High genetic variability revealed in four Nigerian locally-adapted chicken populations using Major Histocompatibility Complex-linked LEI0258 microsatellite marker

Major Histocompatibility Complex (MHC) is a group of genes that influence immune response generally in vertebrates, and it has been explored among different animal species in various countries. However, there is a paucity of information in its application in Nigerian locally-adapted chickens (NLAC). Genetic information of chickens is important for making decision on conservation and improvement in their various production settings. This research investigated genetic polymorphism, allele variability and genetic relationships using LEI0258 major histocompatibility complex-linked microsatellite marker among four NLAC populations namely; Fulani and Yoruba ecotypes, FUNNAB Alpha and Noiler breeds. Blood samples were randomly collected from 50 mature birds in each population and genomic The DNA was extracted and subsequently subjected to PCR, Sanger sequencing and bioinformatic analysis. There were 22 combinations of the two variable numbers of tandem repeats (VNTRs), with 90% of the alleles containing only one R13 and varying numbers of the R12 motifs that ranged from 1 to 19. Additional polymorphism was revealed by the presence of five SNPs and three indels in the upstream and downstream regions of LEI0258. A total of 48 alleles were observed with sizes ranging from 193 to 530 base pairs while the allele frequencies within the populations ranged from 1.9 to 29.2%. However, only 17 out of the 48 alleles had corresponding MHC-B haplotypes. Haplotype B2, B12, and B21 found in this study had been reported to confer resistance to infectious poultry diseases especially avian influenza in locally adapted chickens. High allelic variability and genetic polymorphism were observed across the four NLAC populations.