Student information

Roopika did her thesis on chicken immune response

Roopika Menon from India finished her EMABG thesis in summer 2009 at AgroParisTech in France.

Thesis title

Genetic analysis of immune response in experimental lines of chicken: Identification and validation of signature of selection


Combating disease is a major problem being faced by the poultry industry. A better understanding of the genetic factors involved in immune responses in domestic fowl, can be obtained by studying the basic immunology behind the mechanisms of response to pathogens in chicken. The Major Histocompatibility Complex is a major locus involved in disease resistance in chicken.

This study has analyzed the function of immune response related genes in two aspects- 1) signature of selection based on SNP genotyping and 2) the characterization of the polymorphism of different targets in MHC region. The regions studied for signature of selection includes the Gpc5 gene and the Pcdh gene.  Different methods were compared for genotyping of the desired SNP. The Gpc5 SNP was analyzed using pyrosequencing methods and the Pcdh SNP was analyzed using Restriction Fragment length Polymorphism. The allele frequency was calculated over period of generations and within lines selected for different immune traits.

The CD1A1 and TRIM27.1 regions, located at the ends of the chicken MHC, were analyzed. They are participating in immune responses in chicken. The SNPs were analyzed in both regions and were further mapped to changes in the coding sequence. Certain changes in the base sequence could lead to coding of different proteins, thus increasing or decreasing a specified immune response.

The results obtained could further shed light into the function of the selected genes in eliciting the specified immune response in chicken. The optimal technique in genotyping samples with varying number of SNPs have also been compared in order to get the desired results.