Abstract：
BACKGROUND: On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, in particular regarding animal production. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds likely harbor unique adaptive features and represent a key component of diversity to reach resilience. However, local breeds often suffer from small population sizes, which puts these valuable resources at risk of extinction. In chickens, population management programs were initiated a few decades ago in France, relying on a particular niche market that aims at promoting and protecting local breeds. We conducted a unique comprehensive study of 22 French local breeds, along with four commercial lines, to evaluate their genetic conservation status and the efficiency of the population management programs.
RESULTS: Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds\' selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers\' practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding.
CONCLUSIONS: Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account.
RESULTS: Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds\' selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers\' practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding.
CONCLUSIONS: Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account.
摘要：
背景：持续的气候变化将在未来极大地改变农业，需要更可持续的系统，特别是在动物生产方面。在这种情况下，遗传多样性是适应新条件的关键因素:当地品种可能具有独特的适应特征，代表了达到复原力的多样性的关键组成部分。然而,当地品种往往人口规模较小，这使得这些宝贵的资源面临灭绝的危险。在鸡中,人口管理计划是几十年前在法国发起的，依靠一个特定的利基市场，旨在促进和保护当地品种。我们对22个法国当地品种进行了独特的全面研究，连同四条商业线路，评估其遗传保护状况和种群管理计划的效率。
结果：使用57K单核苷酸多态性（SNP）芯片，我们证明，在法国当地的鸡种群中，品种间和品种内的遗传多样性水平都很高。多样性主要是根据品种的选择和历史来构建的。然而，我们观察到一个突出的子结构的品种，根据农民的做法，在交换方面，导致或多或少孤立的羊群。通过分析人口统计参数和分子信息，我们表明，一致的管理方案在保护遗传多样性方面是有效的，由于早期整合此类计划的品种具有较早的近亲繁殖。
结论：法国本地鸡种的管理计划将其遗传多样性保持在良好水平。我们建议未来的程序样本尽可能多的人，从一开始就强调男性和女性，并专注于人口规模的快速和强劲增长，同时保护尽可能多的家庭。我们还强调了分子工具的有用性，以监测那些家谱并不总是可用的小群体。最后,该品种似乎是保护遗传多样性的适当操作单位，即使是当地品种，对于哪些品种，如果存在，也可以考虑。
结果：使用57K单核苷酸多态性（SNP）芯片，我们证明，在法国当地的鸡种群中，品种间和品种内的遗传多样性水平都很高。多样性主要是根据品种的选择和历史来构建的。然而，我们观察到一个突出的子结构的品种，根据农民的做法，在交换方面，导致或多或少孤立的羊群。通过分析人口统计参数和分子信息，我们表明，一致的管理方案在保护遗传多样性方面是有效的，由于早期整合此类计划的品种具有较早的近亲繁殖。
结论：法国本地鸡种的管理计划将其遗传多样性保持在良好水平。我们建议未来的程序样本尽可能多的人，从一开始就强调男性和女性，并专注于人口规模的快速和强劲增长，同时保护尽可能多的家庭。我们还强调了分子工具的有用性，以监测那些家谱并不总是可用的小群体。最后,该品种似乎是保护遗传多样性的适当操作单位，即使是当地品种，对于哪些品种，如果存在，也可以考虑。
