• A ABBAS Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
  • A ARSHAD Department of Seed Science and Technology, University of Agriculture Faisalabad P.O BOX, 38000, Faisalabad, Pakistan
  • AU REHMAN Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
  • MS BUKHARI Agricultural Research Station Bahawalpur, P.O BOX, 63100, Bahawalpur, Pakistan
  • S ZAMAN College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing 211100, People’s Republic of China



DNA marker, MAS, CRISPR technology, breeding programs, genomic selection


The molecular marker method has come a long way in the last 30 years. Genetic research has advanced from RFLPs to SNPs. Array technology was also used. Sequencing progress has also led to the creation of low-cost NGS systems with high throughput. Phenotyping has been very important in making this progress possible. Markers for important crops like rice, corn, and potatoes have been worked on, but markers for crops that aren't used much haven't been studied as much. Phylogenetics and molecular ecology are other areas that don't know much about molecular markers. Plant breeding and DNA modification have greatly changed since recent improvements to CRISPR technology. To the contrary, some MAS (marker-assisted selection) methods need to know about the genome beforehand, which makes the work even harder. Researchers in plant science might find the methods discussed in this review piece useful as a database. They could use them alone or with other sequence-level characters from different fields.


Aaliya, K., Qamar, Z., Ahmad, N. I., Ali, Q., Munim, F. A., and Husnain, T. (2016). Transformation, evaluation of gtgene and multivariate genetic analysis for morpho-physiological and yield attributing traits in Zea mays. Genetika 48, 423-433. DOI: DOI:

Adhikari, S., Saha, S., Biswas, A., Rana, T., Bandyopadhyay, T. K., and Ghosh, P. (2017). Application of molecular markers in plant genome analysis: a review. The Nucleus 60, 283-297. DOI: DOI:

Ahmar, S., Gill, R. A., Jung, K.-H., Faheem, A., Qasim, M. U., Mubeen, M., and Zhou, W. (2020). Conventional and molecular techniques from simple breeding to speed breeding in crop plants: recent advances and future outlook. International journal of molecular sciences 21, 2590. DOI: DOI:

Ali, Q., Ahsan, M., Ali, F., Aslam, M., Khan, N. H., Munzoor, M., Mustafa, H. S. B., and Muhammad, S. (2013). Heritability, heterosis and heterobeltiosis studies for morphological traits of maize (Zea mays L.) seedlings. Advancements in Life sciences 1.

Ali, Q., Ahsan, M., Kanwal, N., Ali, F., Ali, A., Ahmed, W., Ishfaq, M., and Saleem, M. (2016). Screening for drought tolerance: comparison of maize hybrids under water deficit condition. Advancements in Life Sciences 3, 51-58.

Ali, Q., Ali, A., Ahsan, M., Nasir, I. A., Abbas, H. G., and Ashraf, M. A. (2014). Line× Tester analysis for morpho-physiological traits of Zea mays L seedlings. Advancements in Life sciences 1, 242-253.

Ali, Q., and Malik, A. (2021). Genetic response of growth phases for abiotic environmental stress tolerance in cereal crop plants. Genetika 53, 419-456. DOI: DOI:

Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 7. DOI: DOI:

Andersen, E. J., Ali, S., Byamukama, E., Yen, Y., and Nepal, M. P. (2018). Disease resistance mechanisms in plants. Genes 9, 339. DOI: DOI:

Asif, S., Ali, Q., and Malik, A. (2020). Evaluation of salt and heavy metal stress for seedling traits in wheat. Biological and Clinical Sciences Research Journal 2020. DOI: DOI:

Balqees, N., Ali, Q., and Malik, A. (2020). Genetic evaluation for seedling traits of maize and wheat under biogas wastewater, sewage water and drought stress conditions. Biological and Clinical Sciences Research Journal 2020. DOI: DOI:

Balsalobre, T. W. A., da Silva Pereira, G., Margarido, G. R. A., Gazaffi, R., Barreto, F. Z., Anoni, C. O., Cardoso-Silva, C. B., Costa, E. A., Mancini, M. C., and Hoffmann, H. P. (2017). GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC genomics 18, 1-19. DOI: DOI:

Billerman, S. M., and Walsh, J. (2019). Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions. Molecular Ecology Resources 19, 1115-1130. DOI: DOI:

Boopathi, N. M., and Boopathi, N. M. (2020). Marker-assisted selection (MAS). Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits, 343-388. DOI: DOI:

Bora, S. K. (2023). Applications of Genomic Selection in Animal Breeding: Challenges and Opportunities. World News of Natural Sciences 48, 107-117.

Cobb, J. N., Biswas, P. S., and Platten, J. D. (2019). Back to the future: revisiting MAS as a tool for modern plant breeding. Theoretical and Applied Genetics 132, 647-667. DOI: DOI:

Conway, G. (2019). "The doubly green revolution: food for all in the twenty-first century," Cornell University Press.

Das, G., Patra, J. K., and Baek, K.-H. (2017). Insight into MAS: a molecular tool for development of stress resistant and quality of rice through gene stacking. Frontiers in plant science 8, 985. DOI: DOI:

Deogharia, M., and Gurha, P. (2022). The “guiding” principles of noncoding RNA function. Wiley Interdisciplinary Reviews: RNA 13, e1704. DOI: DOI:

Dinh, X. H. (2020). Molecular genetics of barley (Hordeum vulgare): Leaf rust (Puccinia hordei) interactions.

Duan, L., Wu, T., Li, X., Huang, D., Li, X., Wen, X., Chen, P., Xie, J., and Hu, B. (2022). QTL detection for grain yield and micro-nutrition contents in rice (Oryza sativa) using an interspecific backcross population derived from Dongxiang wild rice (Oryza rufipogon). Crop and Pasture Science 73, 1253-1263. DOI: DOI:

Dwivedi, S. L., Siddique, K. H., Farooq, M., Thornton, P. K., and Ortiz, R. (2018). Using biotechnology-led approaches to uplift cereal and food legume yields in dryland environments. Frontiers in plant science 9, 1249. DOI: DOI:

Farooq, M. U., Bashir, M. F., Khan, M. U. S., Iqbal, B., and Ali, Q. (2021). Role of crispr to improve abiotic stress tolerance in crop plants. Biological and Clinical Sciences Research Journal 2021. DOI: DOI:

Feschotte, C. (2023). Transposable elements: McClintock’s legacy revisited. Nature Reviews Genetics 24, 797-800. DOI: DOI:

Ghafoor, M. F., Ali, Q., and Malik, A. (2020). Effects of salicylic acid priming for salt stress tolerance in wheat. Biological and Clinical Sciences Research Journal 2020. DOI: DOI:

Gouda, G., Gupta, M. K., Donde, R., Mohapatra, T., Vadde, R., and Behera, L. (2020). Marker-assisted selection for grain number and yield-related traits of rice (Oryza sativa L.). Physiology and molecular biology of plants 26, 885-898. DOI: DOI:

Gouveia, B. C., Calil, I. P., Machado, J. P. B., Santos, A. A., and Fontes, E. P. (2017). Immune receptors and co-receptors in antiviral innate immunity in plants. Frontiers in microbiology 7, 2139. DOI: DOI:

Gupta, N., Batra, N., and Bhardwaj, S. C. (2017). Wheat rust research–Status, efforts and way ahead. Journal of Wheat Research 9, 72-86. DOI: 10.25174/2249- 4065/2017/60445 DOI:

Hasan, N., Choudhary, S., Naaz, N., Sharma, N., and Laskar, R. A. (2021). Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Journal of Genetic Engineering and Biotechnology 19, 1-26. DOI: DOI:

Hennessy, C. (2017). Investigating the epigenetic regulation of toll-like receptor 3.

Hernandez, J., Meints, B., and Hayes, P. (2020). Introgression breeding in barley: Perspectives and case studies. Frontiers in plant science 11, 761. DOI: DOI:

Hidalgo-Cantabrana, C., Goh, Y. J., and Barrangou, R. (2019). Characterization and repurposing of type I and type II CRISPR–Cas systems in bacteria. Journal of molecular biology 431, 21-33. DOI: DOI:

Huider, F., Milaneschi, Y., Van der Zee, M. D., De Geus, E. J., Helmer, Q., Penninx, B. W., and Boomsma, D. I. (2021). Major depressive disorder and lifestyle: correlated genetic effects in extended twin pedigrees. Genes 12, 1509. DOI: DOI:

Iqbal, S., Ali, Q., and Malik, A. (2021). Effects of seed priming with salicylic acid on zea mays seedlings grown under salt stress conditions. Biological and Clinical Sciences Research Journal 2021. DOI: DOI:

Iqra, L., Rashid, M. S., Ali, Q., Latif, I., and Mailk, A. (2020). Evaluation for Na+/K+ ratio under salt stress condition in wheat. Life Sci J 17, 43-47. DOI:

Jasrotia, R. S., Iquebal, M. A., Yadav, P. K., Kumar, N., Jaiswal, S., Angadi, U., Rai, A., and Kumar, D. (2017). Development of transcriptome based web genomic resources of yellow mosaic disease in Vigna mungo. Physiology and Molecular Biology of Plants 23, 767-777. DOI: DOI:

Jeffares, D. C., Jolly, C., Hoti, M., Speed, D., Shaw, L., Rallis, C., Balloux, F., Dessimoz, C., Bähler, J., and Sedlazeck, F. J. (2017). Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature communications 8, 14061. DOI: DOI:

Jena, K. K., and Kim, S.-R. (2020). Genomics, biotechnology and plant breeding for the improvement of rice production. Accelerated Plant Breeding, Volume 1: Cereal Crops, 217-232. DOI: DOI:

Johnston‐Monje, D., and Lopez Mejia, J. (2020). Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi. Applications in Plant Sciences 8, e11334. DOI: DOI:

Juma, R. U., Bartholomé, J., Thathapalli Prakash, P., Hussain, W., Platten, J. D., Lopena, V., Verdeprado, H., Murori, R., Ndayiragije, A., and Katiyar, S. K. (2021). Identification of an elite core panel as a key breeding resource to accelerate the rate of genetic improvement for irrigated rice. Rice 14, 1-22. DOI: DOI:

Khanfri, S., Boulif, M., and Lahlali, R. (2018). Yellow rust (Puccinia striiformis): a serious threat to wheat production worldwide. Notulae Scientia Biologicae 10, 410-423. DOI: DOI:

Köhl, J., Kolnaar, R., and Ravensberg, W. J. (2019). Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy. Frontiers in plant science, 845. DOI: DOI:

Kthiri, D. (2017). Genetic and molecular characterization of leaf rust resistance from uncharacterized sources of durum wheat (Triticum turgidum L. ssp. durum), University of Saskatchewan.

Kumar, S. J., Susmita, C., Agarwal, D. K., Pal, G., Rai, A. K., and Simal-Gandara, J. (2021). Assessment of genetic purity in rice using polymorphic SSR markers and its economic analysis with grow-out-test. Food Analytical Methods 14, 856-864. DOI: DOI:

Kumawat, G., Kumawat, C. K., Chandra, K., Pandey, S., Chand, S., Mishra, U. N., Lenka, D., and Sharma, R. (2020). Insights into marker assisted selection and its applications in plant breeding. In "Plant Breeding-Current and Future Views". Intechopen. DOI: DOI:

Lapochkina, I., Baranova, O., Shamanin, V., Volkova, G., Gainullin, N., Anisimova, A., Galinger, D., Lazareva, E., Gladkova, E., and Vaganova, O. (2017). The development of the initial material of spring common wheat for breeding for resistance to stem rust (Puccinia graminis Pers. f. sp. tritici), including the Ug99 race, in Russia. Russian Journal of Genetics: Applied Research 7, 308-317. DOI: DOI:

Lev, I., Seroussi, U., Gingold, H., Bril, R., Anava, S., and Rechavi, O. (2017). MET-2-dependent H3K9 methylation suppresses transgenerational small RNA inheritance. Current Biology 27, 1138-1147. DOI: DOI:

Li, D., Zhou, Z., Lu, X., Jiang, Y., Li, G., Li, J., Wang, H., Chen, S., Li, X., and Würschum, T. (2021a). Genetic dissection of hybrid performance and heterosis for yield-related traits in maize. Frontiers in Plant Science 12, 774478. DOI: DOI:

Li, S., Zhang, C., Li, J., Yan, L., Wang, N., and Xia, L. (2021b). Present and future prospects for wheat improvement through genome editing and advanced technologies. Plant Communications 2. DOI: DOI:

Li, Y., Mo, Y., Li, Z., Yang, M., Tang, L., Cheng, L., and Qiu, Y. (2020). Characterization and application of a gall midge resistance gene (Gm6) from Oryza sativa ‘Kangwenqingzhan’. Theoretical and Applied Genetics 133, 579-591. DOI: DOI:

Manghwar, H., Li, B., Ding, X., Hussain, A., Lindsey, K., Zhang, X., and Jin, S. (2020). CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off‐target evaluation, and strategies to mitigate off‐target effects. Advanced science 7, 1902312. DOI: DOI:

Mazhar, T., Ali, Q., and Malik, M. (2020). Effects of salt and drought stress on growth traits of Zea mays seedlings. Life Science Journal 17, 48-54.

Mefleh, M., Conte, P., Fadda, C., Giunta, F., Piga, A., Hassoun, G., and Motzo, R. (2019). From ancient to old and modern durum wheat varieties: Interaction among cultivar traits, management, and technological quality. Journal of the Science of Food and Agriculture 99, 2059-2067. DOI: DOI:

Milc, J., Bagnaresi, P., Aragona, M., Valente, M., Biselli, C., Infantino, A., Francia, E., and Pecchioni, N. (2019). Comparative transcriptome profiling of the response to Pyrenochaeta lycopersici in resistant tomato cultivar Mogeor and its background genotype—susceptible Moneymaker. Functional & integrative genomics 19, 811-826. DOI: DOI:

Montgomery, D. R. (2017). "Growing a revolution: bringing our soil back to life," WW Norton & Company.

Mores, A., Borrelli, G. M., Laidò, G., Petruzzino, G., Pecchioni, N., Amoroso, L. G. M., Desiderio, F., Mazzucotelli, E., Mastrangelo, A. M., and Marone, D. (2021). Genomic approaches to identify molecular bases of crop resistance to diseases and to develop future breeding strategies. International Journal of Molecular Sciences 22, 5423. DOI: DOI:

Mulima, E. P. (2017). Genetic diversity of sorghum (Sorghum bicolor L. Moench) germplasm and hybrid potential under contrasting environments in Mozambique.

Mustafa, H. S. B., Mahmood, T., Hameed, A., and Ali, Q. (2018). Enhancing food security in arid areas of Pakistan through newly developed drought tolerant and short duration mustard (Brassica juncea L.) Canola. Genetika 50, 21-31. DOI: DOI:

Naseem, S., Ali, Q., and Malik, A. (2020). Evaluation of maize seedling traits under salt stress. Biological and Clinical Sciences Research Journal 2020. DOI: DOI:

Pajares, M. J., Palanca-Ballester, C., Urtasun, R., Alemany-Cosme, E., Lahoz, A., and Sandoval, J. (2021). Methods for analysis of specific DNA methylation status. Methods 187, 3-12. DOI: DOI:

Paul, S. K., Mahmud, N. U., Gupta, D. R., Rani, K., Kang, H., Wang, G.-L., Jankuloski, L., and Islam, T. (2022). Oryzae pathotype of Magnaporthe oryzae can cause typical blast disease symptoms on both leaves and spikes of wheat under a growth room condition. Phytopathology Research 4, 1-12. DOI: DOI:

Peng, F. Y., and Yang, R.-C. (2017). Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.). BMC plant biology 17, 1-17. DOI: DOI:

Piao, M., Sun, L., and Zhang, Q. C. (2017). RNA regulations and functions decoded by transcriptome-wide RNA structure probing. Genomics, proteomics & bioinformatics 15, 267-278. DOI: DOI:

Pomerantz, A., Sahlin, K., Vasiljevic, N., Seah, A., Lim, M., Humble, E., Kennedy, S., Krehenwinkel, H., Winter, S., and Ogden, R. (2022). Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Nature Protocols 17, 1415-1443. DOI: DOI:

Quero-García, J., Letourmy, P., Campoy, J. A., Branchereau, C., Malchev, S., Barreneche, T., and Dirlewanger, E. (2021). Multi-year analyses on three populations reveal the first stable QTLs for tolerance to rain-induced fruit cracking in sweet cherry (Prunus avium L.). Horticulture Research 8. DOI: DOI:

Ramesh, P., Mallikarjuna, G., Sameena, S., Kumar, A., Gurulakshmi, K., Reddy, B. V., Reddy, P. C. O., and Sekhar, A. C. (2020). Advancements in molecular marker technologies and their applications in diversity studies. Journal of biosciences 45, 1-15. DOI: DOI:

Sahu, P. K., Sao, R., Choudhary, D. K., Thada, A., Kumar, V., Mondal, S., Das, B. K., Jankuloski, L., and Sharma, D. (2022). Advancement in the breeding, biotechnological and genomic tools towards development of durable genetic resistance against the rice blast disease. Plants 11, 2386. DOI: DOI:

Shimizu, T., Aka Kacar, Y., Cristofani-Yaly, M., Curtolo, M., and Machado, M. A. (2020). Markers, maps, and marker-assisted selection. The Citrus Genome, 107-139. DOI: DOI:

Silvia, A. L., Shugarts, N., and Smith, J. (2017). A preliminary assessment of the ForenSeq™ FGx System: next generation sequencing of an STR and SNP multiplex. International journal of legal medicine 131, 73-86. DOI: DOI:

Singer, B. D. (2019). A practical guide to the measurement and analysis of DNA methylation. American journal of respiratory cell and molecular biology 61, 417-428. DOI: DOI:

Singh, R. B., Singh, B., and Singh, R. K. (2019). Development of potential dbEST-derived microsatellite markers for genetic evaluation of sugarcane and related cereal grasses. Industrial Crops and Products 128, 38-47. DOI: DOI:

Song, W., Forderer, A., Yu, D., and Chai, J. (2021). Structural biology of plant defence. New Phytologist 229, 692-711. DOI: DOI:

Sun, M., Dong, Z., Yang, J., Wu, W., Zhang, C., Zhang, J., Zhao, J., Xiong, Y., Jia, S., and Ma, X. (2021). Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers. BMC Plant Biology 21, 1-15. DOI: DOI:

Tahir, T., Ali, Q., Rashid, M. S., and Malik, A. (2020). The journey of CRISPR-cas9 from bacterial defense mechanism to a gene editing tool in both animals and plants. Biological and Clinical Sciences Research Journal 2020. DOI: DOI:

Tourrette, E., Falque, M., and Martin, O. C. (2021). Enhancing backcross programs through increased recombination. Genetics Selection Evolution 53, 1-13. DOI: DOI:

van der Loos, L. M., and Nijland, R. (2021). Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Molecular Ecology 30, 3270-3288. DOI: DOI:

Vats, S., Kumawat, S., Kumar, V., Patil, G. B., Joshi, T., Sonah, H., Sharma, T. R., and Deshmukh, R. (2019). Genome editing in plants: exploration of technological advancements and challenges. Cells 8, 1386. DOI: DOI:

Wang, K., Liu, H., Du, L., and Ye, X. (2017). Generation of marker‐free transgenic hexaploid wheat via an Agrobacterium‐mediated co‐transformation strategy in commercial Chinese wheat varieties. Plant Biotechnology Journal 15, 614-623. DOI: DOI:

Wang, M., Wang, S., Liang, Z., Shi, W., Gao, C., and Xia, G. (2018). From genetic stock to genome editing: gene exploitation in wheat. Trends in Biotechnology 36, 160-172. DOI: DOI:

Wilde, P., and Miedaner, T. (2021). Hybrid rye breeding. The Rye Genome, 13-41. DOI: DOI:

Yadavalli, V. R., Balakrishnan, D., Surapaneni, M., Addanki, K., Mesapogu, S., Beerelli, K., Desiraju, S., Voleti, S. R., and Neelamraju, S. (2022). Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon. Planta 256, 71. DOI: DOI:

Zhang, D., Zhang, Z., Unver, T., and Zhang, B. (2021a). CRISPR/Cas: A powerful tool for gene function study and crop improvement. Journal of Advanced Research 29, 207-221. DOI: DOI:

Zhang, F., Shi, Y., Ali, J., Xu, J., and Li, Z. (2021b). Breeding by selective introgression: Theory, practices, and lessons learned from rice. The Crop Journal 9, 646-657. DOI: DOI:

Zhou, L., Peng, R., Zhang, R., and Li, J. (2018). The applications of CRISPR/Cas system in molecular detection. Journal of cellular and molecular medicine 22, 5807-5815. DOI: DOI:




How to Cite


Most read articles by the same author(s)