Genetic variation of LEI0258 locus at major histocompatibility complex (MHC) region in Ethiopian indigenous village chicken
Authors: Kebede Adebabay , Tesfaye Kassahun , Belay Gurja , Kyallo Martina , Githae Dedan , Dessie Tadelle , Sparks Nick , Hanotte Oliver , Pelle Roger 
Published: November 2022

Indigenous chickens are locally adapted to environmental challenges and provide subsistence to millions of farmers in Africa.  However, their productivity remains low compared to exotic strains. Efforts are being made to combine the local adaptation of indigenous chicken with productive traits of exotic chicken. Understanding the link between genetic diversity and environmental challenges leads to marker-assisted breed improvement programs for sustainable chicken production at smallholder level. Genetic variation at LEI0258 VNTR locus located within the MHC region has been linked to infectious disease resistance/susceptibility in commercial breeds. The aim of this study was to investigate allelic variability, genetic diversity and genetic relationships of 24 chicken populations in Ethiopia. Here, the diversity at LEI0258 in 236 chickens from 24 Ethiopian indigenous chicken populations using the major Histo-compatibility Complex linked LEI0258 marker is reported. A total of 236 DNA samples were genotyped by capillary electrophoresis from 24 chicken populations. The number of alleles, allele frequency, and heterozygosity levels were used to measure genetic variation at LEI0258 locus in Ethiopian indigenous village chicken. Twenty-nine LEI0258 alleles were observed using capillary electrophoresis that ranged from 185 to 569 bp with no significant difference in allele frequencies between populations.  The number of alleles ranged from 179 (Meseret) to 569 (Batambie), with an average of 9.6 alleles per population. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Twenty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polympormisms based on the combination of two repeat regions at 12 bp and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 12 bp appeared 2 to 18 times, whereas the region at 13 bp appeared invariant in all populations. Sequence relationships revealed two distinct groups of alleles. The number of indels and mutations were 33 and 17, respectively. From capillary electrophoresis, the fixation coefficient of the sub-population within the total population (FST), inbreeding/fixation/ coefficient of an individual in a sub population (FIS) and total inbreeding /heterozygosity deficit/ coefficient of an individual within the total population (FIT) in the locus was 0.03, 0.08 and 0.11, respectively. Three percent of the genetic diversity was due to differences among populations, where as 8% and 89% were variations among individuals and variations within individuals, respectively. Despite the overall low genetic differentiation, both fragment and sequencing analysis revealed high allelic and genetic variability across the 24 populations. The high diversity at LEI0258 in Ethiopian indigenous village chicken populations supports the importance of the MHC region in relation to the disease challenges faced by smallholder poultry farmers across Ethiopia. We recommend that breed improvement programs ensure the maintenance of this diversity by selecting breeding stock as diverse as possible at the LEI0258 locus.