Proceedings, 10 th World Congress of Genetics Applied to Livestock Production Major histocompatibility complex genetic diversity of Kenyan indigenous chicken populations based on microsatellite markers K. Ngeno *, § , E.H. van der Waaij * , Hendrik-Jan Megens * , A. K. Kahi § , J. A.M. van Arendonk * and R. P. M. A. Crooijmans * . * Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands, § Animal Breeding and Genomics Group, Department of Animal Sciences, Egerton University, Egerton, Kenya, ABSTRACT: The study investigated the genetic make-up of indigenous chicken (IC) ecotypes based on the major histocompatibility complex (MHC) by genotyping mi- crosatellite markers LEI0258 and MCW0371. Blood sam- ples were collected from eight regions of Kenya; Ka- kamega, Siaya, West Pokot, Turkana, Bomet, Narok, Lamu and Taita-Taveta. In total 96 birds per population were sampled whereas 48 birds were genotyped. In total, 56 dif- ferently sized alleles were detected over all the populations. Cluster analysis based on LEI0258 and also in combination with MCW0371 indicated a clear IC subdivision into two genetically distinct groups. Two main population clusters were Lamu and others. Keywords: Indigenous chicken ecotypes ; MHC ; Genetic diversity Introduction Indigenous chicken (Gallus gallus domesticus) are widely distributed throughout Africa and Asia under diver- sified geographical and agro-ecological conditions. Geo- graphically isolated indigenous chicken (IC) populations are subjected to variable climatic conditions and each re- gion is thought to host some unique types of chickens, hereafter called ecotypes. Such ecotypes are anticipated to possess unique combinations of alleles on genes that may constitute adaptation to local environment (Mwacharo et al., 2007). Kenyan IC ecotypes are known for good adapta- bility to harsh scavenging conditions and poor nutrition and tolerance to parasite and diseases in their habitat (Ngeno, 2011). The ecotypes may have evolved independently and become genetically diverged as a result of natural selection imposed by local adaptation to climate, parasites, diseases and nutrition in their habitat. In order to survive, these chicken have to harbour a large plasticity in their immune system to be able to withstand a large number of immune challenges. This plasticity in these IC might be explained by differences in the alleles of the genes in the major histo- compatibility complex (MHC). The MHC is associated with immune response (Parmentier et al., 2004; Fulton et al., 2006; Nikbakht et al., 2013) and disease resistance (La- mont, 1989).The microsatellite marker LEI0258 is a well- studied marker of the MHC, and together with microsatel- lite marker MCW0371 explained already many immune haplotypes (Fulton et al., 2006). Marker LEI0258 has been used in several genetic diversity studies (Izadi et al., 2011; Chang et al., 2012). Relationship between the MHC and IC in different ecosystems has not been studied in depth. The objective of this study was to investigate MHC markers LEI0258 and MCW0371 in IC of different ecotypes in Kenya in order to quantify genetic differences within and between populations. Materials and Methods Sampling. Blood samples were collected from dif- ferent regions (counties) of Kenya. The covered counties included; Kakamega (KK) and Siaya (BN) in the Western region, West Pokot (WP) and Turkana (TK) in the North Rift, Bomet (BM) and Narok (NR) in the South Rift, and Lamu (LM) and Taita-Taveta (TT) in the coastal region. Each county represents an ecotype. Two mature chickens per household located more than 0.5 km away were sam- pled resulting in a total of 768 birds (i.e. 96 samples per ecotype). One bird per household was genotyped to reduce the probability of sampling genetically related birds (i.e. 48 per ecotype). All samples were collected from free ranging IC populations. Blood samples (~2 mL in EDTA) were drawn from the wing vein of each bird. DNA isolation, polymerase chain reaction (PCR) amplification and genotyping. Genomic DNA was obtained by standard phenol–chloroform extraction. Indi- viduals were genotyped with LEI0258 and MCW0371 mi- crosatellite markers located on chromosomes 16. The PCR as described by McConnell et al. (1999) and Fulton et al. (2006) was used. Primer sequences, fluorescent dyes and annealing temperatures (°C) given in supplementary mate- rial Table 1. Table 1. Fluorescent dye, annealing temperatures (°C) and primer sequences Mark- er Fluo- rescent dye Annealing tempera- ture (°C) Primer sequence LEI02 58 Fam 55 Forward: CACGCAG- CAGAACTTGG- TAAGG;Reverse:AGCTG TGCTCAGTCCTCAG- TGC MCW 0371 Ned 55 Forward: TTTCATGG- CATCCTAA- GATGG;Reverse:CTGCT CCGAGCTGTAATCCTG