“Construction and use of molecular marker-based linkage maps” ( Seminar Synopsis)

UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

M.Sc. Seminar - GPB 582 (0+1)

“Construction and use of molecular marker-based linkage maps”

Genetic linkage maps are vital tools in modern plant breeding and genomics. These maps provide the linear order of markers along chromosomes based on recombination frequencies and facilitate the identification of genes or quantitative trait loci (QTLs) associated with desirable traits. The use of molecular markers (DNA-based markers) like SSRs, SNPs, and RFLPs has revolutionized linkage map construction due to their high polymorphism, abundance, and reproducibility.

Linkage maps are constructed based on the recombination frequencies between markers in a segregating population (Mapping populations) including F2, F2:3, RILs, NILs, DHs, and MAGIC populations. Recombination frequencies between markers are converted into map distances using Haldane and Kosambi mapping functions, and linkage groups are established based on LOD scores and recombination data. The resulting maps are instrumental in identifying genes/QTLs associated with important traits.

Bulked Segregant Analysis (BSA) and Mutmap further accelerate the identification of markers linked to specific traits. An integrated genetic linkage map comprising 324 SSR and TRAP markers across 107 linkage groups was developed from a biparental cross (UP 9530 × Co 86,011) in sugarcane. This map offers a robust platform for advancing marker-assisted breeding and genetic improvement in sugarcane. Further, using an F2 population of foxtail millet (Jingu28 × Ai88), a linkage map was constructed and 46 QTLs related to 12 agronomic traits were identified. Two major genes associated with plant height, Seita.5G404900 and heading date Seita.9G020100, were discovered, enabling precise genetic improvement.

Molecular marker-based linkage maps are indispensable tools in modern crop improvement programs. Their construction enables better understanding of genome structure, accelerates gene/QTL discovery, and enhances selection efficiency in breeding.

REFERENCES:

1. GAO, L., ZHU, Q., LI, H., WANG, S., FAN, J., WANG, T., YANG, L., ZHAO, Y., MA, Y., CHEN, L. AND LI, X., 2025, Construction of a genetic linkage map and QTL mapping of the agronomic traits in Foxtail millet (Setaria italica). BMC Genom., 26(1): 152.

2. SEMAGN, K., BJORNSTAD, Å. AND NDJIONDJOP, M.N., 2006, Principles, requirements, and prospects of genetic mapping in plants. Afr. J. Biotechnol., 5(25): 2569-2587.

3. SINGH, S.P., RASOGI, J., CK, C., SINGH, R.K., NIGAM, A. AND SINGH, R.B., 2025, Construction of an integrated linkage map of sugarcane using unigene-derived microsatellite (SSR) markers. Reprod. Breed., 5(1): 12-22.