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 situand 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 andex 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.
Key Words: Chinese domestic chicken, Genomic diversity,
Adaptation, Breed-specific characteristics, Conservation genomics