Population Structure and Genetic Diversity of Indigenous Chicken Populations (Gallus Gallus Domesticus) using MHC-Linked Microsatellite LEI0258 in South Kivu, Eastern Democratic Republic of Congo

Abstract

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 by many poor small farmers for their meat and eggs. They 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 to support breeding programs and genetic resource conservations. The LEI0258 microsatellite marker within the major histocompatibility complex gene region was used for genotyping. 2-5 mL of blood sample was collected by venipuncture of the jugular vein from each bird and stored onto Whatman FTA filter paper. Three punches of dried blood spot per sample were used to isolate the total genomic DNA using Invitrogen DNA extraction Kit and boiling method. Then PCR amplification was performed followed by Sanger sequencing. The number of R13 and R12 repeats varied from 1 to 21 and 3 to 21, respectively; whereas several combinations of indels and single-nucleotide polymorphisms (SNPs) 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 (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) showed the relationships among the chicken populations. The present study showed the existence of high genetic diversity in chicken populations from South Kivu. This study provides information useful for better conservation and breeding strategies of indigenous chicken populations in South Kivu.