Quantitative genetics: pan-genomes, SVs, and k-mers for GWAS
1Molecular Biology Laboratory, Department of Genetics and Plant Breeding, CCS University Meerut, Meerut, India.
Trends in Genetics : TIG
|June 29, 2021
Summary
Genome-wide association studies (GWAS) identify marker-trait associations for complex traits. Methodologies have evolved from using reference genomes and SNPs to incorporating pan-genomes and structural variations.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- Marker-trait associations (MTAs) are crucial for understanding complex traits in agriculture and animal breeding.
- Thousands of genome-wide association studies (GWAS) have been conducted over the last 20 years to identify these associations.
- Methodological advancements have been central to the progress of GWAS.
Purpose of the Study:
- To review the evolution of methodologies used in genome-wide association studies (GWAS).
- To highlight the shift from traditional markers to more advanced genomic resources.
- To underscore the importance of these studies for identifying marker-trait associations in complex traits.
Main Methods:
- Review of methodologies employed in genome-wide association studies (GWAS) over the past two decades.
- Comparison of initial approaches using reference genomes and single nucleotide polymorphisms (SNPs).
- Examination of recent advancements incorporating pan-genomes and structural variations (SVs)/k-mers as markers.
Main Results:
- Early GWAS relied on reference genomes and SNPs for marker-trait association identification.
- Current GWAS methodologies increasingly utilize pan-genomes and structural variations (SVs)/k-mers.
- These advancements allow for a more comprehensive analysis of complex traits.
Conclusions:
- The field of genome-wide association studies (GWAS) has seen significant methodological improvements.
- The adoption of pan-genomes and structural variations enhances the power to detect marker-trait associations.
- Continued methodological innovation is vital for dissecting complex traits in diverse organisms.
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