Discover rare functional variants that play an important role in determining the phenotype
Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation.
Pooled multiplexed PCR products or custom hybridization-capture are used for focused sequencing in order to identify natural or induced mutations over large amount of samples as in reverse genetics studies. Rare functional variants in targeted genes, follow-up to genome-wide association studies are usually carried with the help of hybridization-capture systems. In particular multi-dimensional pooling of samples is carried to allow screening of hundreds or thousands of individuals in a cost-effective manner.
Our workflow can be used to identify common and rare SNPs in any organism. Given its ability to discriminate true from false positive SNPs, it is particularly suited for the screening of large populations in the search for rare variants that could be immediately used in breeding programs.
Studies aimed at genetic characterization of various populations of a given organism may take advantage of our workflow since individuals belonging to each population are pooled, and population genetics parameters can be accurately estimated for each population. Finally, researchers investigating qualitative phenotypes may create pools based on the phenotypic category, accurately estimate the allele frequency of SNPs in the two phenotypic classes, and perform pooled association studies.
The method has high sensitivity and specificity, and it accurately estimates allele frequencies and population genetic parameters in large samples. In addition, it is cost-effective compared to individual sequencing.
Read here on how we detected mutations in candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions.