Next-Generation Ecotilling

Discover rare functional variants that play an important role in determining the phenotype

Efficient and accurate method to screen a large number of individuals for mutations


Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation.

We use pooled multiplexed sequencing of PCR products to identify SNPs in different candidate genes involved in a particular phenotype in order to screen large populations for rare functional variants in targeted genes, as well as a follow-up to genome-wide association studies to extensively sequence regions surrounding associated variants.


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.