Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa

Abstract

BackgroundChickens represent an important animal genetic resource for improving farmers’ income in Africa. The present study provides a comparative analysis of the genetic diversity of village chickens across a subset of African countries. Four hundred seventy-two chickens were sampled in 23 administrative provinces across Cameroon, Benin, Ghana, Côte d’Ivoire, and Morocco. Geographical coordinates were recorded to analyze the relationships between geographic distribution and genetic diversity. Molecular characterization was performed with a set of 22 microsatellite markers. Five commercial lines, broilers and layers, were also genotyped to investigate potential gene flow. A genetic diversity analysis was conducted both within and between populations.ResultsHigh heterozygosity levels, ranging from 0.51 to 0.67, were reported for all local populations, corresponding to the values usually found in scavenging populations worldwide. Allelic richness varied from 2.04 for a commercial line to 4.84 for one population from Côte d’Ivoire. Evidence of gene flow between commercial and local populations was observed in Morocco and in Cameroon, which could be related to long-term improvement programs with the distribution of crossbred chicks. The impact of such introgressions seemed rather limited, probably because of poor adaptation of exotic birds to village conditions, and because of the consumers’ preference for local chickens. No such gene flow was observed in Benin, Ghana, and Côte d’Ivoire, where improvement programs are also less developed. The clustering approach revealed an interesting similarity between local populations found in regions sharing high levels of precipitation, from Cameroon to Côte d’Ivoire. Restricting the study to Benin, Ghana, and Côte d’Ivoire, did not result in a typical breed structure but a south-west to north-east gradient was observed. Three genetically differentiated areas (P < 0.01) were identified, matching with Major Farming Systems (namely Tree Crop, Cereal-Root Crop, and Root Crop) described by the FAO.ConclusionsLocal chickens form a highly variable gene pool constituting a valuable resource for human populations. Climatic conditions, farming systems, and cultural practices may influence the genetic diversity of village chickens in Africa. A higher density of markers would be needed to identify more precisely the relative importance of these factors.

Review: Sustainability of crossbreeding in developing countries; definitely not like crossing a meadow…

“…A study of the same data revealed a greater rate of European introgression in closer proximity to animal markets (Mbole-Kariuki et al, 2014). A study of African village chickens from multiple locations (Leroy et al, 2012) reported evidence of introgression in some of the countries, including Morocco and Cameroon, whereas finding negligible gene flow in some other countries such as Benin or Ghana.…”

“…However, in developing countries, pedigree and performance recording remain a bottleneck for the implementation of selection schemes . More generally, genomics provides effective tools to assess and monitor the level of introgression within local population (Leroy et al, 2012;Murray et al, 2013). Genome-wide analysis of crossbred and improved livestock under tropical conditions may also reveal the genomic regions submitted to recent selection and therefore linked to adaptation, as investigated by Kim and Rothschild (2014) in Kenyan dairy cattle.…”

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

“…In addition, free-range scavenging village chickens (Dessie et al, 2011;Leroy et al 2012;Desta et al, 2013) also offer large potential to understand the genetic control of phenotypic diversity. Since village chickens possess a richness of accumulated recombination and a number of adaptive characteristics for extreme environments such as high temperature, they provide a useful genetic resource for high-resolution genetic mapping (Wragg et al, 2012;Megens and Groenen, 2012).…”

The role of mitochondrial DNA to determine the origin of domestic chicken

“…A combination of SSR and mtDNA markers is a complementary approach that combines the highly polymorphic microsatellites whose high mutation rates allow for small scale resolution of more recent demographic event with mtDNA which shed light on phylogeographic events dating back further in time (Feulner et al, 2004). Microsatellites have been used to asses genetic diversity of a number of native chicken population in Africa (Leroy et al, 2012;Goraga et al, 2012;Eltanany et al, 2011), Europe Wilkinson et al, 2012;Zanetti et al, 2011;Bodzsar et al, 2009) and Asia (Pham et al, 2013;Cuc et al, 2010;Berthouly et al, 2009;Ngo Thim et al, 2006). The first chicken genome sequence draft was completed in 2004 (International Chicken Consortium, 2004); its availability offers new opportunities in the evaluation of chicken genetic diversity using SNPs (Gholami et al, 2014;Granevitze et al, 2014;Siwek et al, 2013;Groenen et al, 2009;Muir et al, 2008).…”