Conservation of genomic diversity and breed-specific characteristics of
domestic chickens in China
Abstract
Effective conservation and utilization of farm animals are fundamental
for realizing sustainable increases in food production. In situ and ex
situ conservation are the two main strategies currently used to protect
domestic chicken in China. However, genomic diversity and population
structure have not been compared in these conserved populations. One
potential risk is that the use of genome-wide SNPs to optimize genomic
diversity might not preserve particular alleles that are associated with
breed-specific characteristics. Here, 361 individuals from three Chinese
domestic chicken breeds were collected from populations conserved in
situ and ex situ, and genotyped using GBS (genotyping-by-sequencing). We
estimated the genomic diversity, analyzed population structures, and
found that the small ex situ conserved populations that have been
maintained in controlled environments retained less genetic diversity
than the in situ’s. In addition, genetic differentiation was detected
between in situ and ex situ conserved populations within a single breed.
We next analyzed selective signatures (FST, Pi, and XPEHH) to examine
the genetic mechanisms underlying differentiation between in situ and ex
situ conserved populations. We concluded that differentiation might be
caused by genetic drift, or the differences were due to variants from
the original populations. Finally, based on sequencing data obtained
from the ex situ conserved populations, we used Di and Pi to identify
“genomic conservation units” for breed-specific characteristics. Loci
associated with the “genomic conservation unit” could be used to
preserve breed-specific characteristics in the conservation program.