“Types of Marker Systems and Their Applications in Plant Breeding” ( Seminar synopsis)

UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

Seminar – GPB 682 (0+1)

“Types of Marker Systems and Their Applications in Plant Breeding”

Genetic markers are essential tools in modern plant breeding, enabling scientists to track the inheritance of traits without relying solely on visible characteristics. Traditionally, phenotypic markers (plant height, flower color) and biochemical markers (isozyme patterns) were used to study genetic variation. However, these markers had limited resolution and were heavily influenced by environmental conditions and the ontogeny of the crop. With advancements in molecular biology, DNA-based markers have revolutionized crop improvement by providing precise, stable, and high-throughput methods for selecting desirable traits.

DNA-based markers are categorized into three generations. First-generation markers, such as RFLP (Restriction Fragment Length Polymorphism) were the earliest tools developed in the 1980s. Though they played a foundational role in genetic mapping, their time-consuming nature and lack of automation were major drawbacks. The second-generation markers, including SSR (Simple Sequence Repeats or microsatellites) and AFLP (Amplified Fragment Length Polymorphism), offered improved polymorphism detection, better reproducibility, and higher information content. SSRs became particularly popular due to their co-dominant nature, locus specificity, and ease of use in genotyping. These markers were widely applied in QTL mapping, diversity analysis, and marker-assisted selection (MAS), significantly accelerating the breeding of crops for traits like drought tolerance, pest resistance, and grain quality.

The recent advent of third-generation markers, derived from next-generation sequencing (NGS) technologies, has enabled the development of high-resolution markers such as SNPs (Single Nucleotide Polymorphisms). These markers allow genome-wide association studies (GWAS), genomic selection (GS), and high-density linkage mapping. SNPs, in particular, have become the gold standard due to their abundance and suitability for automation. Third-generation markers are being used in cutting-edge breeding strategies and the development of climate-resilient and nutritionally enhanced crops.

Badri et al. (2022) developed 196 rice introgression lines (ILs) of the elite cultivar ‘Krishna Hamsa’ through marker-assisted inter-crossing with six donor lines. These ILs incorporated resistance genes for bacterial blight (BB), blast, and brown planthopper (BPH), along with drought-tolerant QTLs. Foreground selection was performed using tightly linked polymorphic markers during the inter-crossing process. Seven distinct phenotypic classes (PCs) were identified, each exhibiting varied resistance and tolerance combinations. Notably, five ILs in the first phenotypic class showed resistance to blast and BB, and were drought-tolerant, although none displayed resistance to BPH despite possessing the relevant gene.

In conclusion, the transition from phenotypic and biochemical markers to DNA-based markers—especially the shift from first to third-generation molecular markers—has fundamentally transformed plant breeding. These technologies have enhanced the precision, speed, and scope of crop improvement programs. As molecular tools continue to evolve, integrating them with traditional breeding will be crucial for developing the next generation of crops capable of meeting global challenges such as food security and climate change.

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REFERENCES:

1. Badri, J., Lakshmidevi, G., Jaividhya, L.R.K., Prasad, M.S., Laha, G.S., Lakshmi, V.J., Isetty, S.R., Padmashree, R., Balakrishnan, D., Varanasi, Y.V.P., & Jukanti, A.K. (2022). Multiparent-derived, marker-assisted introgression lines of the elite Indian rice cultivar ‘Krishna Hamsa’ show resistance against bacterial blight and blast and tolerance to drought. Plants, 11(5): 622.

2. Chaudhary, D., Joshi, S., & Arora, A. (2025). Advances in Crop Breeding: Molecular markers and its breeding approaches in crop improvement. In U.G. Reddy, S.K. Deshpande, K. Priyanka, & S. Jahagirdar (Eds.), Cornous Publications LLP, Puducherry, pp: 108-127.

3. Singh, B.D., & Singh, A.K. (2015). Marker-Assisted Plant Breeding: Principles and Practices. Springer.