Diversity and population structure of indigenous chicken in Congo, using MHC-linked microsatellite LEI0258

Context: Chickens are the most important livestock in the Democratic Republic of Congo in particular and in Africa in general; they are kept for their meat and eggs for nutrition and economic status. The availability of chicken diversity information is very important in selection of breeds and in conservation of genetic resources. Aims: This study aimed to determine allelic variability, genetic diversity, and genetic relationships of the indigenous chicken populations from the South Kivu region to support breeding programs and genetic resource conservations. Methods: The LEI0258 microsatellite marker within the major histocompatibility complex gene region was used for genotyping. The LEI0258 locus amplicon sequences of 163 indigenous chickens were analysed. Key results: The number of R13 and R12 repeats varied from 1 to 21 and from 3 to 21 respectively, whereas several combinations of indels and single-nucleotide polymorphisms were observed in the microsatellite flanking regions. In total, 45 different LEI0258 alleles ranging from 193 to 473 bp were determined, including 14 private alleles (N-p). Expected heterozygosity (H-e) varied from 0.864 (Mwenga) to 0.938 (Bukavu), with a mean of 0.911, and observed heterozygosity (H-o) ranged from 0.417 (Uvira) to 0.667 (Mwenga), with a mean of 0.519. The analysis of molecular variance (AMOVA) showed higher genetic variation within individuals (56%) than among individuals (43%) and among chicken populations (1%). Clustering into three admixed gene pools (K = 3) showed the relationships among the chicken populations. Conclusion: The present study showed the existence of high genetic diversity in chicken populations from South Kivu. Implications: This study provides information useful for better conservation and breeding strategies of indigenous chicken populations in South Kivu.