Genome-Wide Association Study (GWAS) for Economically Important Traits in Tea Plant

Genome-wide association study (GWAS), also known as association mapping, is a method of identifying markers or candidate genes through the association analysis between genotype and phenotype based on linkage disequilibrium (LD). Usually, restriction-site associated DNA sequencing (RAD-seq) or genotyping-by-sequencing (GBS) approaches are used for sequencing and GWAS of a specific species population. Compared with whole genome resequencing, RAD-seq or GBS approaches can only obtain sequence information uniformly distributed near enzyme cleavage sites in the genome, reducing the complexity and cost of the genome, especially suitable for research with large species genomes and sample sizes. GWAS identify variations statistically associated with specific traits by testing numerous genetic variants across genomes. This approach has generated a large number of associations for many traits, and the number of related variations will grow steadily with the increase of GWAS sample sizes. The results of GWAS are widely used in the study of phenotype biology, calculation of genetic correlations, estimation of heritability, identification of excellent genes, development of molecular markers and marker-assisted breeding. In this chapter, we introduced GWAS, explained their statistical basis and use, described the most advanced methods, introduced the application of GWAS in tea plant, and discussed the future perspectives for GWAS.