Genetic evaluation of South African indigenous chickens for disease resistance.

Abstract

An alternative standard disease control method would be selective breeding in order to increase disease resistance. To set up marker assisted selection programmes, knowledge of the genetic diversity of the chickens is required. To date, indigenous South African chicken lines have received little scientific attention and has never been subjected to purposive selective breeding for any particular trait. The objective of the study was to investigate genetic variation within genes involved in innate and adaptive immune system response. The innate immune system genes which were studied were the Toll Like Receptor-4 (TLR-4), Myeloid Differential protein-2 (MD-2) and Solute Carrier Family 11 member A1 (SCL11A1) genes. The PCR-RFLP method was used to detect single nucleotide polymorphisms in these genes and thereafter, the electrophoretic patterns were analysed and used to compute population genetic analyses. The indigenous chickens were moderately outbred at the TLR-4-Sau 96I and INOS-Alu I loci as indicated by high observed heterozygosity figures of 0.78 and 0.51 respectively and low fixation indices. The hypothesis of indigenous chicken population having a more genetic variation was supported by the results that showed the high observed homozygosity in commercial chickens at the SLC11A1-Sac I locus. The Major Histocompatibility Complex is composed of genes responsible for the adaptive immune system response. The genetic variation in the LEI0258 microsatellite marker within the MHC was investigated in indigenous chicken populations in South Africa and across the 3 populations, 36 alleles were detected and of these, 11 of them were private alleles. Observed heterozygosity levels and high fixation indices suggested a level of inbreeding at this locus. It was concluded that the sampled South African chicken populations were moderately inbred at the MHC locus and that the inbreeding may be due to natural selection of certain alleles in order to acclimate to the natural environment more effectively.