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.