The yield and purity of DNA extracts from seeds of eight six accessions of Treculia species using Zymo Research mini-prep DNA extraction kit
Article Sidebar
Main Article Content
Abstract
There is a need for the use of efficient DNA extraction methods that will yield good quality and quantity of DNA for molecular studies. Several commercial kits are available that are used in place of conventional extraction methods due to cost, speed, and safety. Therefore, the Zymo Research mini plant/seed DNA extraction kit was used to determine the yield and purity of DNA extracts of 86 accessions of Treculia africana varieties. Nanodrop Thermo Scientific™ NanoDrop™ One Microvolume UV-Vis Spectrophotometer was used to determine the quality and quantity of the extracted DNA. The extracted DNA was amplified by a polymerase chain reaction using
Internal Transcribed Spacer 1 and 2 (ITS 1 and ITS 2). The amplicon was run on 1% agarose gel electrophoresis. The concentration (ng/µl) at the A260/280 and A260/230 ratios of the samples were recorded. The concentration and purity values varied among the accessions. The purity at A260/280 ratio ranged from 1.5 to 2.18, obtained from accessions B22 and B43 respectively while A260/230 ratio ranged from 0.93 to 39.56, obtained from accessions C46 – Ab6 respectively. The values derived at the A260/280 ratio and A260/230 ratio
were majorly within the acceptable range of 1.8 – 2.0 suggesting that the ZR kit could eliminate contaminants. Thus, further downstream applications such as PCR and sequencing could conveniently be carried out. The suitability and efficiency of using Zymo research mini prep as a DNA extraction kit were revealed on the agarose gel images. Zymo Research DNA extraction kit is appropriate for the extraction of DNA from seeds of Treculia species.
Downloads
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
References
Abdel-Latif, A. and Osman, G. (2017). Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods, 13: 1 Doi: 10.1186/s13007-016-0152-4.
Aboul-Maaty N. AF. and Oraby, H. AS. (2019). Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method.Bulletin of the National Research Centre, 43(25) doi.org/10.1186/s42269-019-0066-1.
Abdullah, F. I., Chus, L. S., Rahmat, Z., Samad, A. A. and Wagiran, A. (2016). Genomic DNA extraction for herbs and sequencing their Internal Transcribed Spacer Regions amplified by specific primers. Natural Product Communication, 11(10): 1491 –1496
Abouseadaa, H. H., Osman, G. H., Ramadan, A. M., Hassanein, S. E., Abdelsattar, M. T., Morsy, Y. B., Alameldin, H. F., El-Ghareeb, D.K., Nour-Eldin, H. A., Salem, R., Gad, A. A., Elkhodary, S. E. and Shehata, M. M., Mahfouz, H. M., Eissa, H. F. and Bahieldin, A. (2015). Development of transgenic wheat (Triticum aestivum L.) expressing avidin gene conferring resistance to stored product insects. BMC Plant Biology, 15:183– 190.
Alfi, S., Ratna, P., Muindar, E. P. J. and Muhammad, L. A. (2021). Analysis of purity and concentration of DNA extracted from intron patho gene-spin extraction on processed crab food product samples Asian Journal of Tropical Biology, 19: 21-24. DOI: 10.13057/biofar/f190104.
Amujiri, A. N., Eze, P. C., Amadi, C. C. and Njoku, E. U. (2020). Effects of seed origin on the germination, seedling development, and morphology of African breadfruit (Treculia africana decne, moraceae) seeds. Bioscience Research, 17(4): 3060-3068.Bhattacharjee, R. (2009). Harnessing biotechnology for conservation and increased utilization of orphan crops. African Technology Development Journal, 6(3/4): 24- 33.
Chen, S. L., Pang, X. H., Song, J.Y., Shi, L., Yao, H., Han, J. and Leon, C. (2014). A renaissance in herbal medicine identification: from morphology to DNA. Biotechnology Advancement, 32(7): 1237-1244. 10.1016/j.biotechadv.2014.07.004.
Community Reference Laboratory for GM Foods and Feed Biotechnology and GMO Unit (CRL-GFF) (2007). Soybean seeds sampling and DNA extraction. Accessed from https://gmocrl.jrc.ec.europa.eu/summaries/A2704-12_soybean_DNAExtr_report.pdf.
Cornejo, O. E., Muh-Ching, Y., Dominguez, V., Andrews, M., Alexandra, S., Strandberg, D., Livingstone III, Conrad, S., Alberto, Ro, Pathmanathan, U., Stefan, R., Nilesh, R., Tawari, P., Osman, G., Wilbert, P., Mockaitis, K., Carlos, D., Motamayor, B. and Motamayor, J. C. (2018). Population genomic analyses of the chocolate tree, Theobroma cacaoL., provide insights into its domestication process. Communications Biology, 1(167) DOI: 10.1038/s42003-018-0168
Devi, K. D., Punyarani, K., Singh, S. and Devi, H. S. (2013). An efficient protocol for total DNA extraction from the members of order Zingiberales - suitable for diverse PCR based downstream applications. Springer Plus 2:669. https://doi.org/10.1186/2193-180-2-669.
Ekanade, O., Salami, A.T. and Odekunle, T. (1998). Adoption of modern farming techniques in rural southwestern Nigeria. Journal of Science Research, 4(1):63-67.
Ezennaya, C. F. and Ezeigwe, O. C. (2023). A comparative study on the nutritional compositiom of raw, boiled and roasted Treculia africana (African breadfruit). The Bioscientsis Journal, 11(1):15- 25.
Ganiyu, S. A., Ysuuf, S. M., Agbolade, J. O and Imonmion, J. E. (2017). The levels of yield and purity of geneomic DNA from five tomato cultivars subjected to two DNA extraction techniques. Nigerian Journal of Biotechnology, 33: 131 – 135.
Holden, M., Blasic, J., Bussjaeger, L., Kao, C., Shokere, L., Kendall, D., Freese, L. and Jenkins, G. (2003). Evaluation of extraction methodologies for corn kernel (Zea mays) DNA for detection of trace amounts of biotechnology-derived DNA. Journal of Agriculture and Food Chemistry, 51:2468–2474.
Healy, A., Furtado, A., Cooper, T. and Henry, R. (2014). Protocol a simple method for extracting next generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods, 10(21): wwwttp://www.plantmethods.com/content/10/1/21.
Japelaghi, R. H., Raheem, H. and Garoosi, G. A. (2011). Rapid and efficient isolation of high-quality nucleic acids from plant tissues rich in polyphenols and polysaccharides. Molecular Biotechnology, 49, 129-137.
Kapa Biosystems (2014). KAPA2G Fast HotStart PCR Kit Technical Data Sheet. Kapa Biosystems Inc., Wilmington, MA. Retrieved from https://ngenetics.com/files/co/Documents/manual/kapa_11065.pdf.
Moreira, P. and Oliveira, D. A. (2011). Leaf age affects the quality of DNA extracted from Dimorphandra mollis (Fabaceae), a tropical tree species from the Cerrado region of Brazil. Genetics and Molecular Research, 10(1):353-8. Doi: 10.4238/vol10-1gmr1030.
Moeller, J. R., Moehn, N.R., Waller, D. M and Givnish, T. J. (2014). Paramagnetic cellulose DNA isolation improves DNA yield and quality among diverse plant taxa. Applications in Plant Science, 2(10): 1400048 https://doi.org/10.3732%2Fapps.1400048
Navarro, J. A. R., Phillips-Mora, W., Arciniegas-Leal, A., Mata-Quirós, A., Haiminen, N., Mustiga, G., Livingstone, D., van Bake, H., Kuhn, D. N., Parida, L., Kasarskis, A. and Motamayor, J. C. (2017). Application of genome-wide association and genomic prediction for improvement of Cacao
productivity and resistance to black and frosty pod diseases. Frontiers in Plant Science, 14(8):1905. Doi: 10.3389/fpls.2017.01905. eCollection 2017.
Nuga, O. O. and Ofodile, E. A. U. (2010). Potentials of Treculia africana Decne- an endangered species of southern Nigeria. Journal of Agriculture and Social Research 10(2): 1- 9 Doi: 10.4314/jasr.v10i2.67577.
Nurhaimi-Haris, A. H., Toruan-Mathius, N. and Purwantara, A. (2003). Kemiripan genetik klon karet (Hevea brasiliensis Muell. Arg.) berdasarkan metode Amplified Fragment Length Polymorphisms (AFLP). Menara Perkeb,71: 1–15
Nurhaimi-Haris, A. H., Toruan-Mathius, N. and Purwantara, A. (2003). Kemiripan genetik klon karet (AFLP) Menara Perkeb, 71:1–15
Oderinde, A. A., Ibikunle, A. A., Bakre, L. G. and Babarinde, N. A. A. (2020). Modification of African breadfruit (Treculia africana, Decne) kernel starch: Physicochemical, morphological, pasting, and thermal properties. International Journal of Biological Macromolecules, 153: 78 -87.
Ogunkanmi, A. L., Amusa, O. D., Bola, K. and Oyekunle, S. M. (2019). Optimization and assessment of DNA extraction protocols in cowpea (Vigna ungiculata L. Walp.). African Scientist, 20(1): 9 – 15.
Okoronkwo, K. A., Nwagboso, O. C. and Okoronkwo, B. C. (2020). Chemical and amino acid composition of African breadfruit (Treculia africana).
International Network Organization for Scientific Research (Inosr) Applied Sciences 6(1): 1-10.
Pervaiz, Z., Turi, N., Khaliq, I., Rabbani, M., and Malik, S. A modified method for high-quality DNA extraction for molecular analysis in cereal plants
(2011). Genetic and Molecular Research Journal, 10:1669–73.
Ramlah, I. R., Aziz, M., Pabendon, P. B. and Daryono, B. S. (2020). Method of DNA extraction of local maize (Zea mays l.) Tana Toraja, South
sulawesi, Indonesia using modification of buffer CTAB (cethyl trimethyl ammonium bromide) without liquid nitrogen. IOP Conference Series:
Earth and Environmental Science, 575: 012163 doi:10.1088/1755-1315/575/1/012163
Raimundo, J., Reis, C.M.G. and Ribeiro, M. M. Rapid, simple and potentially universal method for DNA extraction from Opuntia spp. Fresh cladode
tissues suitable for PCR amplification. Molecular Biology Reports. 2018, 45(5), 1405-1412.
Runsewe-Abiodun, T. I., Aliyu, A. O. and Oritogu, K. S. (2018). Evaluation of nutrients of anti- nutrients properties of Treculia africana (Bread fruit diet and toasted seeds). African Journal of Food and Agriculture, Nutrition and Development, 18(2):1372-13286.
Sahu, S. K., Thangaraj, M. and Kathiresan, K. (2012). DNA Extraction Protocol for Plants with High Levels of Secondary Metabolites and
Polysaccharides without Using Liquid Nitrogen and Phenol. ISRN Molecular Biology, 205049 Doi: 10.5402/2012/205049
Schenk, J. J., Becklund, L. E., Carey, J. S. and Fabre, P. P. (2023). What is the “modified” CTAB protocol? Characterizing modifications to the
CTAB DNA extraction protocol. Applications in Plant Science, 11(3): e11517 Doi.10.1002%2Faps3.11517
Srisutham, S., Saralamba. N., Malleret. B. and Re, L. (2017). Four human Plasmodium species quantification using droplet digital PCR. PLoS
One, 12 (4): e0175771. Doi: 10.1371/journal.pone.0175771
Huaqiang, T., Haitao, H., Manman, T., Jianyao, M. and Huanxiu, Li. (2013). Comparative analysis of six DNA Extraction methods in Cowpea (Vigna
unguiculata L. Walp). Journal of Agricultural Science, 5(7). Doi.org/10.5539/jas.v5n7p82.
Ugwu, C. S. and Iwuchukwu, J. C. (2013). Processing and preservation of African bread fruit (Treculia africana) by women in Enugu north agricultural zone, Enugu State, Nigeria. African Journal of Agricultural Research, 8(11): 984-994
Wang, Q., Shen, X., Qiu, T., Wu, W., Li, L., Wang, Z. and Shou, H. (2021). Evaluation and application of an efficient plant DNA extraction protocol for
laboratory and field testing. Journal of Zhejiang University Science B, 22(2): 99–111. Doi: 10.1631/jzus.B2000465
Wati, S. I. (2014). Analisis keragaman pola pita DNA antar varietas ganyong (Canna edulis Ker.) dari daerah karanganyar, solo dan boyolali
berdasarkan penanda RAPD. EL-VIVO 2(1)
Weising K, Nybom H, Wolff K, Kahl G. (2005) DNA fingerprinting in plants: principles, methods and applications. CRC press, Boca Raton. 472pp
Wullandari, D. R., Martin, A. F., Ermayanti, T. M., Sinanga. K. A. and Ratnadwei, D. (2023). Morpho- genetic characterization of diploid and
tetraploid taro (Colocasia esculenta L. Schott). Kaliurang- an Indonesian local cultivar. Czech Journal of Genetic and Plant Breeding, 59(3):
- 175
Xia, Y., Chen, F., Du,Y., Liu, C., Bu, G., Xin, Y. and Liu, B. (2019). A modified SDS-based DNA extraction method from soybean. Bioscience
Report, 39(2): BSR20182271. https://doi.org/10.1042%2FBSR20182271
Xin, Z. and Chen, J. (2012). A high throughput DNA extraction method with high yield and quality. Methodology, 8(26). Doi.org/10.1186/1746-
-8-26
Zymo research (2022). How to Extract DNA from plant leaves and seeds. An easy and practical protocol for DNA extraction from plants and
seeds. Retrieved from https://zymoresearch.eu/blogs/blog/how-toextract-dna-from-plant-leaves-seedsZymo Research Cooperation (Undated) Instruction manual Quick -DNA TM Plant /Seed Miniprep Kit Catalog Np D6020. Retrieved from https://files.zymoresearch.com/protocols/_d6020
_quick-dna_plant-seed_miniprep_kit.pdf