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.