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.