Introduction
Because of its long history of animal husbandry and diversified geographical conditions, China has a rich diversity of domestic chicken breeds. To date 107 Chinese breeds have been described (Rescources, 2011), among which are some with striking appearance and valuable traits. Genetic diversity provides the raw material for breed improvement and for the adaptation of livestock populations to changing environments and market demands. However, genetic diversity is at risk for many species throughout the world. Among domesticated avian species, chickens have by far the highest number of breeds at risk . In China alone 21 breeds are at risk, representing 1/5 of the total number of domestic chicken breeds (Rescources, 2011). Effective conservation and use of farm animals are necessary to obtain sustainable increases in food production. Conservation plans are commonly classified into three categories: in situ conservation; ex situ in vivoconservation; and ex situ in vitro conservation.In vivo methods are primarily used in China for the management of animal genetic resources, including both in situ and ex situconservation. In situ conservation can best be described as the sustainable breeding of an endangered livestock breed in the normal adaptive production environment, or as close to it as practically possible, to conserve genetic diversity over a long period. Ex situ conservation is the preservation of endangered livestock outside of normal production systems . In China, two national gene banks (National Chicken Genetic Resources in Jiangsu and Zhejiang) and 23 national conservation farms have been established. However, few studies have compared the actual efficacy of in situ and ex situefforts to conserve chickens, although the FAO has recommended that livestock breed conservation status should be monitored regularly .
A comprehensive knowledge of genetic diversity within and between breed populations is required to manage animal genetic resources (Groeneveld et al., 2010). DNA markers are the most reliable molecular tools for the assessment of genetic diversity (Liu and Cordes, 2004b). RFLPs (Thurston et al., 2002), mtDNA (Avise et al., 1987; Avise et al., 1986; Harrison, 1989; Kocher et al., 1989; Zhang and Hewitt, 1996), RAPD (Ali et al., 2004; Dodgson et al., 1997; Koh et al., 1998; Levin et al., 1993), AFLPs (Parsons and Shaw, 2001; Savelkoul et al., 1999), Y-chromosome markers (Bruford et al., 2003; Zeder et al., 2006), VNTRs (Zane et al., 2002), and SNPs (Andersson and Georges, 2004; Liu and Cordes, 2004a; McMahon et al., 2014; Morin et al., 2004; Vignal et al., 2002) have been the most widely used marker systems. In addition, conservation programs have been based on pedigree information. The development of high-throughput genotyping techniques has made it possible to obtain large numbers of genomic markers that can be used to correct and reconstruct pedigrees. Genome-wide marker data is also regarded as a useful tool for the maintenance of genetic diversity (de Cara et al., 2011). However, conservation programs designed using genome-wide SNPs alone risk losing the genetic variations associated with some traits, resulting in reduced performance. In particular, domestic chicken breeds have specific performance traits that constitute an important genetic resource. The maintenance of genetic diversity must therefore include the preservation of these valuable phenotype variations. Because conservation populations are usually small, gene drift can also occur easily, and alleles that contribute to special traits might be lost. It is thus crucial to monitor and maintain the genetic diversity specifically responsible for breed characteristics as well as the general genetic diversity across the genome.
Here, we integrated genomic data from in situ and ex situconserved chicken breeds in China, compared breeds to determine genomic diversity, and then used whole-genome SNP markers to assess the efficacy of ongoing in situ and ex situ conservation efforts. The data were examined to detect genomic signatures resulting from genetic differentiation between breeds managed using the two conservation practices, and selective signature analysis was also used to identify “genomic conservation units” to study the molecular breed-specific characteristics conservation. Our results provide insights into the genomic effects of ongoing conservation efforts, and establish a foundation for optimizing conservation programs for in situ andex situ populations of Chinese domestic chickens.