Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

Abstract On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, for animal production in particular. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds are likely to harbor unique adaptive features and represent a key component of diversity to reach resilience. Nevertheless, they are often suffering from small population size putting these valuable resources at risk of extinction. In chickens, management programs have been initiated a few decades ago in France, relying on a particular niche market aiming at promoting and protecting local breeds. We conducted a unique comprehensive study of 23 French local populations, along with 4 commercial lines, to evaluate their genetic conservation status and the efficiency of management programs. Using a 57K SNP chip we demonstrated that both between and within breeds genetic diversity were high in French populations. Diversity was mainly structured according to selection and breeds’ history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmer’s practices in terms of exchange, leading to more or less isolated flocks. Analysing demographic parameters as well as molecular information, we showed the efficiency of consistent management programs to conserve genetic diversity, since the earlier the breeds integrated programs the lower was the inbreeding. Finally we stressed that management programs can benefit from molecular markers and runs of homozygosity, ROH, in particular, as a valuable and affordable tool to monitor genetic diversity of local breeds which often lack pedigree information.