Immunogenetics and genetic variations in indigenous chicken in the tropics using SNP data

Abstract

This study used data from 150 indigenous chicken from four agro-ecological zones in Rwanda to provide deep insight of the population structure and variation of the immunogenetics using several approaches based on phenotypic and SNP data. The population structure of indigenous chicken was analysed using Principal Component Analysis (PCA), ADMIXTURE analysis, and phylogenetic relationships for the whole genome and at chromosome 16. The study used 65,945 SNPs from the collected chicken. Phenotypic analysis was done for the Newcastle disease titer (ab) alongside bodyweight at 20 weeks with the highest having 1.6kg. The genome analysis was done using the genotyping-by-sequencing approach. The grouped the indigenous chicken into two genetic clusters, which was confirmed by ADMIXTURE analysis that revealed that the lowest cross-validation (CV) error (0.51) was at K=2. The analysis of Population structure at chromosome 16 showed that the population had the lowest CV error (0.50) at K=1. The mean body weight and antibody titer were 1673.61 ±237.14 g and .5±55.35, 1311.34±121.9 g and 8832.5±55.36, respectively, depicting an inverse relationship between bodyweight and antibody titers. The cluster means for body weight and antibody titers were significantly different (P