Genome-wide association study in indigenous poultry breeds and varieties

Objective

• To assess diversity of Indian breeds in comparison with tropically adapted exotic chicken breeds
• To identify Indian breeds specific candidate signature of selection for adaptive and productivity traits
• To design and develop SNP chip for Indian chicken breeds

Methods

• For conducting divergence study among Indian and tropically adapted chicken breeds, 6 to 8 breeds will be taken in to account.
• Blood samples will be collected from all the animals. Genomic DNA will be isolated.
• The whole genome sequence of all the breeds studied here will be explored through NGS. The sequence will be aligned with the reference chicken assembly available in the public domain to prepare the Indigenous chicken specific assembly. Based on frequencies of SNPs within and among chicken breeds, and their distribution across the genome, putative SNPs will be detected.
• Genetic divergence among breeds will be determined and distantly related breeds will be further used for establishing candidate signature of selection for adaptive and productivity traits.
• On the basis of genetic divergence among breeds, one layer based and one meat based Indian breed will be identified for conducting GWAS experiment.
• Phenotypes pertaining to productivity (Growth and egg production traits) and adaptive traits will be measured in all the animals of Indian breeds selected for GWAS study.
• SNPs of all the animals of selected breeds will be explored through NGS.
• SNPs-traits association will be estimated with statistical models. The SNPs significantly associated with the traits will be used to establish Indigenous chicken specific candidate signature of selection for growth, egg production and adaptive traits. The association between traits and SNPs in the promoter/5’upstream region of the candidate genes will be substantiated by transcriptome analysis in the animals.
• All the putative SNPs identified in the Indigenous and tropically adapted chicken breeds will be employed to develop a comprehensive SNP chip for use in selection programme.
• The SNP chip will be validated in one Indian chicken breed for confirmation and to use further for improvement of Indian chicken breeds.

Expected outcomes

• Array of SNP based diversity of Indian Chicken breeds will be established.
• SNP chip for Indian native chicken will be developed.
• Indian breeds specific candidate signature of selection for selection for growth and adaptive traits will be established.