Molecular markers have revolutionized crop improvement by enabling the accurate and efficient selection of desirable traits. This chapter provides a comprehensive overview of the role of molecular markers in plant breeding, emphasizing their use in disease resistance, tolerance to abiotic stress, and improving quality traits. The chapter delves into various types of molecular markers, including RFLPs, RAPDs, AFLPs, SSRs, SNPs, and their respective advantages and limitations in breeding programs. It also explores marker-assisted selection and genomic selection as key strategies for accelerating the breeding process. The combination of molecular markers with traditional breeding methods is explored, with case studies illustrating the effective use of these tools in advancing crop improvement. The chapter concludes by emphasizing the potential of molecular markers to enhance crop resilience and productivity in the face of global challenges, such as climate change and food security.
Molecular markers, Genetic diversity, Gene pyramiding, QTL mapping
Agarwal, M., Shrivastava, N., & Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant cell reports, 27, 617-631.
Ahmad, R., & Anjum, M. A. (2018). Applications of molecular markers to assess genetic diversity in vegetable and ornamental crops-a review. Journal of Horticultural Science and Technology, 1, 1-7.
Arbelaez, J. D., Tandayu, E., Reveche, M. Y., Jarana, A., van Rogen, P., Sandager, L., ... & Cobb, J. (2019). Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice. Plant Methods, 15, 1-11.
Asins, M. J., Bernet, G. P., Villalta, I., & Carbonell, E. A. (2009). QTL analysis in plant breeding. Molecular Techniques in Crop Improvement: 2nd Edition, 3-21.
Ayenan, M. A. T., Danquah, A., Hanson, P., Ampomah-Dwamena, C., Sodedji, F. A. K., Asante, I. K., & Danquah, E. Y. (2019). Accelerating breeding for heat tolerance in tomato (Solanum lycopersicum L.): an integrated approach. Agronomy, 9(11), 720.
Banoth, M., Nunavath, U. S., Bhimireddy, S., Konne, D., Govada, V., & Lavudya, S. (2023). Conventional and molecular breeding strategies for improvement of drought tolerance cultivars in rice: Recent approaches and outlooks. Environment Conservation Journal, 24(4), 367-381.
Belisle, C. E., Sargent, S. A., Brecht, J. K., Sandoya, G. V., & Sims, C. A. (2021). Accelerated shelf-life testing to predict quality loss in romaine-type lettuce. HortTechnology, 31(4), 490-499.
Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American journal of human genetics, 32(3), 314.
Chase, K., Belisle, C., Ahlawat, Y., Yu, F., Sargent, S., Sandoya, G., ... & Liu, T. (2024). Examining preharvest genetic and morphological factors contributing to lettuce (Lactuca sativa L.) shelf-life. Scientific Reports, 14(1), 6618.
Chen, F., Zhu, S. W., Xiang, Y., Jiang, H. Y., & Cheng, B. J. (2010). Molecular marker-assisted selection of the ae alleles in maize. Genetics and Molecular Research, 9(2), 1074-1084.
Chu, Y., Wu, C. L., Holbrook, C. C., Tillman, B. L., Person, G., & Ozias‐Akins, P. (2011). Marker‐assisted selection to pyramid nematode resistance and the high oleic trait in peanut. The plant genome, 4(2).
Chukwu, S. C., Rafii, M. Y., Ramlee, S. I., Ismail, S. I., Oladosu, Y., Muhammad, I. I., ... & Yusuf, B. R. (2020). Recovery of recurrent parent genome in a marker-assisted backcrossing against rice blast and blight infections using functional markers and SSRs. Plants, 9(11), 1411.
Collard, B. C., Jahufer, M. Z. Z., Brouwer, J. B., & Pang, E. C. K. (2005). An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica, 142, 169-196.
Demir, K. Ö. K. S. A. L., Bakir, M. E. L. İ. K. E., Sarikamis, G. Ö. L. G. E., & Acunalp, S. (2010). Genetic diversity of eggplant (Solanum melongena) germplasm from Turkey assessed by SSR and RAPD markers. Genetics and Molecular Research, 9(3).
Deokar, A., Sagi, M., Daba, K., & Tar'an, B. (2019). QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea. Plant Biotechnology Journal, 17(1), 275-288.
Dormatey, R., Sun, C., Ali, K., Coulter, J. A., Bi, Z., & Bai, J. (2020). Gene pyramiding for sustainable crop improvement against biotic and abiotic stresses. Agronomy, 10(9), 1255.
Ellur, R. K., Khanna, A., Bhowmick, P. K., Vinod, K. K., Nagarajan, M., Mondal, K. K., ... & Singh, A. K. (2016). Marker-aided incorporation of Xa38, a novel bacterial blight resistance gene, in PB1121 and comparison of its resistance spectrum with xa13+ Xa21. Scientific Reports, 6(1), 1-8.
Ferreira, J. R., Pereira, J. F., Turchetto, C., Minella, E., Consoli, L., & Delatorre, C. A. (2016). Assessment of genetic diversity in Brazilian barley using SSR markers. Genetics and molecular biology, 39(1), 86-96.
Gasbarra, D., Pirinen, M., Sillanpaa, M. J., & Arjas, E. (2009). Bayesian quantitative trait locus mapping based on reconstruction of recent genetic histories. Genetics, 183(2), 709-721.
Gaur, P. M., Samineni, S., Thudi, M., Tripathi, S., Sajja, S. B., Jayalakshmi, V., ... & Dixit, G. P. (2019). Integrated breeding approaches for improving drought and heat adaptation in chickpea (Cicer arietinum L.). Plant Breeding, 138(4), 389-400.
Gedil, M., Mengesha, W., Ilesanmi, O., & Menkir, A. (2024). Advances in Genetic Enhancement of Nutritional Quality of Tropical Maize in West and Central Africa. Agriculture, 14(4), 577.
Geng, X., Qu, Y., Jia, Y., He, S., Pan, Z., Wang, L., & Du, X. (2021). Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in upland cotton (Gossypium hirsutum L.). BMC genomics, 22, 1-11.
Hasan, N., Choudhary, S., Naaz, N., Sharma, N., & 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), 128.
Hoffstetter, A., Cabrera, A., Huang, M., & Sneller, C. (2016). Optimizing training population data and validation of genomic selection for economic traits in soft winter wheat. G3: Genes, Genomes, Genetics, 6(9), 2919-2928.
Ince, A., & Karaca, M. (2019). Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.). International Journal of Agriculture Environment and Food Sciences, 3(4), 240-244.
Jannink, J. L., & Walsh, B. (2002). Association mapping in plant populations, editor. Quantitative genetics, genomics and plant breeding. Oxford: CAB International; p. 59–68.
Jiang, G. L. (2013). Molecular markers and marker-assisted breeding in plants. Plant breeding from laboratories to fields, 3, 45-83.
Jiang, H., Li, Z., Liu, J., Shen, Z., Gao, G., Zhang, Q., & He, Y. (2019). Development and evaluation of improved lines with broad-spectrum resistance to rice blast using nine resistance genes. Rice, 12, 1-11. https://doi.org/10.1186/s12284-019-0292-z
Kang, J. H., Yang, H. B., Jeong, H. S., Choe, P., Kwon, J. K., & Kang, B. C. (2014). Single nucleotide polymorphism marker discovery from transcriptome sequencing for marker-assisted backcrossing in Capsicum. Horticultural Science & Technology, 32(4), 535-543.
Kaur, G., Joshi, A., & Jain, D. (2018). SSR-Marker assisted evaluation of Genetic Diversity in Mungbean (Vigna radiata (L.) Wilcezk) genotypes. Brazilian Archives of Biology and Technology, 61, e16160613.
Kim, M. S., Yang, J. Y., Yu, J. K., Lee, Y., Park, Y. J., Kang, K. K., & Cho, Y. G. (2021). Breeding of high cooking and eating quality in rice by marker-assisted backcrossing (MABc) using KASP markers. Plants, 10(4), 804.
Kumar, S., Knox, R. E., Singh, A. K., DePauw, R. M., Campbell, H. L., Isidro-Sanchez, J., ... & Fedak, G. (2018). High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross. PLoS One, 13(2), e0192261.
Kwabena Osei, M., Danquah, A., Adu-Dapaah, H., Danquah, E., Blay, E., Massoudi, M., & Maxwell, D. (2022). Marker assisted backcrossing of alcobaca gene into two elite tomato breeding lines. Frontiers in Horticulture, 1, 1024042.
Li, C., Yu, H., Li, C., Zhao, T., Dong, Y., Deng, X., ... & Zhu, S. (2018). QTL mapping and heterosis analysis for fiber quality traits across multiple genetic populations and environments in upland cotton. Frontiers in plant science, 9, 1364.
Li, D., Lu, X., Zhu, Y., Pan, J., Zhou, S., Zhang, X., ... & Zhang, C. (2022). The multi‐omics basis of potato heterosis. Journal of Integrative Plant Biology, 64(3), 671-687.
Li, X., Wei, Y., Ma, Y., Cao, G., Ma, S., Zhang, T., ... & Piao, Z. (2022). Marker-assisted pyramiding of CRa and CRd genes to improve the clubroot resistance of Brassica rapa. Genes, 13(12), 2414.
Liu, R., Lu, J., Zhou, M., Zheng, S., Liu, Z., Zhang, C., ... & Zhang, L. (2020). Developing stripe rust resistant wheat (Triticum aestivum L.) lines with gene pyramiding strategy and marker-assisted selection. Genetic Resources and Crop Evolution, 67, 381-391.
Mammadov, J., Buyyarapu, R., Guttikonda, S. K., Parliament, K., Abdurakhmonov, I. Y., & Kumpatla, S. P. (2018). Wild relatives of maize, rice, cotton, and soybean: treasure troves for tolerance to biotic and abiotic stresses. Frontiers in plant science, 9, 886.
Mathivathana, M. K., Jagadeeshselvam, N., Madhumitha, B., Karthikeyan, A., Pandiyan, M., Karthikeyan, G., ... & Sudha, M. (2018). Screening and identification of SSR markers for genetic diversity for mungbean (Vigna radiata (L.) Wilczek). Journal homepage: http://www. ijcmas. com, 7(04), 2018.
Meuwissen, T. H., Hayes, B. J., & Goddard, M. (2001). Prediction of total genetic value using genome-wide dense marker maps. genetics, 157(4), 1819-1829.
Michel, S., Löschenberger, F., Ametz, C., & Bürstmayr, H. (2021). Genomic selection of parents and crosses beyond the native gene pool of a breeding program. The Plant Genome, 14(3), e20153.
Milc, J., Sala, A., Bergamaschi, S., & Pecchioni, N. (2011). A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database. Database, 2011, baq038.
Mohammed, S. B., Ongom, P. O., Togola, A., & Boukar, O. (2024). Enhancing cowpea tolerance to elevated temperature: achievements, challenges and future directions. Agronomy, 14(3), 513.
Mukri, G., Patil, M. S., Motagi, B. N., Bhat, J. S., Singh, C., Jeevan Kumar, S. P., ... & Simal-Gandara, J. (2022). Genetic variability, combining ability and molecular diversity-based parental line selection for heterosis breeding in field corn (Zea mays L.). Molecular Biology Reports, 49(6), 4517-4524.
Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Comertpay, G., Yıldız, M., ... & Baloch, F. S. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32(2), 261-285.
Oliveira, L. K., Melo, L. C., Brondani, C., DEL PELOSO, M. J., & Brondani, R. P. V. (2008). Backcross assisted by microsatellite markers in common bean.
Patella, A., Palumbo, F., Galla, G., & Barcaccia, G. (2019). The molecular determination of hybridity and homozygosity estimates in breeding populations of lettuce (Lactuca sativa L.). Genes, 10(11), 916.
Patil, A., & Ram, M. (2024). Breeding for heat stress tolerance in wheat: A review. Journal of Advances in Biology & Biotechnology, 27(7), 227-237.
Peng, P., Jiang, H., Luo, L., Ye, C., & Xiao, Y. (2023). Pyramiding of multiple genes to improve rice blast resistance of photo-thermo sensitive male sterile line, without yield penalty in hybrid rice production. Plants, 12(6), 1389. https://doi.org/10.3390/plants12061389
Pollock, C. J., Stoddart, J. L., Thomas, H., & JOHNES, T. (1987). Protein electrophoresis: Isoenzymes as genetic markers. 1BPGR Lecture Series-1. Collection, Characterization and Utilization of Genetic Resources of Temperate Forage Grass and Clover, 41-53.
Prasanna, B. M., Palacios-Rojas, N., Hossain, F., Muthusamy, V., Menkir, A., Dhliwayo, T., ... & Fan, X. (2020). Molecular breeding for nutritionally enriched maize: status and prospects. Frontiers in genetics, 10, 1392.
Proite, K., Leal-Bertioli, S. C., Bertioli, D. J., Moretzsohn, M. C., da Silva, F. R., Martins, N. F., & Guimarães, P. M. (2007). ESTs from a wild Arachis species for gene discovery and marker development. BMC plant biology, 7, 1-10.
Pundir, S., Sharma, R., Kumar, D., Singh, V. K., Chaturvedi, D., Kanwar, R. S., ... & Sharma, S. (2022). QTL mapping for resistance against cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.). Scientific reports, 12(1), 9586.
Rasheed, A., Hao, Y., Xia, X., Khan, A., Xu, Y., Varshney, R. K., & He, Z. (2017). Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Molecular plant, 10(8), 1047-1064.
Richardson, B. J., Baverstock, P. R., & Adams, M. (2012). Allozyme electrophoresis: a handbook for animal systematics and population studies. Academic press.
Rocha, R. B., Barros, E. G., Cruz, C. D., Rosado, A. M., & Araújo, E. F. D. (2007). Mapping of QTLs related with wood quality and developmental characteristics in hybrids (Eucalyptus grandis x Eucalyptus urophylla). Revista Arvore, 31, 13-24.
Sachan, D. S., Naimuddin, S. K., Patra, D., Subha, L., Senthilkumar, T., Chittibomma, K., ... & Prasad, S. V. (2024). Advancements in enhancing oil quality in rapeseed and mustard: A Comprehensive Review. Journal of Experimental Agriculture International, 46(5), 181-193.
Saha, P., Ghoshal, C., Saha, N. D., Verma, A., Srivastava, M., Kalia, P., & Tomar, B. S. (2021). Marker-assisted pyramiding of downy mildew-resistant gene Ppa3 and black rot-resistant gene Xca1bo in popular early cauliflower variety pusa meghna. Frontiers in Plant Science, 12, 603600.
Schmidthoffer, I., Szilák, L., Molnár, P., Csontos, P., & Skribanek, A. (2018). Drought tolerance of European barley (Hordeum vulgare L.) varieties. Agriculture (Pol'nohospodárstvo), 64(3), 137-142.
Soriano, J. M. (2020). Molecular marker technology for crop improvement. Agronomy, 10(10), 1462.
Tomkowiak, A., Bocianowski, J., Kwiatek, M., & Kowalczewski, P. Ł. (2020). Dependence of the heterosis effect on genetic distance, determined using various molecular markers. Open Life Sciences, 15(1), 1-11.
Tong, Z., Xiu, Z., Ming, Y., Fang, D., Chen, X., Hu, Y., ... & Xiao, B. (2021). Quantitative trait locus mapping and genomic selection of tobacco (Nicotiana tabacum L.) based on high-density genetic map. Plant Biotechnology Reports, 15, 845-854.
Ullah, M., Akram Babar, H. M., Malik, and M. F. (2023). Assessing Intraspecific Genetic Variability in Cannabis sativa Populations of Punjab Pakistan Using RAPD and DNA Barcode Markers. Phytopathogenomics and Disease Control, 2, 111–118.
Varshney, R. K., Graner, A., & Sorrells, M. E. (2005). Genic microsatellite markers in plants: features and applications. TRENDS in Biotechnology, 23(1), 48-55.
Varshney, R. K., Pandey, M. K., Janila, P., Nigam, S. N., Sudini, H., Gowda, M. V. C., ... & Nagesh, P. (2014). Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theoretical and Applied Genetics, 127, 1771-1781.
Veerendrakumar, H. V., Barmukh, R., Shah, P., Bomireddy, D., Jamedar, H. V. R., Roorkiwal, M., ... & Pandey, M. K. (2024). Genomic Selection in Crop Improvement. In Frontier Technologies for Crop Improvement (pp. 187-222). Singapore: Springer Nature Singapore.
Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. V. D., Hornes, M., ... & Zabeau, M. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic acids research, 23(21), 4407-4414.
Wang, N., Wang, H., Zhang, A., Liu, Y., Yu, D., Hao, Z., ... & Zhang, X. (2020). Genomic prediction across years in a maize doubled haploid breeding program to accelerate early-stage testcross testing. Theoretical and Applied Genetics, 133, 2869-2879.
Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews genetics, 10(1), 57-63.
Wen, Y. J., Zhang, Y. W., Zhang, J., Feng, J. Y., Dunwell, J. M., & Zhang, Y. M. (2019). An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2. Briefings in bioinformatics, 20(5), 1913-1924.
Wu, J., Zhao, Q., Zhang, L., Li, S., Ma, Y., Pan, L., ... & Sun, D. (2018). QTL mapping of fiber-related traits based on a high-density genetic map in flax (Linum usitatissimum L.). Frontiers in Plant Science, 9, 885.
Wu, Y. B., Li, G., Zhu, Y. J., Cheng, Y. C., Yang, J. Y., Chen, H. Z., ... & Ying, J. Z. (2020). Genome-wide identification of QTLs for grain protein content based on genotyping-by-resequencing and verification of qGPC1-1 in rice. International Journal of Molecular Sciences, 21(2), 408.
Xiao, N., Pan, C., Li, Y., Wu, Y., Cai, Y., Lu, Y., ... & Li, A. (2021). Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice. Genome Biology, 22, 1-22.
Yang, Y., Wang, B., Wang, J., He, C., Zhang, D., Li, P., ... & Li, Z. (2022). Transcription factors ZmNF-YA1 and ZmNF-YB16 regulate plant growth and drought tolerance in maize. Plant Physiology, 190(2), 1506-1525.
Zambelli, A. (2019). The impact of molecular genetics in plant breeding: realities and perspectives. BAG, J. basic appl. genet. (Online), 11-15.
Zhang, M., Montooth, K. L., Wells, M. T., Clark, A. G., & Zhang, D. (2005). Mapping multiple quantitative trait loci by Bayesian classification. Genetics, 169(4), 2305-2318.
Zhao, Y., & Su, C. (2019). Mapping quantitative trait loci for yield-related traits and predicting candidate genes for grain weight in maize. Scientific reports, 9(1), 16112.
