GWAS(Genome Wide Association Studies): SNPs detection using R
Figure 1: An illustration of Manhattan plot depicting loci associated with sperm mobility trait in F3 population.
GWAS also known as Genome Wide Association Study or Whole Genome Association study is a tool widely used in genetics to detect statistically significant genomic loci associated with a respective trait under investigation. Genome wide variants between individuals are analyzed for identifying genomic regions containing associated SNPs that might explain the observable trait.
Figure 2: A graphical representation of sperm mobility of F2 population. Samples for GWAS analysis were taken from low end and high end of the F2 population.
We are using Genome Wide Association Studies (GWAS) in High and low sperm mobility chicken lines, and crosses between the lines to elucidate the gene regions affecting the sperm mobility trait. Sperm mobility is a significant determinant of male fertility in commercial chickens and has been shown to be a highly heritable trait. GWAS analysis will allow us to identify gene regions and gene networks responsible for variability of the mobility phenotype. Initially we performed a GWAS between the High and Low lines. We then performed a GWAS on the tails of the mobility distribution within the Low line and on an F2 cross of the two lines. The results implicate the Z chromosome as a major determinant of mobility phenotype, consistent with previous work that demonstrated a strong maternal effect. However, the specific regions on chromosome Z do not seem to be shared between the different GWAS experiments suggesting a strong epistatic effect.