The major histocompatibility complex region and diversity of the local chicken populations in Niger

Introduction: The major histocompatibility complex (MHC) of chicken is highly polymorphic, and it is linked to several disease resistance or susceptibility traits. Therefore, the current study aimed to analyze the genetic diversity in the MHC region of Nigerien local chicken (Dourgou, Goggori, Kolonto, Tchagara, Gouzou-gouzou, and Popular) using a high polymorphic microsatellite marker named LEI0258 to determine the diversity of chickens kept at the four agroecological zones in Niger.

Materials and methods: A total of 601 chickens from six local Nigerien chickens were sampled. By capillary electrophoresis using LEI0258 marker, 403 samples with different fragment sizes were randomly chosen and sequenced.

Results: The findings indicated 80 different alleles ranging in size from 181 to 474 bp. A total of 22 new alleles and 39 private alleles (that existed in only one breed) were detected. The alleles 309, 295, and 193 were the most predominant in the Nigerien local chicken population. Nine polymorphisms were observed along the LEI0258 sequence, including three in the upstream (one indel and two Single Nucleotide Polymorphism [SNP]), one in the repeat region at the last R12 (SNP), and five in the downstream (two indels and three SNPs).

Conclusion: The chickens are not clustering according to their agroecological zone of origin. They are randomly distributed across the four investigated agroecological zones. The information found in this study is invaluable in breeding and conservation programs associated with several disease resistance or susceptibility traits.