Diversity and population structure of indigenous chicken populations (Gallus gallus domesticus) in South Kivu, Democratic Republic of Congo, using MHC-linked microsatellite LEI0258. DR Congo local chicken genetic diversity

Chickens are the most important and widely distributed of all livestock in Africa. They play very significant socio-cultural and economic roles in African societies. In the Democratic Republic of Congo, chickens are generally kept for their meat and eggs which provide a source of nutrition and income in rural and peri-urban areas. The availability of information on chicken population structure and diversity is important in the conservation of genetic resources which is critical in the selection of breeds that are important in diverse production systems. This study aimed to determine allelic variability, genetic diversity, and genetic relationships of the indigenous chicken populations from the South Kivu region using the LEI0258 microsatellite marker within the major histocompatibility complex gene region. For genotyping, LEI0258 locus amplicon sequences of 163 indigenous chickens were analyzed. The number of R13 and R12 repeats varied from 1 to 21 and 3 to 21, respectively; whereas several combinations of indels and SNPs were observed in the microsatellite flanking regions. A total of 45 different LEI0258 alleles ranging from 193 to 473 bp were determined, including 14 private alleles (Np). Expected heterozygosity (He) varied from 0.864 (Mwenga) to 0.938 (Bukavu) with a mean of 0.911 and observed heterozygosity (Ho) ranged from 0.417 (Uvira) to 0.667 (Mwenga) with a mean of 0.519. The analysis of molecular variance (AMOVA) revealed higher genetic variation within individuals (56%) than among individuals (43%) and among chicken populations (1%). Clustering into three admixed gene pools (K=3) revealed the relationships among the chicken populations. The present study reveals the existence of high genetic diversity in chicken populations from South Kivu and provides information useful for conservation and breeding strategies.