Breeding history and candidate genes responsible for black skin of Xichuan blackbone chicken

- responsible for black skin of Xichuan black- bone chicken.
- Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs.
- We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype..
- Results: Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds.
- Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds.
- The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago.
- This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection.
- A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3 , might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis..
- Conclusions: These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals..
- Keywords: Xichuan black-bone chicken, Structural variants, Selective sweep, Black skin, Integration of whole genome and transcriptome.
- Domesticated ani- mals have spread to every region of the globe along with their human domesticators.
- The study of domestic ani- mals contributes to our understanding of the evolution of animals under artificial selection, the influence of domestication or adaptive evolution on the animal genome, the genetic basis of evolution and phenotypic.
- The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material.
- Full list of author information is available at the end of the article Li et al.
- Chicken is one of the major sources of animal protein for humans.
- The Xichuan black-bone chicken (XBC), named for the Chinese prefecture of Xichuan, typically has five black parts (beak, skin, bones, legs, and meat) that dis- tinguish it from other chicken breeds.
- Black-bone chick- ens are commonly believed to have medicinal properties and have been used as remedies to enhance the human immune system [19], prevent emaciation [20], treat dia- betes [21], and cure conditions such as menstrual abnor- malities and postpartum complications [22].
- Xichuan black-bone chickens were primarily developed in a mountainous and inaccessible region in Xichuan County, China.
- Xichuan black-bone chickens are highly prized, and be- came major income producers for farmers in the region..
- However, the breeding history has not been examined in any detail, and the identity of the genetic factors responsible for the black body parts are unknown, particularly at the genomic level.
- the extent to which the Xichuan black-bone chickens has contributed germplasm to other breeds has not been studied..
- In this study, we used whole genome resequencing to identify genomic features that illuminate the breeding history of the Xichuan black-bone chicken, and to cor- relate these features with the black characteristics of the breed.
- Genes with Xichuan black-bone chicken specific genomic variants were identified.
- Some genes in this class have undergone positive selection, and may be clues to the adaptive evolutionary history of the breed..
- Our results provide insight into the genetic factors underlying traits specific to Xichuan black-bone chick- ens.
- Genetic variation in Xichuan black-bone chicken.
- To identify genetic variations, we resequenced the ge- nomes of 5 Xichuan black-bone chickens.
- Around 98.45% of Xichuan black-bone chicken sequences were identical to those of red jungle fowl.
- To examine genome-wide relationships and divergence between Xichuan black-bone chickens and other.
- a Geographical origins of the 9 chicken breeds used in this study.
- b Summary of genomic resequencing data from 5 Xichuan black-bone chickens.
- Chromosomes are represented in different colors in the outermost circle.
- a NJ tree generated using polymorphisms detected in the 29 individual chickens.
- Each of the 9 breeds has been assigned a distinct color.
- K is the number of presumed ancestral groups, which was varied in the analysis from 2 to 10.
- The scale bar shows 10 times the average standard error of the entries in the sample covariance matrix.
- in five of the populations 5 ka years ago (Fig.
- In addition, a large difference in the pi value was also observed within this sweep between black and non-black groups.
- The pi value in the black-skin group was lower, suggesting that the sweep has been positively selected in the black-skin population (Fig.
- We analyzed differences between black-bone chick- ens and other domesticated chickens to detect selection signatures associated with black skin.
- Genes associated with pigmentation that play important roles in the regu- lation of melanin deposition in mammals were identified in several genomic regions within selective sweeps.
- To better understand the evolution of the selected genes, we hybridized Gushi chickens with Xichuan black-bone chickens to obtain F2 full-sibs with different.
- Xichuan black-bone chickens are rare in China and else- where, and have not been the focus for many studies..
- Due to the limited information available, we performed in-depth whole-genome sequencing of 5 black-bone chickens to explore the population structure, genetic diversity, and history of this breed.
- 5 Identification of genomic regions in Xichuan black-bone chickens with strong selective sweep signals.
- a Selective sweep signals are located to the left and right of the vertical dashed lines (representing Pi ratio values >.
- 7 Histomorphological examination of Xichuan black-bone chickens with black (a) and yellow (b) skin.
- This is because breeds such as XBC were do- mesticated in the middle or lower reaches of the Yellow River, and then brought to many other regions by humans [36].
- Obviously, the role of human activities cannot be ignored in the domestication history of native breeds.
- Membrane-associated transporter SLC45A2 is a member of the free vector family of SLC45A (solute carrier family 45) [50].
- SLC45A2 is differ- entially expressed in the skins of 1-month-old grey and white Lander geese [53].
- The results suggest that the differential expression of SLC45A2 affects the depos- ition of melanin in black skin of the XBC, although the specific regulatory mechanism remained unknown..
- Green shanks are another typical characteristic of Xichuan black-bone chickens.
- A mutation in the noncoding region of exon 4 of GRAMD3 may be linked to shank color in chickens [63]..
- Mutations in the flanking region of GRAMD3 cause abnormal expression of the gene in green shank [64]..
- When MCHR1 is distributed in the peripheral tissues of mice, it affects the synthesis of fat and is related to obesity [71, 72].
- We suggest that MCHR1 might play an important role in the meat quality and pigmentation in XBC..
- SLCO2B1 is a member of the OATP gene family.
- The results provide new insight into Xichuan black-bone chickens and their unique qualities..
- Whole blood samples from five 30-week-old female Xichuan black-bone chickens were collected from Xichuan County (32°56′11″N E) in Henan Province, which come from different conservation popu- lations and have no genetic relationship.
- The data were used to analyze the evolutionary history of Xichuan black-bone chickens and other populations (Fig.
- Finally, gene-based annotation of the variants was ac- complished using SnpEff [83], for which the corre- sponding chicken gene annotation file was downloaded from Ensembl.
- To compare the Xichuan black-bone chicken with the other breeds, we adjusted the sequencing data for the Xichuan black-bone chicken so that the average sequencing depth was similar across breeds..
- LD for five breeds was calculated on the basis of the correlation coefficient R 2 statistics of two loci using PopLDdecay [91]..
- TreeMix [27] was used to construct a population phylo- genetic tree for gene flow analysis of the 9 breeds.
- A tree file was one of the out- puts generated by Beast2.
- We used a pairwise sequentially Mar- kovian coalescent (PSMC) model [93] to detect changes in the effective ancestral population sizes of the XBC population at a high level of detail.
- Finally, we per- formed a functional enrichment analysis of the candidate genes, using Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
- To determine whether novel allelic variants located in the top 5% of Fst regions of the genome affect gene expres- sion, we utilized RNA-Seq to construct six cDNA libraries from black (BS) and yellow (YS) dorsal skin of a Xichuan black-bone chickens hybrid population.
- The hybrid F2 population was obtained by crossing the Gushi chickens with Xichuan black-bone chickens.
- To verify the accuracy of the data obtained from RNA-seq, the results were confirmed by qRT-PCR.
- Statistics of genetic variants in Xichuan black-bone chickens..
- GO analysis of candidate genes under selection in Xichuan black-bone chickens..
- Gene annotation of genomic regions with strong selective sweep signals in Xichuan black- bone chickens..
- Difference in expression for dorsal skin between black skin (BS) and yellow skin (YS) in Xichuan black-bone chickens by RNA-Seq..
- XBC: Xichuan black-bone chicken.
- YC, CZ, WL, FL, YF, YW and YT collected the samples and performed most of the experiments.
- CARS-40-K04), the Program for Innovation Research Team of the Ministry of Education (IRT16R23), the Key Science and Technol- ogy Research Project of Henan Province and the Young Backbone Teacher Training Program of Henan Higher Educational Institution (2017GGJS036).
- Data for the 5 Xichuan black-bone chickens used in the whole-genome rese- quencing analysis, and for the 6 Xichuan black-bone chickens used in the RNA-Seq analysis are accessible at NCBI under BioProject accession numbers PRJNA642410 and PRJNA418694, respectively.
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