a Ege University, Izmir, Turkey
Все права защищены ©Aslanbay Guler и др. Это статья с открытым доступом, распространяемая на условиях международной лицензии Creative Commons Attribution 4.0. (http://creativecommons.org/licenses/by/4.0/
), позволяет другим распространять, перерабатывать, исправлять и развивать произведение, даже в коммерческих целях, при условии указания автора произведения.
Получена 07 Ноября, 2022 |
Принята в исправленном виде 04 Апреля, 2023 |
Опубликована 21 Апреля, 2023
Marker-assisted technologies in the field of plant biotechnology have attracted great interest of scientists seeking to determine the genetic variety and improve specific characteristics of species. Among several types, molecular markers hold great promise due to their high efficiency, adequate accuracy, and good reproducibility. This review aimed to present different molecular markers used in genetic biodiversity studies of common food plants, including potato, corn, and tomato.
We presented some of the most frequent molecular markers in terms of their methodologies, advantages, challenges, and applications. We also reviewed the latest advances in the genetic diversity studies of common food plants that contribute to agricultural activities.
According to latest progress, Simple Sequence Repeats, Sequence Characterized Amplified Region, and Single Nucleotide Polymorphism are the most common molecular markers in plant diversity studies due to their co-dominancy, high level of polymorphism, great reproducibility, and adequate specificity. Considering common food plants like potato, corn, and tomato, Simple Sequence Repeats and Single Nucleotide Polymorphisms provide detailed information about polymorphisms, resistance to pathogens or diseases, genome maps, and population dynamics. However, more research should be conducted to apply the latest and more efficient technologies, such as Next Generation Sequencing, Diversity Array Technologies, and omics, to the genetic diversity studies of plant species.
Within the scope of recent progress, this review has a strong potential in providing relevant material for further research. It can serve as a guide to adopt the latest and most efficient sequencing platforms for examining various plant species, primarily potato, corn, and tomato.
, genome sequencing
, Amplified Fragment Length Polymorphism (AFLP)
, Single Nucleotide Polymorphism (SNP)
, Random Amplified Polymorphic DNA (RAPD)
, polymerase chain reaction (PCR)
Bahar Aslanbay Guler conceptualized the research and wrote the original draft. Esra Imamoglu conceptualized and supervised the research, as well as reviewed and edited the manuscript.
The authors declare that there is no conflict of interest.
- Sadigov R. Rapid growth of the world population and its socioeconomic results. Scientific World Journal. 2022;2022. https://doi.org/10.1155/2022/8110229
- Jones RAC, Naidu RA. Global dimensions of plant virus diseases: Current status and future perspectives. Annual Review of Virology. 2019;6:387–409. https://doi.org/10.1146/annurev-virology-092818-015606
- Ahmar S, Gill RA, Jung K-H, Faheem A, Qasim MU, Mubeen M, et al. Conventional and molecular techniques from simple breeding to speed breeding in crop plants: Recent advances and future outlook. International Journal of Molecular Sciences. 2020;21(7). https://doi.org/10.3390/ijms21072590
- Kersey PJ, Collemare J, Cockel C, Das D, Dulloo EM, Kelly LJ, et al. Selecting for useful properties of plants and fungi – Novel approaches, opportunities, and challenges. Plants, People, Planet. 2020;2(5):409–420. https://doi.org/10.1002/ppp3.10136
- Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 2021;7(10). https://doi.org/10.1016/j.heliyon.2021.e08093
- Cheng A, Mayes S, Dalle G, Demissew S, Massawe F. Diversifying crops for food and nutrition security – a case of teff. Biological Reviews. 2017;92(1):188–198. https://doi.org/10.1111/brv.12225
- Saeed F, Khan MA, Sharif M, Mittal M, Goyal LM, Roy S. Deep neural network features fusion and selection based on PLS regression with an application for crops diseases classification. Applied Soft Computing. 2021;103. https://doi.org/10.1016/j.asoc.2021.107164
- Lema M. Marker assisted selection in comparison to conventional plant breeding: Review article. Agricultural Research and Technology. 2018;14(2). https://doi.org/10.19080/ARTOAJ.2018.14.555914
- Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Journal of Genetic Engineering and Biotechnology. 2021;19(1). https://doi.org/10.1186/s43141-021-00231-1
- Mondini L, Noorani A, Pagnotta MA. Assessing plant genetic diversity by molecular tools. Diversity. 2009;1(1):19–35. https://doi.org/10.3390/d1010019
- Singh HP, Raigar OP, Chahota RK. Estimation of genetic diversity and its exploitation in plant breeding. The Botanical Review. 2021;88:413–435. https://doi.org/10.1007/s12229-021-09274-y
- Kim HC, Kim K-H, Song K, Kim JY, Lee B-M. Identification and validation of candidate genes conferring resistance to downy mildew in corn (Zea mays L.). Genes. 2020;11(2). https://doi.org/10.3390/genes11020191
- Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. The Nucleus. 2017;60:283–297. https://doi.org/10.1007/s13237-017-0214-7
- Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F. Trends in plant research using molecular markers. Planta. 2018;247(3):543–557. https://doi.org/10.1007/s00425-017-2829-y
- Kumar A, Swapnil, Perween S, Singh RS, Singh DN. Prospect of molecular markers in precision plant breeding. In: Swapnil, editor. Recent advances in chemical sciences and biotechnology. New Delhi Publishers; 2020. pp. 131–142.
- Al-Hadeithi ZSM, Jasim SA. Study of plant genetic variation through molecular markers: An overview. Journal of Pharmaceutical Research International. 2021;33(45B):464–473. https://doi.org/10.9734/jpri/2021/v33i45B32828
- Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, et al. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology and Biotechnological Equipment. 2017;32(2):261–285. https://doi.org/10.1080/13102818.2017.1400401
- Sesli M, Yegenoglu ED. Genetic relationships in wild olives (Olea europaea ssp. oleaster) by ISSR and RAPD markers. Biotechnology and Biotechnological Equipment. 2017;31(5):897–904. https://doi.org/10.1080/13102818.2017.1344107
- Al-Khayri JM, Mahdy EMB, Taha HSA, Eldomiaty AS, Abd-Elfattah MA, Latef AAHA, et al. Genetic and morphological diversity assessment of five kalanchoe genotypes by SCoT, ISSR and RAPD-PCR markers. Plants. 2022;11(3). https://doi.org/10.3390/plants11131722
- Tikendra L, Amom T, Nongdam P. Molecular genetic homogeneity assessment of micropropagated Dendrobium moschatum Sw. – A rare medicinal orchid, using RAPD and ISSR markers. Plant Gene. 2019;19. https://doi.org/10.1016/j.plgene.2019.100196
- Choudhury A, Deb S, Kharbyngar B, Rajpal VR, Rao SR. Dissecting the plant genome: through new generation molecular markers. Genetic Resources and Crop Evolution. 2022;69(1):2661–2698. https://doi.org/10.1007/s10722-022-01441-3
- Sharma P, Nath AK, Dhiman SR, Dogra S, Sharma V. Characterization of carnation (Dianthus caryophyllus L.) genotypes and gamma irradiated mutants using RAPD, ISSR and SSR markers. South African Journal of Botany. 2022;148:67–77. https://doi.org/10.1016/j.sajb.2022.04.012
- Lin W-J, Tung C-Y, Yen M-Y, Chan Y-J, Lin C-H, Hsueh P-R. A novel target pathogen identification and tracking system using capillary electrophoresis-random amplified polymorphic DNA. Scientific Reports. 2018;8(1). https://doi.org/10.1038/s41598-018-33702-6
- Ramesh P, Mallikarjuna G, Sameena S, Kumar A, Gurulakshmi K, Reddy BV, et al. Advancements in molecular marker technologies and their applications in diversity studies. Journal of Biosciences. 2020;45(1). https://doi.org/10.1007/s12038-020-00089-4
- Leipold M, Tausch S, Hirtreiter M, Poschlod P, Reisch C. Sampling for conservation genetics: How many loci and individuals are needed to determine the genetic diversity of plant populations using AFLP? Conservation Genetic Resources. 2020;12(4):99–108. https://doi.org/10.1007/s12686-018-1069-1
- Negi MS, Sharma SS, Singh A, Chauhan S, Adholeya A, Tripathi SB. Analysis of genetic diversity of Indian tea accessions using two modified amplified fragment length polymorphism methods. Proceedings of the National Academy of Sciences India, Section B: Biological Sciences. 2018;88:621–632. https://doi.org/10.1007/s40011-016-0798-8
- Li X, Qiao L, Chen B, Zheng Y, Zhi C, Zhang S, et al. SSR markers development and their application in genetic diversity evaluation of garlic (Allium sativum) germplasm. Plant Diversity. 2022;44(5):481–491. https://doi.org/10.1016/j.pld.2021.08.001
- Shahabzadeh Z, Mohammadi R, Darvishzadeh R, Jaffari M. Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers. Molecular Biology Reports. 2020;47(1):655–669. https://doi.org/10.1007/s11033-019-05173-z
- Buddhachat K, Changtor P, Ninket S. An accurate and rapid method for species identification in plants: Melting fingerprint-high resolution melting (MFin-HRM) analysis. Plant Gene. 2019;20. https://doi.org/10.1016/j.plgene.2019.100203
- Stavridou E, Lagiotis G, Kalaitzidou P, Grigoriadis I, Bosmali I, Tsaliki E, et al. Characterization of the genetic diversity present in a diverse sesame landrace collection based on phenotypic traits and EST-SSR markers coupled with an HRM analysis. Plants. 2021;10(4). https://doi.org/10.3390/plants10040656
- Ambreetha S, Balachandar D. SCAR marker: A potential tool for authentication of agriculturally important microorganisms. Journal of Basic Microbiology. 2022;63(1):4–16. https://doi.org/10.1002/jobm.202200419
- Dar AA, Mahajan R, Sharma S. Molecular markers for characterization and conservation of plant genetic resources. The Indian Journal of Agricultural Science. 2019;89(11):1764–1772. https://doi.org/10.56093/ijas.v89i11.95286
- Asande LK, Ombori O, Nyaboga EN, Oduor RO. Efficient shoot organogenesis using leaf disc and nodal explants of passion fruit (Passiflora edulis Sims) and genetic fidelity assessment using sequence-related amplified polymorphism (SRAP) markers. International Journal of Agronomy. 2020;2020 https://doi.org/10.1155/2020/3205710
- Loera-Sánchez M, Studer B, Kölliker R. DNA-based assessment of genetic diversity in grassland plant species: Challenges, approaches, and applications. Agronomy. 2019;9(12). https://doi.org/10.3390/agronomy9120881
- Emrey TM. Application of molecular markers SNP and DArT in plant breeding: A review paper. Journal of Agricultural and Crops. 2018;4(8):86–92.
- Nguyen KL, Grondin A, Courtois B, Gantet P. Next-generation sequencing accelerates crop gene discovery. Trends in Plant Science. 2019;24(3):263–274. https://doi.org/10.1016/j.tplants.2018.11.008
- Pervez MT, Hasnain MJU, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A comprehensive review of performance of next-generation sequencing platforms. BioMed Research International. 2022;2022. https://doi.org/https://doi.org/10.1155/2022/3457806
- Manivannan A, Kim J-H, Yang E-Y, Ahn Y-K, Lee E-S, Choi S, et al. Next-generation sequencing approaches in genome-wide discovery of single nucleotide polymorphism markers associated with pungency and disease resistance in pepper. BioMed Research International. 2018;2018. https://doi.org/10.1155/2018/5646213
- Hess JF, Kohl TA, Kotrová M, Rönsch K, Paprotka T, Mohr V, et al. Library preparation for next generation sequencing: A review of automation strategies. Biotechnology Advances. 2020;41. https://doi.org/10.1016/j.biotechadv.2020.107537
- Soltabayeva A, Ongaltay A, Omondi JO, Srivastava S. Morphological, physiological and molecular markers for salt-stressed plants. Plants. 2021;10(2). https://doi.org/10.3390/plants10020243
- Munaweera TIK, Jayawardana NU, Rajaratnam R, Dissanayake N. Modern plant biotechnology as a strategy in addressing climate change and attaining food security. Agriculture and Food Security. 2022;11. https://doi.org/10.1186/s40066-022-00369-2
- Spanoghe M, Marique T, Nirsha A, Esnault F, Lanterbecq D. Genetic diversity trends in the cultivated potato: A spatiotemporal overview. Biology. 2022;11(4). https://doi.org/10.3390/biology11040604
- Duan Y, Duan S, Xu J, Zheng J, Hu J, Li X, et al. Late blight resistance evaluation and genome-wide assessment of genetic diversity in wild and cultivated potato species. Frontiers in Plant Science. 2021;12. https://doi.org/10.3389/fpls.2021.710468
- del Rio AH, Bamberg JB. Detection of adaptive genetic diversity in wild potato populations and its implications in conservation of potato germplasm. American Journal of Plant Science. 2020;11(10):1562–1578. https://doi.org/10.4236/ajps.2020.1110113
- del Rio A, Bamberg J. An AFLP marker core subset for the cultivated potato species Solanum phureja (Solanum tuberosum L. subsp. andigenum). American Journal of Potato Research. 2021;98(1):374–383. https://doi.org/10.1007/s12230-021-09849-w
- Pandey J, Scheuring DC, Koym JW, Coombs J, Novy RG, Thompson AL, et al. Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA. Scientific Reports. 2021;11. https://doi.org/10.1038/s41598-021-87284-x
- Jo KR, Cho S, Cho J-H, Park H-J, Choi J-G, Park Y-E, et al. Analysis of genetic diversity and population structure among cultivated potato clones from Korea and global breeding programs. Scientific Reports. 2022;12. https://doi.org/10.1038/s41598-022-12874-2
- Javed R, Iqbal M, Ullah S, Khan MR, Iqbal A, Ullah MS, et al. Phenotypic and molecular divergence in corn (Zea mays L.) ecotypes. Pakistan Journal of Agricultural Science. 2021;58:1777–1787.
- Mahato A, Shahi JP, Singh PK, Kumar M. Genetic diversity of sweet corn inbreds using agro-morphological traits and microsatellite markers. 3 Biotech. 2018;8(8). https://doi.org/10.1007/s13205-018-1353-5
- Roy NS, Park K-C, Lee S-I, Im M-J, Ramekar RV, Kim N-S. Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays. Genetica. 2018;146(1):1–12. https://doi.org/10.1007/s10709-017-9985-7
- Kasoma C, Shimelis H, Laing MD, Shayanowako AIT, Mathew I. Revealing the genetic diversity of corn (Zea mays L.) populations by phenotypic traits and DArTseq markers for variable resistance to fall armyworm. Genetic Resources and Crop Evolution. 2021;68(4):243–259. https://doi.org/10.1007/s10722-020-00982-9
- Osuman AS, Badu-Apraku B, Ifie BE, Tongoona P, Obeng-Bio E, Garcia-Oliveira AL. Genetic diversity, population structure and inter-trait relationships of combined heat and drought tolerant early-maturing corn inbred lines from west and central africa. Agronomy. 2020;10(9). https://doi.org/10.3390/agronomy10091324
- Pidigam S, Thuraga V, Munnam SB, Amarapalli G, Kuraba G, Pandravada SR, et al. Genetic diversity, population structure and validation of SSR markers linked to Sw-5 and I-2 genes in tomato germplasm. Physiology and Molecular Biology of Plants. 2021;27(1):1695–1710. https://doi.org/10.1007/s12298-021-01037-8
- Tranchida-Lombardo V, Mercati F, Avino M, Punzo P, Fiore MC, Poma I, et al. Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array. Plant Biosystems – An International Journal Dealing with all Aspects of Plant Biology. 2019;153(2):288–297. https://doi.org/10.1080/11263504.2018.1478900
- Alzahib RH, Migdadi HM, Al Ghamdi AA, Alwahibi MS, Afzal M, Elharty EH, et al. Exploring genetic variability among and within hail tomato landraces based on sequence-related amplified polymorphism markers. Diversity. 2021;13(3). https://doi.org/10.3390/d13030135
- Gonias ED, Ganopoulos I, Mellidou I, Bibi AC, Kalivas A, Mylona PV, et al. Exploring genetic diversity of tomato (Solanum lycopersicum L.) germplasm of genebank collection employing SSR and SCAR markers. Genetic Resources and Crop Evolution. 2019;66(4):1295–1309. https://doi.org/10.1007/s10722-019-00786-6
- Ahmed S, Zhou X, Pang Y, Xu Y, Tong C, Bao J. Genetic diversity of potato genotypes estimated by starch physicochemical properties and microsatellite markers. Food Chemistry. 2018;257:368–375. https://doi.org/10.1016/j.foodchem.2018.03.029
- Belalia N, Lupini A, Djemel A, Morsli A, Mauceri A, Lotti C, et al. Analysis of genetic diversity and population structure in Saharan corn (Zea mays L.) populations using phenotypic traits and SSR markers. Genetic Resources and Crop Evolution. 2019;66:243–257. https://doi.org/10.1007/s10722-018-0709-3
- Iboyi JE, Abe A, Adetimirin VO. Microsatellite marker-based genetic diversity of tropical-adapted shrunken-2 corn inbred lines and its relationship with normal endosperm inbred lines of known heterotic classification. Plant Genetic Resources. 2020;18(6):454–461. https://doi.org/10.1017/S1479262120000489
- Herison C, Sutjahjo SH, Sulastrini I, Rustikawati R, Marwiyah S. Genetic diversity analysis in 27 tomato accessions using morphological and molecular markers. AGRIVITA. Journal of Agricultural Science. 2018;40(1):36–44. https://doi.org/10.17503/agrivita.v40i1.726
- Kiani G, Siahchehreh M. Genetic diversity in tomato varieties assessed by ISSR markers. International Journal of Vegetable Science. 2018;24(4):353–360. https://doi.org/10.1080/19315260.2017.1419397
Aslanbay Guler B, Imamoglu E. Molecular marker technologies in food plant genetic diversity studies: an overview. Foods and Raw Materials. 2023;11(2):282–292. https://doi.org/10.21603/2308-4057-2023-2-575