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

BMC Genetics Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa Grgoire Leroy 1 2 Boniface B Kayang 0 Issaka AK Youssao 6 Chia V Yapi-Gnaor 5 Richard Osei-Amponsah 0 N'Goran E Loukou 4 5 Jean-Claude Fotsa 3 Khalid Benabdeljelil 7 Bertrand Bed'hom 1 Michle Tixier-Boichard 1 Xavier Rognon 1 2 0 University of Ghana , Legon Ghana 1 INRA, UMR1313 Genetique Animale et Biologie Integrative , Jouy-en-Josas 78352 France 2 AgroParisTech, UMR1313 Genetique Animale et Biologie Integrative , Paris 05 F-75231 France 3 Station Specialisee de Recherche Agricole de Mankon (SRRAD) , Bamenda BP 4099 Cameroun 4 Universite de Cocody , Abidjan 22 BP 1244 Cote d'Ivoire 5 Centre National de la Recherche Agronomique , Abidjan 01 BP 1740 Cote d'Ivoire 6 Universite d'Abomey-Calavi, Ecole Polytechnique d'Abomey-Calavi , Cotonou 01 BP 2009 Benin 7 Institut Agronomique et Veterinaire Hassan II, DPBA, Rabat Instituts , 10101, Rabat BP 6202 Maroc Background: Chickens 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, Cte 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. Results: High 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 Cte 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 Cte 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 Cte d'Ivoire. Restricting the study to Benin, Ghana, and Cte 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. Conclusions: Local 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. - Background Knowledge-based management of animal genetic resources (AnGR) is critical to answer the current agricultural, socioeconomic, and environmental challenges. Consequently, characterization of AnGR constitutes one of the priorities of the FAO global plan of action for AnGR [1], in particular in developing countries, where there is a lack of information regarding what and how to conserve, develop, and select among local breeds. Village poultry make a significant contribution to poverty alleviation and household food security in many developing countries [2]. About 1.5 billion chickens are raised in Africa, 80% of them belonging to local chicken populations [3]. Indigenous chickens are considered to make a significant contribution to food security and the economical sustainability of rural households [4-6]. However, little is known about their genetic diversity. A recent FAO survey has shown that economic drivers and poor livestock sector policies are the main threats to AnGR: intensification of agriculture, importation of exotic breeds, and indiscriminate cross-breeding [7]. In the case of poultry, poor conservation strategies represent a relatively important threat, and incentives for a continued and sustainable use of local populations are lacking. Conservation strategies require a good knowledge of the genetic structure of these local populations, within or between countries, as well as an assessment of their diversity at the molecular level, to provide recommendations regarding their future management. Several studies of the genetic diversity and structure of local chicken populations in Africa have been done separately for different countries [8-15], and very few have considered a larger region such as East Africa [16]. More specifically, possible relationships between genetic diversity and environmental conditions have been investigated for chicken populations with contrasted results depending on the country of study [9,11,16]. Thus, an integrated study encompassing several African countries is still lacking but is undoubtedly required in order to give a more complete analysis of the current diversity of local chickens on this continent, where domestic chickens arrived from various origins such as India and the Mediterranean area [17,18]. The aim of the present study was to provide a largescale analysis of the genetic diversity of local chickens in several countries from the central, western and northern parts of the African continent, in order to address questions important for further conservation strategies. These questions deal with (i) the amount of genetic diversity found within these populations, (ii) the search for a possible correlation between the genetic structure and agroecological distribution, and (iii) the detection of a possible gene flow between local populations and commercial lines. Methods Sample collection and genotypes The sampling design involved 5 countries (Benin, Cte dIvoire, Ghana, Cameroon, and Morocco). Blood samples were drawn from the wing vein of 472 local adult chickens. Samples representative of Benin, Cte dIvoire, and Ghana chicken populations were collected throughout each country (Table 1, Figure 1). These populations have been independently investigated in previous studies [12-14] respectively). For a given village investigated, a mean number of 2 households was randomly chosen, and, for a given household, 2 chickens were sampled on average (80% of females). The number of villages investigated for a given administrative region range (...truncated)