“Linkage Disequilibrium and Its Application in Plant Breeding” ( Seminar Synopsis)

 

UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

“Linkage Disequilibrium and Its Application in Plant Breeding”

Many traits of agricultural and evolutionary significance are complex, being controlled by multiple quantitative trait loci (QTLs), their interactions, environmental influences, and QTL-by-environment interactions. Traditionally, linkage analysis has been employed to unravel the genetic basis of such traits. However, its resolution is often limited to broad genomic regions (typically 10–20 cM) because of the limited recombination events in mapping populations and the high costs associated with developing and phenotyping large numbers of lines.

Over the past two decades, although numerous linkage studies have been conducted in plants, only a limited number of the identified QTLs have been fine-mapped or characterised at the gene level. To address these limitations, association mapping—also referred to as linkage disequilibrium (LD) mapping—has emerged as a powerful alternative. By leveraging historical and evolutionary recombination events within natural populations, LD mapping offers significantly higher resolution, reduced research time, and enhanced ability to detect a broader spectrum of allelic variation underlying complex traits.

Since its introduction in plant research, association mapping has gained significant traction, driven by advancements in high-throughput genomics, a growing interest in uncovering superior alleles, and the development of robust statistical tools. Depending on the study's objectives, it can be implemented as candidate-gene association mapping for specific traits or as genome-wide association studies (GWAS) for comprehensive exploration of trait-associated loci across the genome. Linkage disequilibrium (LD) plays a crucial role in various applications, including genomic selection for predicting breeding values, LD decay-based positional gene cloning, inference of population demographic history, and gene mapping in non-model species such as perennial trees.

LD-based approaches have proven effective in accurately positioning previously unassigned SNPs onto existing genetic maps, thereby enhancing the accuracy of genome-wide association studies (GWAS) and genomic prediction. A notable example is the application of the LODE-based algorithm in crops such as sugarcane, wheat, and barley, which enables the precise localization of un-positioned SNPs. This strategy offers a practical solution for refining genetic maps, even in the absence of fully assembled reference genomes.

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REFERENCES:

1. Singh, B.D., and Singh, A.K. (2015). Marker-Assisted Plant Breeding: Principles and Practices, pp. 260-289.

2. Sved, J.A., and Hill, W.G. (2018). One hundred years of linkage disequilibrium. Genet., 209(3):629-636.

3. Yadav, S., Ross, E.M., Aitken, K.S., Hickey, L.T., Powell, O., Wei, X., Voss-Fels, K.P., and Hayes, B.J. (2021). A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genom., 22(1): 773.