.889 57.600 0.0 40 0.0 19 2.105 G4 123.600 0.29 0 0.16 0 1.813 448.800 0.37 0 0.20 0 1.850 248.400 0.2 10 0.1 20 1.750 G5 350.400 0.39 0 0.22 0 1.773 355.200 0.29 0 0.16 0 1.810 80.400 0.0 60 0.0 29 2.069 G6 224.400 0.18 0 0.08 0 2.250 490.800 0.40 0 0.20 0 2.000 127.200 0.2 30 0.1 10 2.091 G8 96.000 0.09 0 0.05 0 1.800 66.000 0.07 2 0.04 0 1.800 440.400 0.3 60 0.1 90 1.895 G9 98.400 0.10 0 0.05 0 2.000 369.600 0.30 0 0.15 0 2.000 361.200 0.3 00 0.1 80 1.667 G10 92.400 0.06 0 0.03 0 2.000 104.400 0.08 0 0.04 0 2.000 238.800 0.1 90 0.1 10 1.727 G11 60.000 0.09 0 0.05 0 1.800 361.200 0.26 0 0.13 0 2.000 165.600 0.2 30 0.1 00 2.300 G12 183.600 0.25 0 0.12 0 2.083 309.600 0.25 0 0.13 0 1.920 333.600 0.3 70 0.1 90 1.947 G13 121.200 0.27 0 0.13 0 2.077 306.000 0.25 0 0.13 0 1.920 319.200 0.2 60 0.1 50 1.733 G15 225.600 0.21 0 0.12 0 1.750 645.600 0.49 0 0.25 0 1.960 308.400 0.3 50 0.1 50 2.333 G16 14.400 0.14 0 0.08 0 1.750 321.600 0.26 0 0.13 0 2.000 132.000 0.4 10 0.2 40 1.708 G19 112.800 0.21 0 0.11 0 1.909 135.600 0.23 0 0.12 0 1.917 21.600 0.4 30 0.2 10 2.048 G1= NGB 00695; G2=NGB 00696, G3=NGB 00708, G5=NGB 00713, G6= NGB 00714 G8=NGB 00721, G9=NGB 00724, G10=NGB 00725, G11=NGB 00726, G13=NGB 00729, G15=NGB 00735, G16=NGB 00737, G19=NGB 0075
More Articles from JOURNAL OF BIOLOGY AND GENETIC RESEARCH
Information Processing Speed and Cognitive Style as Joint Predictors of Secondary School Students’ Achievement in Biology in Anambra State, Nigeria
Author: Okigbo, Ebele Chinelo, Pat-Anyaeji, Veronica Nnenna
Effect of Inquiry-Based Instructional Strategy on Senior Secondary Students’ Interest, Achievement and Retention in Biology in Federal Capital Territory, Abuja
Author: Ubom, A. E. B., Ojelade, I. A. and Ekpruke, Oghenekevwe Jennifer
Influence of Soil Amendment, Season and Environment on the Germination Potential of Okra
Author: Sallet I., Chuku E. C., Nmom F. W. and Worlu C. W.
Biochemical Evaluation and Fungi Pathogens Associated with Fresh and Boiled Detarium microcarpum (Ofor) in Rivers State, Nigeria
Author: Emiri, U. N. and Chukwu, E. C.
Assessment of Sedimentation Rate of Aero-Pathogens in Health Centres in Port Harcourt
Author: Renner Renner Nrior & Gladden Karasira Lucky