Abstract
The human genome project, which ended in 2003, provided a human genome map with 99.99 % accuracy. This project stimulated association studies between traits and genes and allowed the discovery of new genes. In 2006, an innovational method known as genome-wide association study (GWAS) was developed. GWAS is different from the traditional method of studying associations between a few candidate genes and traits in that GWAS can handle about one million single-nucleotide polymorphisms (SNPs) simultaneously.
These days, GWAS is widely used to study genetic factors related to phenotype in many species, including plants. The advances in next generation sequencing (NGS) have allowed large amounts of genetic data to be obtained at a relatively low cost.
In this chapter, we will review GWAS including the associated statistical concepts and available software packages. We describe the use of GAPIT (Genomic Association and Prediction Integrated Tool) and demonstrate SNP calling using the widely used commercial CLC Genomic Workbench with re-sequenced cucumber genome data. Finally, we examine the current status of genomics research worldwide that requires whole-genome resequencing, one of the requirements of GWAS.
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Lee, CY., Kim, TS., Lee, S., Park, YJ. (2015). Concept of Genome-Wide Association Studies. In: Koh, HJ., Kwon, SY., Thomson, M. (eds) Current Technologies in Plant Molecular Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9996-6_6
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DOI: https://doi.org/10.1007/978-94-017-9996-6_6
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