Breed characteristics
The chicken conservation programs use random mating and random selection in in situ conservation, and random mating with within-family selection in ex situ conservation. Genome-wide SNP markers are often used to assess genetic diversity in programs that conserve animal genetic resources for specific populations. However, this approach can result in the loss of genetic diversity for some breed-specific traits, thereby reducing performance (Sun et al., 2018).
The three chicken breeds in this study have specific performance traits and phenotypes of value, as discussed in our previous study (Zhang et al., 2018). Because these characteristics are important, programs that maintain the overall genetic diversity of each breed must also maintain the distinct phenotypic variations. Since the size of a conservation population is usually small (30 males and 300 females), genetic drift can easily occur and alleles that contribute to special traits can be lost. Therefore, it is crucial to monitor and maintain the genetic diversity associated with these special traits. Here, we utilized Di and Pi to sweep the selective signatures to identify genomic regions related with breed characteristics. We then compared these regions to the Chicken QTL database (Hu et al., 2013) (http://www.animalgenome.org/cgi-bin/QTLdb). Regions or SNPs that overlapped with QTLs were classified tentatively as the “genomic conservation unit” for a specific breed.
Based on the population-scale genetic differences between Beijing You chicken and the other breeds, we hypothesized that specific genome signals have appeared in the Beijing You chicken population during domestication. To localize these selective sweeps in the Beijing You chicken genome, we calculated two genome-wide statistics, Di and the Pi ratio, for the Beijing You chicken vs. the Baier Yellow and Langshan populations. Focusing on the regions in the top 5% of the Di and Pi ratio empirical distribution (Figure 9), we identified 59 significant regions (Di > 0.5036 and log2 Pi ratio > 0.9433) harboring 255 candidate genes (Table S5b). Comparing the genomic regions with the Chicken QTL database (Hu et al., 2013), we found that these selected regions were related to important economic traits such as growth, body weight, and feed conversion ratio. In the Baier Yellow chicken, we identified 50 candidate genomic regions (Di >0.4762 and log2 Pi ratio >0.6137) harboring 202 genes (Figure 10, Table S5a). These genomic regions overlapped with QTLs for body weight (day of first egg), egg number, egg production rate, and earlobe color. Finally, 36 genomic regions were identified in Langshan chickens (Di>0.5064 and log2 Pi ratio>0.6572) (Figure 11 and Table S5c).
A phylogenetic tree reflects the genetic distance among animals and enables the selection of individuals for breeding (Sun et al., 2018). Based on the pairwise distance matrix, a phylogenetic tree for the threeex situ populations was constructed using the neighbor-joining method (Saitou and Nei, 1987) (Figure S6a). SNPs located in the selected genome regions were defined as breed-specific markers, and the selected genome regions were defined as the “genomic conservation unit”. Using these criteria, 9029, 7260, and 3907 SNPs located within genomic conservation units were identified in the Beijing You chicken, Baier Yellow chicken, and Langshan chicken populations, respectively. The phylogenetic trees were then reconstructed using these SNPs (Figure S6b).
Using the phylogenetic trees together, it is possible to identify individuals that embody whole genomic diversity as well as breed-specific characteristics. For example, consider the 6 pedigrees in Figure S7a and 7 pedigrees in Figure S6b for the Beijing You chicken. If the conservation program was constructed using only the genome-wide SNPs, individuals 2, 4, 7, 23, 39, and 52 might not be chosen for breeding, resulting in the loss of the genetic diversity associated with important economic traits. It is therefore critical to select individuals that represent both pedigrees in Figure S6a and Figure S6b. Similar precautions would need to be observed for the Baier Yellow and Langshan populations. These additional steps improve the ability of the conservation program to retain critical breed characteristics.