Elucidating biological pathways bridging genotype and phenotype is one of the fundamental challenges in genetic and genomic research. Gene variants that control phenotypes are typically discovered by combined linkage analysis and molecular validation. However, these genotype-phenotype associations do not expose the underlying biological pathways through which gene variants operate on phenotype. We explore genomic and computational approaches to uncover the biological pathways through which genetic loci influence phenotypes and predict the effects of genetic and transcriptional variations/ interventions on gene expression and physiological/ behavioral phenotypes of individuals with different genetic background. In last few decades, genome wide association studies (GWAS) in several species have led to the discovery of numerous loci for a range of complex diseases and many economically important traits in plants. mRNA expression data leads to the identification of expression quantative trait loci (eQTL), a genomic loci which is responsible to regulate the expression levels of various mRNA and proteins.

The trait value measured by mRNA or proteins is always a product of single gene with a specific chromosomal location. Expression QTL are empirically divided into two classes cis and trans. We identify cis-QTL region in which eQTL region is mapped to approximate location of their gene-of-origin i.e when both eQTL and gene position overlap, the eQTL is considered to be cis-regulated. While trans eQTL region are those regions which are far from the location of their gene-of-origin i.e if the eQTL and gene location are non-overlapping, eQTL is considered to be trans-acting. Any eQTL identified can be either cis regulated or trans regulated. The polymorphism of the regulatory elements directly regulates the abudance of a gene transcript. The combination of whole genome-wide association studies with the measurement of global gene expression allows the systematic identification of eQTL. Xcelris has developed a pipeline where we simultaneously assay gene expression along with the genetic variation on a genome wide basis in large number of individuals along with statistical genetic methods which are used to map the genetic factors that determine the expression of many thousands of transcripts.

Global eQTL analysis in yeast, mice and humans have detected significant levels of eQTL traits that simultaneously regulate a large fraction of transcriptome. In yeasts, the complex inheritance of transcript levels has been revealed by detecting significant levels of nonadditive genetic variance, epistasis interactions and transgenic segregation. However, comparable studies in plants have yet to be reported. At Xcelris, we will provide eQTL analysis service both for the animal as well as plant samples.