Chinese Indigenous Chicken Research Articles

The Effect of Breed and Age on the Growth Performance, Carcass Traits and Metabolic Profile in Breast Muscle of Chinese Indigenous Chickens.

Indigenous chickens possess desirable characteristics and account for considerable proportions of the total chicken production in China. The current study examined the growth performance, carcass characteristics and muscle metabolites among a crossbred broiler and two indigenous, yellow-feathered chickens (Mahuang and Tuer) with different ages (60 and 75 days). Results indicated that the crossbred broiler had better feed efficiency, higher breast and thigh muscle yield, as well as a lower abdominal fat percentage than Mahuang and Tuer chickens (p < 0.05). Gas chromatography–mass spectrometry-based metabolomics and multivariate analysis revealed sugars, amino acids and organic acids were the predominant metabolites that differed among the three chicken breeds. Growth performance and carcass traits of yellow-feathered chickens exhibited significant differences with the extension of the feeding period (p < 0.05). Moreover, differential metabolites reflected altered aminoacyl-tRNA biosynthesis, ATP-binding cassette transporters, pantothenate and CoA biosynthesis, as well as glutathione metabolism in yellow-feathered chickens affected by age. Collectively, this study contributes to a deeper understanding of the production efficiency and chemical composition of precursor flavor in Chinese indigenous, yellow-feathered chicken.

Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler.

Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.

Effects of Dietary Ginsenoside Rg1 Supplementation on Growth Performance, Gut Health, and Serum Immunity in Broiler Chickens.

The restriction and banning of antibiotics in farm animal feed has led to a search for promising substitutes for antibiotics to promote growth and maintain health for livestock and poultry. Ginsenoside Rg1, which is one of the most effective bioactive components in ginseng, has been reported to have great potential to improve the anti-inflammatory and anti-oxidative status of animals. In this study, 360 Chinese indigenous broiler chickens with close initial body weight were divided into 5 groups. Each group contained 6 replicates and each replicate had 12 birds. The experimental groups were: the control group, fed with the basal diet; the antibiotic group, fed basal diet + 300 mg/kg 15% chlortetracycline; and three Rg1 supplementation groups, fed with basal diet + 100, 200, and 300 mg/kg ginsenoside Rg1, respectively. The growth performance, immune function, and intestinal health of birds were examined at early (day 1–28) and late (day 29–51) stages. Our results showed that dietary supplementation of 300 mg/kg ginsenoside Rg1 significantly improved the growth performance for broilers, particularly at the late stage, including an increase in final body weight and decrease of feed conversion ratio (P < 0.05). Additionally, the integrity of intestinal morphology (Villus height, Crypt depth, and Villus height/Crypt depth) and tight junction (ZO-1 and Occludin), and the secretion of sIgA in the intestine were enhanced by the supplementation of Rg1 in chicken diet (P < 0.05). The immune organ index showed that the weight of the thymus, spleen, and bursa was significantly increased at the early stage in ginsenoside Rg1 supplementation groups (P < 0.05). Our findings might demonstrate that ginsenoside Rg1 could serve as a promising antibiotic alternative to improve the growth performance and gut health for broiler chickens mainly through its amelioration of inflammatory and oxidative activities.

Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations.

The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.

Comparative analysis of hypothalamus transcriptome between laying hens with different egg-laying rates

Egg-laying performance is one of the most important economic traits in the poultry industry. Commercial layers can lay one egg almost every day during their peak-laying period. However, many Chinese indigenous chicken breeds show a relatively low egg-laying rate, even during their peak-laying period. To understand what makes the difference in egg production, we compared the hypothalamus transcriptome profiles of Lushi blue-shelled-egg chickens (LBS), a Chinese indigenous breed with low egg-laying rate and Rhode Island Red chickens (RIR), a commercial layer with relatively high egg-laying rate using RNA-seq. A total of 753 differentially expressed genes (DEGs) were obtained. Of these DEGs, 38 genes were enriched in 2 Gene Ontology (GO) terms, namely reproduction term and the reproductive process term, and 6 KEGG pathways, namely Wnt signaling pathway, Oocyte meiosis, GnRH signaling pathway, Thyroid hormone signaling pathway, Thyroid hormone synthesis and MAPK signaling pathway, which have been long known to be involved in egg production regulation. To further determine the core genes from the 38 DEGs, protein-protein interaction (PPI) network, co-expression network and transcriptional regulatory network analyses were carried out. After integrated analysis and experimental validation, 4 core genes including RAC1, MRE11A, MAP7 and SOX5 were identified as the potential core genes that are responsible for the laying-rate difference between the 2 breeds. These findings paved the way for future investigating the mechanism of egg-laying regulation and enriched the chicken reproductive regulation theory.

Hepatic lipid metabolomics in response to heat stress in local broiler chickens breed (Huaixiang chickens).

High‐temperature environment‐induced heat stress (HS) is a hazard environmental element for animals, leading to dramatic changes in physiological and metabolic function. However, the metabolomic‐level mechanisms underlying lipid metabolism in liver of slow‐growing broilers are still obscure. The present study investigated the effects of HS on hepatic lipidomics in Chinese indigenous slow‐growing broilers (Huaixiang chickens). The study includes two treatments, each treatment had 5 replicates with 4 broilers per cage, where a total of 40 eight‐week‐old female Huaixiang chickens (average initial body weight of 840.75 ± 20.79 g) were randomly divided into normal temperature (NT) and HS groups for 4 weeks, and the broilers of NT and HS groups were exposed to 21.3 ± 1.2℃ and 32.5 ± 1.4℃ respectively. The relative humidity of the two groups was maintained at 55%–70%. The liquid chromatography‐mass spectrometry (LC‐MS)‐based metabolomics were conducted to evaluate the changes in hepatic lipidomics of broilers. The results showed that there were 12 differential metabolites between the two treatments. Compared with the NT group, HS group reduced the levers of hepatic phosphatidylcholine (PC) (16:0/16:0), PC (16:0/18:2), triglyceride (TG) (16:0/16:1/18:1), TG (18:0/18:1/20:4) (VIP > 1 and p < 0.05), while increased PC (18:1/20:3), PC (18:0/18:1), PC (18:1/18:1), PC (18:0/22:5), dimethyl‐phosphatidyl ethanolamine (dMePE) (14:0/18:3), dMePE (18:0/18:1) and dMePE (16:0/20:3) levels (Variable Importance in the Projection; VIP > 1 and p < 0.05). In addition, according to the analysis of metabolic pathway, the pathways of linoleic acid, alpha‐linolenic acid, glycerolipid and glycerophospholipid metabolism were involved in the effects of HS on hepatic lipid metabolism of broilers (p < 0.05). In conclusion, HS altered the hepatic lipid metabolism mainly through linoleic acid, alpha‐linolenic acid, glycerolipid and glycerophospholipid metabolism pathway in indigenous broilers. These findings provided novel insights into the role of HS on hepatic lipidomics in Chinese indigenous broiler chickens.

Population Structure and Genetic Diversity of Seven Chinese Indigenous Chicken Populations in Guizhou Province.

To investigate the population structure and genetic diversity of indigenous chicken breeds in Guizhou, a total of 150 individual samples were collected from 12 breeds, including seven local chicken breeds in Guizhou Province, three Chinese native breeds found in other provinces, and two commercial breeds. The genotype datasets were obtained using a 50K single nucleotide polymorphism array method, and then a series of population analyses were performed. The obtained population parameters and linkage disequilibrium decay indicated a higher degree of genetic diversity in Guizhou chickens than in commercial breeds. Two Guizhou local breeds, Wumeng black-bone and Weining, were clustered with a breed from a neighboring province, Xinwen black-bone, which exhibited similar ancestral composition patterns. A newly found breed, Wumeng crested, had high genetic diversity and displayed genetic differences from other Guizhou breeds. These findings provide insight into the establishment of efficient conservation and utilization programs for Guizhou chicken breeds.

Improving read alignment through the generation of alternative reference via iterative strategy

There is generally one standard reference sequence for each species. When extensive variations exist in other breeds of the species, it can lead to ambiguous alignment and inaccurate variant calling and, in turn, compromise the accuracy of downstream analysis. Here, with the help of the FPGA hardware platform, we present a method that generates an alternative reference via an iterative strategy to improve the read alignment for breeds that are genetically distant to the reference breed. Compared to the published reference genomes, by using the alternative reference sequences we built, the mapping rates of Chinese indigenous pigs and chickens were improved by 0.61–1.68% and 0.09–0.45%, respectively. These sequences also enable researchers to recover highly variable regions that could be missed using public reference sequences. We also determined that the optimal number of iterations needed to generate alternative reference sequences were seven and five for pigs and chickens, respectively. Our results show that, for genetically distant breeds, generating an alternative reference sequence can facilitate read alignment and variant calling and improve the accuracy of downstream analyses.

Heat stress alters serum lipid metabolism of Chinese indigenous broiler chickens-a lipidomics study.

Heat stress (HS) by high-temperature environment reduced the production performance of poultry and caused losses to the breeding industry. The present study was conducted to investigate the effects of HS on serum lipidomics in Chinese indigenous slow-growing broiler chickens (Huaixiang chickens). A total of 40 8-week-old female Huaixiang chickens were randomly allocated to two groups, including normal temperature (NT, fed basal diet) and HS (fed basal diet), and each group consisted of five replicates with four birds per replicate. NT and HS groups were exposed to 21.3 ± 1.2 °C and 32.5 ± 1.4 °C for 4 weeks, respectively. Serum lipidomics in broilers was determined by liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. The results indicated that there were significant differences in metabolic spectra between the groups, and a total of 17 differential metabolites were screened. Compared with NT group, HS group reduced the serum ceramide (cer) (d18:1/22:0), cer (d18:1/24:1), cer (d20:2/22:2), lyso-phosphatidylcholine (LPC) (18:0), phosphatidylcholine (PC) (18:0/20:4), PC (15:0/23:4), PC (18:0/22:6), PC (18:2/18:2), phosphatidylethanolamine (PE) (18:1/18:1), polyethylene terephthalate (PEt) (37:3/8:0), phosphatidylglycerol (PG) (32:1/16:2), phosphatidyl methyl ethanolamine (PMe) (19:3/13:0), PMe (26:1/9:0), sphingomyelin (SM) (d16:0/18:1), triglycerides (TG) (18:0/18:1/18:2), and TG (19:4/21:6/21:6) levels [variable importance in the projection (VIP > 1 and P < 0.05)], while HS group increased serum PC (17:0/17:0) content (VIP > 1 and P < 0.05). Also, metabolic pathway analysis showed that the pathways of glycerolphospholipid, linoleic acid and α-linolenic acid metabolism, and glycosylphosphatidylinositol (GPI)-anchored biosynthesis were changed (P < 0.05). In conclusion, HS led to the disorders of serum lipid metabolism in broilers, and mainly downregulated serum content of phospholipids. These findings provide novel insights into the effects of HS on serum lipidomics in indigenous slow-growing chickens.

Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken

Gamecock chickens are one of the earliest recorded birds in China, and have accumulated some unique morphological and behavioral signatures such as large body size, muscularity and aggressive behavior, whereby being excellent breeding materials and a good model for studying bird muscular development and behavior. In this study, we sequenced 126 chicken genomes from 19 populations, including four commercial chicken breeds that are commonly farmed in China, 13 nationwide Chinese typical indigenous chicken breeds (including two Chinese gamecock breeds), one red jungle fowl from Guangxi Province of China and three gamecock chickens from Laos. Combined with 31 published chicken genomes from three populations, a comparative genomics analysis was performed across 157 chickens. We found a severe confounding effect on potential cold adaptation exerted by introgression from commercial chickens into Chinese indigenous chickens, and argued that the genetic introgression from commercial chickens into indigenous chickens should be seriously considered for identifying selection footprint in indigenous chickens. LX gamecock chickens might have played a core role in recent breeding and conservation of other Chinese gamecock chickens. Importantly, AGMO (Alkylglycerol monooxygenase) and CPZ (Carboxypeptidase Z) might be crucial for determining the behavioral pattern of gamecock chickens, while ISPD (Isoprenoid synthase domain containing) might be essential for the muscularity of gamecock chickens. Our results can further the understanding of the evolution of Chinese gamecock chickens, especially the genetic basis of gamecock chickens revealed here was valuable for us to better understand the mechanisms underlying the behavioral pattern and the muscular development in chicken.

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

BackgroundYellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration.ResultsThe whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 (LGR4), solute carrier family 23 member 2 (SLC23A2), and solute carrier family 2 member 14 (SLC2A14), besides the classical beta-carotene dioxygenase 2 (BCDO2), as major candidates pigment determining genes in the YFCs.ConclusionWe provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs.

Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations

BackgroundModern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line.ResultsBased on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line.ConclusionsOur observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations.

Evaluation of the genetic diversity of six Chinese indigenous chickens.

ObjectiveThe extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China.MethodsIn the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds.ResultsTwenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious.ConclusionThe genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

Effects of exercise on carcass composition, meat quality, and mRNA expression profiles in breast muscle of a Chinese indigenous chicken breed

In this study, we evaluated the effects of exercise on the growth performance, carcass composition, meat quality, and mRNA expression profile of breast muscle in a Chinese indigenous chicken breed. Briefly, 300 female Huainan chickens (60-day-old) with similar BW were selected and raised in a free-range environment. Daily steps were counted by pedometer for all birds from 61 to 140 D of age. At 140 D of age, based on the average counts of steps per day, 15 birds with the highest number of steps (HS), 15 birds with a medium number of steps (MS), and 15 birds with low numbers of steps (LS) were selected for use in subsequent experiments. The HS group had heavier BW than the other two groups (P < 0.05). Compared with the LS group, the HS group displayed higher meat redness and lower shear force, drip loss, cooking loss values, and the percentage of breast muscle weight (P < 0.05). Moreover, a total of 150 differentially expressed genes were identified from the pectoralis major muscles of the HS and LS group. Therefore, enhanced exercise increased BW, improved meat quality by increasing WHC and decreasing shear force values, and decreased percentage of breast muscle weight but had no effect on others carcass parameters. Additionally, the differentially expressed genes in breast muscle between the HS and LS groups were mainly associated with skeletal muscle tissue development and meat quality traits.

Effects of husbandry systems and Chinese indigenous chicken strain on cecum microbial diversity.

ObjectiveThis study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions.MethodsA total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment.Resultsi) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens.ConclusionThe core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

Whole-genome resequencing analysis of Pengxian Yellow Chicken to identify genome-wide SNPs and signatures of selection.

Chinese indigenous chickens have experienced strong selective pressure in genes or genomic regions controlling critical agricultural traits. To exploit the genetic features that may be useful in agriculture and are caused by artificial selection, we performed whole-genome sequencing of six Pengxian Yellow Chickens and downloaded the sequence data of five Red Jungle fowls from the NCBI. Through selective sweep analysis, we detected several regions with strong selection signals, containing 497 protein-coding genes. These genes were involved in developmental processes, metabolic processes, the response to external stimuli and other biological processes including digestion (ABCG5, ABCG8 and ADRB1), muscle development and growth (SMPD3, NELL1, and BICC1) and reduced immune function (CD86 and MTA3). Interestingly, we identified several genes with extremely strong selection signals associated with the loss of visual capability of domestic chickens relative to their wild ancestors. Amongst them, we propose that CTNND2 is involved in the evolutionary changes of domestic chickens toward reduced visual ability through the diopter system. VAT1 was also likely to contribute to these processes through its regulation of mitochondrial fusion. In summary, these data illustrate the patterns of genetic changes in Pengxian yellow chickens during domestication and provide valuable genetic resources that facilitate the utilization of chickens in agricultural production.

Identification and characterization of a novel natural recombinant avian leucosis virus from Chinese indigenous chicken flock.

Avian leukosis virus (ALV) caused tremendous economic losses to poultry industry all over the world, especially in China. One natural recombinant ALV strain, designated as HB2015032, was isolated from indigenous chickens with neoplastic diseases in Hubei, China. The complete proviral genome of HB2015032 is 7703bp in length. Sequence analysis showed that the Env of HB2015032 exhibited 99.3% similarity with that of a ALV subgroup K (ALV-K) isolate JS11C1 at amino acid level. Phylogenetic analysis revealed that both gp85 and gp37 of HB2015032 were clustered in the same branch with JS11C1 and other ALV-K strains isolated from Chinese indigenous chickens in recent years. However, the pol gene, the 3' untranslated region (3' UTR), and the 3' long terminal repeat (3' LTR) of HB2015032 were more closely related to ALV-J prototype HPRS-103, and clustered in the same branch with ALV-J strains. Furthermore, the pol gene of HB2015032 contained a premature stop codon that resulted in a truncated Pol protein with 22 amino acid residues missing, which was a unique feature of the pol gene of ALV-J. 3'UTR of HB2015032 containing entire DR1, E element and U3. E element of HB2015032 contained one base deletion, which resulted in a c-Ets-1 binding site. In addition, U3 region of HB2015032 contains most of the transcription regulatory elements of ALV-J, including two CAAT boxes, Y boxes, CArG boxes, PRE boxes, NFAP-1 boxes, and one TATA box. These results suggest that isolate HB2015032 was a novel recombinant ALV-K containing the ALV-K env gene and the ALV-J backbone and exhibiting high pathogenicity.

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds.

The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).

Widespread introgression in Chinese indigenous chicken breeds from commercial broiler.

Chinese indigenous chickens (CICs) constitute world‐renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.

Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences

ABSTRACT Chinese indigenous chicken breeds are geographically widespread, and a total of 116 indigenous chicken breeds are listed as Chinese national genetic resources. However, these indigenous chicken breeds are facing serious challenges as declining population and germplasm degeneration because lots of commercial chicken breeds had been introduced. In this study, the genetic variations of eleven Chinese indigenous chicken breeds of Sichuan province and three commercial chicken breeds were investigated based on the partial mitochondrial DNA D-loop of 487bp in length. 147 individuals from 14 breeds were examined and 34 haplotypes were observed. Genetic diversity analysis showed that the highest haplotype diversity level was found in Dahen Chicken (DH) population, while the Arbor Acres Chicken (WF) and Roman layer (RM) showed lower genetic diversity levels. The long-term artificial selection may lead to reduced nucleotide diversity. Genetic population differentiation analysis indicated that most of the variation (80.80%) was attributed to variations among breeds. Phylogenetic analysis revealed that these individuals were divided into four distinct genetic clades, including cluster A, B, C and D. Eighteen haplotypes were classified as cluster A, eight haplotypes were classified as cluster B, five haplotypes were classified as cluster C and three haplotypes were classified as cluster D. There was no breed-specific clade. Our study firstly identified the population’s genetic structure of Chinese indigenous chickens and the most important commercial breeds in Sichuan province, though the genetic diversity of indigenous breeds did not suffer obvious decrease, but could be helpful for efficient artificial breeding selection and genetic resources conservation.