Discussion
Because China has a long history of animal husbandry and diverse
geographical conditions, it has developed extensive genetic resources
for the chicken, with 107 different indigenous breeds. Chickens are one
of the most widely distributed livestock animals in China. Worldwide,
they also have a significant role as a source of income and high-quality
protein. Indigenous chickens possess enormous genetic diversity,
especially in adaptative traits, including the ability to survive harsh
conditions, shifting climate,
urbanization,
disease epidemics, selection errors, and many other potential stresses
(Anderson, 2003; Anderson and Centonze, 2007). Most Chinese domestic
chicken breeds also have unique meat and /or egg qualities, as well as
other useful breed characteristics. However, the majority of these
chickens are currently maintained as small populations. Generally, the
smaller a livestock population, the greater is its vulnerability to
extinction (Biscarini et al., 2015; Henson et al., 1992; Ramstad et al.,
2004). Many favorable alleles can be lost as a result of selection or
genetic drift. The successful preservation and utilization of these
local breeds depend on the accurate assessment of conservation
efficiency, which is the essential measure of an effective conservation
program. Both in situ and ex situ programs have been
established for the management of poultry genetic resources in China. In
this study, we used SNPs obtained by high-throughput genome sequencing
to assess genomic diversity for chickens managed in in situ andex situ conservation programs, and proposed a strategy for
conserving the specific breed characteristics of three Chinese domestic
chicken breeds (Beijing You chicken, Langshan chicken, and Baier Yellow
chicken).
The results show that all three chicken breeds, conserved both inin situ and ex situ , have maintained rich genetic
diversity as measured by heterozygosity (Ho, He), proportion of
polymorphic markers (PN ), and allelic richness
(AR ). Breeds conserved in situ exhibited
higher genetic diversity than those conserved ex situ . Although
conservation time was longer for the in situ than the ex
situ populations, the in situ populations were larger. We
estimated the effective population size (Ne) based on whole genome SNPs
for the conserved populations, and evaluated Ne based on the
macrochromosome class (gga1–5). For all three breeds, Ne was larger for
chickens enrolled in in situ conservation programs (Figure 6 and
Table S4). We also estimated inbreeding coefficients based on whole
genome SNPs markers. As expected, the inbreeding coefficient for Baier
Yellow chickens and Beijing You chickens conserved in situ were
lower than for those conserved ex situ . However, the opposite was
true for Langshan chickens. The discrepancy may reflect the fact that
the in situ conservation time for the Langshan chicken was the
longest among the three breeds, and is currently 60 years. The largest
inbreeding coefficient was 0.0958 for the Beijing You chicken (ex
situ ), which meets our program goal to maintain 90% of whole genomic
diversity from the initial population, and limit the inbreeding
coefficient to less than 0.1 for 100 years .
Based on assessments using NJtree, PCA, STRUCTURE, FST,
and the distribution of ROH, genetic differentiation has occurred
between the two conserved populations for all three chicken breeds. The
adaptation may have been driven by environmental differences, or
selection may differ between the in situ and the ex situprograms. Few studies have examined and compared the structures ofin situ and ex situ conserved populations, and it is not
known how the genetics of domestic chickens may change in response to a
shift from the in situ to the ex situ conditions over
several decades. To explore the genetic mechanisms underlying the
differentiation between the in situ and ex situ conserved
chickens, we used FST, Pi and XP-EHH to detect regions
that were different between the two populations. Based on the gene
functions revealed by KEGG and GO term analysis, we hypothesize that the
genetic differences may be related to adaptation to local environmental
conditions. For example, the selection and conservation of the Beijing
You chicken began at the BAAFS institute of Animal Husbandry and
Veterinary Medicine in 1972. This in situ conservation program
reached its 47th year in 2018. In 1976, Beijing You
chickens were obtained from the Beijing program and transferred to
Yangzhou, Jiangsu (National Chickens Genetic Resources) to establish anex situ program, which reached its 40th year in
2015. Climate conditions in the two locations are markedly different. In
contrast, the conservation programs for Baier Yellow chickens and
Langshan chickens were conducted under nearly identical climate
conditions at Zhejiang and Jiangsu. The population sizes for these
chickens were very small at the onset of the conservation program, so it
is possible that the genetic differentiation has been caused by genetic
drift over several decades. Alternatively, the very small founder
populations used in these programs may have sampled different variants
from the original populations simply by chance.
Breed conservation has recently entered the genomic era. For bothin situ and ex situ conservation, breeders now use genomic
markers to estimate genomic diversity and reconstruct pedigrees,
enabling them to reveal relationships among animals in a population and
select individuals for mating. However, this cannot be pursued blindly.
In the case of domestic chickens, some breeds have special
characteristics and it is important to preserve these traits. More
specifically, utilization of markers for the sole purpose of optimizing
genomic diversity will not necessarily preserve breed-specific
characteristics. This shortcoming can be addressed by genome sequencing,
which makes it possible to identify and conserve variations responsible
for breed-specific characteristics. We first used Di and Pi to identify
the “genomic conservation unit” that is associated with specific breed
characteristics. SNP markers located in these regions can be used to
safeguard breed-specific characteristics in a conservation program.
Specifically, trait-specific markers are not only useful for rebuilding
phylogenetic trees for identifying valuable individuals, but are also
useful as reference markers for custom SNP chips that can track
breed-specific characteristics at the molecular level to monitor
conservation efficiency.