Indigenous Chicken Breeds Research Articles

Association of antioxidant defense system with semen attributes vis a vis fertility in exotic and indigenous chicken breeds

The present study was designed to ascertain the association of antioxidant defense system with semen attributes and fertility in RIR (Rhode Island Red), PR (Punjab Red), RIR x local cross, Aseel and Kadaknath breeds. Based on sperm attributes, roosters of each breed were divided into two group i.e. G-I (exhibiting >50% sperm attributes) and G-II (exhibiting <50% sperm attributes). Motility, viability, membrane-, acrosome-, DNA-integrity and fertility differed significantly (p < 0.05) among the breeds, representing maximum in PR roosters and least in Aseel roosters. Values of sperm attributes and fertility rate were also significantly (p < 0.05) higher in G-I compared to G-II roosters in exotic as well as indigenous breeds. MDA content differed significantly (p < 0.05) in spermatozoa of five breeds. It indicated a least oxidant stress in PR and highest in Aseel. MDA concentration was significantly (P < 0.05) higher in G-II (28.36 ± 2.40–96.0 ± 6.4) than G-I (13.65 ± 1.81–52.22 ± 6.4) roosters in all breeds. Antioxidant enzyme activity varied significantly (p < 0.05) among the breeds and groups within the breeds. Significantly (p < 0.05) higher activity of four enzymes was evident in G-II as compared to G-I roosters irrespective of the breed. A moderate to strong negative correlation was perceived among LPO, SOD, GPX, catalase, GRE and sperm attributes/fertility rate. A moderate to strong positive correlation (0.21–0.92) among LPO and antioxidant enzymes revealed that with the increase in LPO, antioxidant enzymes increase too and vice versa in all breeds. Likewise, positive correlation between sperm attributes and fertility revealed that higher sperm attributes contribute to the high fertility of roosters. This is one of the first reports on complete set of antioxidant enzymes and oxidative stress in relation to sperm attributes and fertility in different five chicken breeds. A complete antioxidant enzyme system seems to modulate the oxidative stress, sperm attributes and fertility. It may be possible to use LPO as a fertility marker to select the roosters for breeding purpose in the chicken breeds.

Meat quality traits of Vietnamese indigenous Noi chicken at 91 days old

Indigenous chicken breeds have showed slower growth rate and yield lower meat production, compared to commercial broilers. However, their meat quality is valued by modern consumers. The present study aimed at analyzing the quality traits of breast meat samples of Noi broilers, one of the famous indigenous chicken breeds in Vietnam. A total of 355 breast fillet samples were collected to evaluate quality meat traits such as pH, surface color, drip loss, and cooking loss at different time points of 3, 24, and 48 hours after slaughtering as well as to analyze chemical compositions such as dry matter, crude protein and ether extract. As result, sex and cold-storage time significant affect some of quality traits of breast meat, whereas their interaction did not associate among the observed properties. After 3 hour-storage, the pH value was determined at 5.63, then decrease to 5.56 and 5.55 after 24 and 48 hours, respectively. The color values (L*, a*, and b*) were in the normal range reported from previous studies. Meat samples of two sexes did not vary in the cooking loss and drip loss values, whereas it was significantly different due to cold-storage time. The ether extract content of the meat was found negatively correlated with the cooking loss. The higher dry matter content of breast meat resulted in the lower drip loss value after 3h coldstorage (r=-0.12, P&lt;0.05). There is a negative relationship between L* and a*. The variation demonstrated in this study can be used in breeding schemes in order to improve meat quality of Noi chicken lines.

Analysis of Population Structure and Differentially Selected Regions in Guangxi Native Breeds by Restriction Site Associated with DNA Sequencing.

Guangxi indigenous chicken breeds play a very important role in promoting the high-quality development of the broiler industry in China. However, studies on genomic information of Guangxi indigenous chicken to date remain poorly explored. To decipher the population genetic structure and differentially selected regions (DSRs) in Guangxi indigenous chickens, we dug into numerous SNPs from seven Guangxi native chickens (GX) by employing the restriction site associated with DNA sequencing (RAD-seq) technology. Another three breeds, Cobb, White Leghorn, and Chahua (CH) chicken, were used as a control. After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. The results showed a significant difference in population structure, and the control breeds were distinctly separate from the Guangxi native breeds, which was also strongly supported by the phylogenetic tree. Distribution of FST indicated that there were three SNPs with big genetic differentiation (FST value all reach to 0. 9427) in GX vs. CH group, which were located on chr1-96,859,720,chr4-86,139,601, and chr12-8,128,322, respectively. Besides, we identified 717 DSRs associated with 882 genes in GX vs. Cobb group, 769 DSRs with 476 genes in GX vs. Leghorn group, and 556 DSRs with 779 genes in GX vs. CH group. GO enrichment showed that there were two significant terms, namely GPI-linked ephrin receptor activity and BMP receptor binding, which were enriched in GX vs. Leghorn group. In conclusion, this study suggests that Guangxi native chickens have a great differentiation with Cobb and Leghorn. Our findings would be beneficial to fully evaluate the genomic information on Guangxi native chicken and facilitate the application of these resources in chicken breeding.

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.

Rapid behavioral assay using handling test provides breed and sex differences in tameness of chickens.

BackgroundJapanese indigenous chicken breeds are often used to improve meat quality rather than broilers in the Jidori industry. There are sometimes severe crowding accidents caused by many birds frightened by environmental stimuli. To prevent the economic loss, the chickens need to be more gentle, tame, and imperturbable.MethodsIn this study, a new handling test for tameness in adult chickens in individual cages was performed with 100 birds from each sex of Shamo, Rhode Island Red, Nagoya, Australorp, and Ukokkei, as well as 10 hens of F1 hybrid between Shamo and Rhode Island Red, to measure both active and passive tameness. We counted the number heading toward human hands (heading) and retreating in other directions (avoiding) in both active and passive tameness phases, as well as the number of steps taken (step) during the handling test.ResultsMale chickens exhibited higher avoidance behavior than females. Nagoya females displayed the lowest level of avoidance behavior, which implies passive tameness. In terms of active tameness, a variety of phenotypes can be obtained in different combinations of breed and sex. These results suggested the handling test will be good method for rapid screening of individual differences in tameness. In addition, there were heterosis effects on avoidance and locomotive behaviors. Since F1 is often used in the Jidori industry, the breeders should be tested not only for meat production but also for tameness.ConclusionsIn the future, combining both the behavioral screening and the population genomics will establish typical evidence about mechanisms of tameness and domestication in animals.

Whole-genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China.

Ten indigenous chicken breeds were originally distributed in Jiangxi Province, China, and they define a critical component of Chinese chicken genetic resources. We have investigated the population genetics of seven Jiangxi chicken breeds using 600K chicken BeadChip SNP data. To provide a genome-wide perspective for the population structure of all 10 Jiangxi chicken breeds, we herein genotyped 78additional individuals from the seven breeds and 63 chickens from three uninvestigated breeds-Yugan Black (YG), Nancheng Black (NC) and Wanzai Yellow using 55K chicken SNP arrays. We then explored merged data of 17101 SNPs from 235 individuals to infer the population structure of the 10 breeds. We showed that NC and YG are two regional populations of the same breed, as individuals from the two populations clustered together to form a branch separate from the other breeds in the neighbor-joining tree, they always grouped together in multidimensional principal component analyses and they displayed an identical pattern of ancestral lineage composition. Hence, NC and YG should be considered a single breed in the state-supported conservation scheme. Moreover, we conducted a genome scan for signatures of selection for black plumage. bayescan and hapflk analyses of two contrasting groups (three black-feathered breeds vs. six non-black-feathered breeds) consistently detected 25 putative regions under selection. Nine pigmentation- associated genes (DCT, SLC24A5, SLC30A4, MYO5A, CYP19A1, NADK2, SLC45A2, GNAQ and DCP2) reside within these regions, and these genes are interesting candidates for black plumage and provide a starting point for further identification of causative mutations for black feathers in chicken.

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).

Sequence Variability in the NRAMP1 Gene among Indigenous and Exotic Chicken Types

The natural resistance-associated macrophage protein 1 ( NRAMP1 ) gene in chickens, which exists on chromosome 7, is thought to play a significant role in disease resistance. Variations in this gene have been documented and have played crucial roles in the variations in the resistance and/or susceptibility that is expressed by individuals and different groups of animal species. In this study, the NRAMP1 gene was studied for single nucleotide polymorphism (SNP) variability between indigenous and exotic chicken breeds. The gene was amplified using the polymerase chain reaction (PCR) method and sequenced and analyzed. Six SNPs, both synonymous and non-synonymous (C3700T, G3702C, A3712C, C3714G, C3693G, and G3705T), were detected in the gene in both indigenous and exotic chicken types. One allele form was detected among all the sample animals that were studied. A phylogenetic tree revealed that the indigenous chicken type and the exotic broiler chicken type are genetically similar with respect to this gene. However, the exotic layer chicken type is genetically suggested to be distantly related to both the indigenous and broiler chicken types, indicating that the gene has probably been evolving both within and among different poultry species.

Genomic Analysis Reveals Pleiotropic Alleles at EDN3 and BMP7 Involved in Chicken Comb Color and Egg Production.

Artificial selection is often associated with numerous changes in seemingly unrelated phenotypic traits. The genetic mechanisms of correlated phenotypes probably involve pleiotropy or linkage of genes related to such phenotypes. Dongxiang blue-shelled chicken, an indigenous chicken breed of China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The red comb line chicken produces significantly higher number of eggs than the dark comb line chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. Based on the genome-wide association study results, we identified a genomic region on chromosome 20 involving EDN3 and BMP7, which is associated with hyperpigmentation of chicken comb. Further analyses by selection signatures in the two divergent lines revealed that several candidate genes, including EDN3, BMP7, BPIFB3, and PCK1, closely located on chromosome 20 are involved in the development of neural crest cell and reproductive system. The two genes EDN3 and BMP7 have known roles in regulating both ovarian function and melanogenesis, indicating the pleiotropic effect on hyperpigmentation and egg production in blue-shelled chickens. Association analysis for egg production confirmed the pleiotropic effect of selected loci identified by selection signatures. The study provides insights into phenotypic evolution due to genetic variation across the genome. The information might be useful in the current breeding efforts to develop improved breeds for egg production.

Differential proteomic analysis to identify proteins associated with beak deformity in chickens

The beak is the dominant avian facial feature, and beak deformity occurs in 0.5 to 2.5% of some indigenous chicken breeds, resulting in difficulties when eating, drinking, and performing natural behaviors. Previous studies on beak deformity focused largely on candidate molecules associated with skeletogenic development, providing insight into the molecular and genetic underpinnings of beak deformity. The present study was performed to identify candidate proteins related to this malformation in chickens. Three 12-day-old Beijing-You roosters with deformed beaks (D1, D2, and D3) and 3 with normal beaks (N1, N2, and N3) were used, and total beak proteins were isolated and subjected to standard iTRAQ labeling, strong cation-exchange chromatography, and liquid chromatography-tandem mass spectrometry. Mascot 2.3.02 was used to identify and quantitatively analyze proteins. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to identify functions and metabolic pathways of differentially expressed proteins, and key proteins were further validated using western blot. A total of 2,370, 2,401, and 2,378 proteins were reliably quantified in 3 biological replicates, among which, 2,345 were common to all, and 92 were differentially expressed between the 2 groups. These included 37 upregulated and 55 downregulated proteins in deformed beaks. Pentraxin-related protein 3, hemopexin, lipoprotein lipase, retinoid-binding protein 7, and biliverdin reductase A were downregulated in all 3 sets, while parvalbumin, peptidyl-prolyl cis-trans isomerase, and ubiquitin-fold modifier 1 were upregulated. Pathway analysis returned no enriched pathways, and western blot validated the iTRAQ results. Parvalbumin and lipoprotein lipase could be firstly selected as key proteins in view of their known functions in regulating the buffering of intracellular free Ca2+ in both cartilage and bone cells and bone mass, respectively. Their potential roles in beak deformity, however, deserve further studies. In summary, the onset of beak deformity could be very complex, and this study will be helpful for future investigation of mechanistic explanation for beak deformity.

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.

A Survey Study on Productive and Reproductive Performance of Indigenous Poultry

A survey study was conducted to analyze the reproductive and productive performances of four indigenous chicken breeds (Potchefstroom Koekoek, Venda, Naked Neck and Ovambo) under different rearing system. Six villages located in Eastern Cape, South Africa were used for the study from July 2017 to June 2018. Data on Clutch Per Year (CPY), hatchability (HATCH), Egg Per Clutch (EGC), survivability at 10-12 weeks (SURV), Egg Per Year (EPY), Recovery Period (RP), average age at production (AA), Duration of Rearing (DR), mortality, egg laying length (EGL), Natural Brooding Period (NBP) and Natural Incubating Period (NIP) were obtained from Seven thousand, five hundred and thirty eight (7538) indigenous chicken. Four different breeds were sampled such as Venda breeds (2748), Potchefstroom Koekoek (2088), Ovambo (1838) and Naked Neck (864) breeds respectively. Potchefstroom Koekoek is observed to be a good egg producing breed with 15.11±0.25 eggs per clutch. Venda breed possess good mothering ability (hatchability) and high survivability with 86.03±0.31days and 82.70±0.26 days respectively. Naked Neck is known to be more prone to diseases with least (survivability) 60.08±0.25 days. Village was positively correlated with EGC and HATCH, EGY and SURV at p≤0.01 and p≤0.05 respectively. Rearing system was positively correlated with EGC. Rearing system was positively correlated at p≤0.05 on EGC than CPY, HATCH, EGY and SURV. Breed and village interactions were significant at p≤0.05 on RP, AA, DR, EGL, NBP and NIP. Therefore, productive and reproductive traits of indigenous chicken differ across different rearing systems, breeds and villages.

Population genetic analyses of seven Chinese indigenous chicken breeds in a context of global breeds.

Jiangxi province in China is rich in indigenous chicken breeds, which have diverse phenotypes and represent a valuable genetic resource for further genetic improvement of modern breeds. Here, we conducted a series of analyses to reveal genetic diversity, phylogenetic relationships and population structure of seven chicken breeds in Jiangxi province in the context of nine non-local chicken breeds, using 600K SNP data. We show that Jiangxi indigenous breeds have more abundant nucleotide diversity than do European local and commercial breeds. Among Jiangxi breeds, Dongxiang Blue-eggshell (DX) and Chongren Partride (CR) display remarkably reduced genetic diversity, as the two breeds exhibit increased inbreeding coefficients, runs of homozygosity, extent of linkage disequilibrium and reduced expected heterozygosity. DX, CR and Taihe Silkie (TH) represent three ancestral lineages of the Jiangxi chicken and display genetic differentiation from the other four Jiangxi breeds, which show a signature of admixture with European commercial breeds. These findings provide insight for the establishment of an efficient conservation program for Jiangxi chicken breeds. Considering the current status of genetic diversity and ancestral representativeness, particular attention should be paid to DX, CR and TH chickens.

Polymorphisms in pattern recognition receptor genes of indigenous and White Leghorn breeds of chicken.

Functional polymorphisms in pattern recognition receptors (PRRs) modulate innate immunity and play a crucial role in resistance or susceptibility to diseases. The present study was carried out to explore polymorphic patterns in the coding sequences of PRR genes TLR3, TLR1LA (TLRs), MDA5, LGP2 (RLRs) and NOD1 (NLR) in chicken breeds of India, namely Ghagus (GH), Nicobari (NB) and the exotic White Leghorn (WLH) breed. Out of 209 SNPs observed in five genes among three breeds, 117 were synonymous (Syn) and 92 were non-synonymous (NS) SNPs. In TLR genes the highest polymorphism was observed in NB (16, 28) compared to GH (14, 16) and WLH (13, 19) breeds. In the MDA5 gene the highest polymorphism was observed in GH (12) compared to NB (eight) and WLH (four) breeds. However, an almost similar level of polymorphism was observed in the LGP2 gene among the three breeds. In the NOD1 gene, the highest polymorphism was observed in NB (27), followed by WLH (11) and GH (10) breeds. The overall highest number of SNPs was observed in NB (90), followed by GH (62) and the WLH (57) breed. With regard to variation in polymorphism among different classes of PRRs, the study revealed the highest polymorphism in TLRs compared to NOD1 and the RLR class of PRRs. Further, the domain locations of various Syn and NS SNPs in each PRR among the three breeds were identified. In silico analysis of NS SNPs revealed that most of them had a neutral effect on protein function. However, two each in TLR1LA and LGP2 and one in the MDA5 gene were predicted to be deleterious to protein function. The present study unravelled extensive polymorphism in the coding sequences of the TLR and NLR class of PRR genes, and the polymorphism was higher in indigenous chicken breeds.

Genetic Diversity of TLR4 and IL2 Loci Involved In Immune System in Some Iranian Indigenous Chicken Breeds

Genetic Diversity of TLR4 and IL2 Loci Involved In Immune System in Some Iranian Indigenous Chicken Breeds

Knowledge and perception of pelung keepers’s toward chicken contests in West Java, Indonesia

Asmara IY, Garnida D, Sulisytati M, Tejaningsih S, Partasasmita R. 2018. ­­­­Knowledge and perception of pelung keepers’s toward chicken contests in West Java, Indonesia. Biodiversitas 19: 2232-2237. Pelung chicken is an indigenous chicken breed which has social and cultural functions in particular communities in Indonesia. Contests are conducted regularly as a media to show the singing ability of Pelung chickens and the activities are considered important to maintain the existence of the chickens. The objective of this study was to determine the knowledge and perceptions of chicken keepers toward chicken contests for Pelung chickens. A survey using open and structured questionnaire was conducted to collect data involving 133 Pelung keepers. The study was carried out in four districts in West Java Province, Indonesia including Cianjur, Sukabumi, Bandung, and Garut Districts. The data were analyzed using descriptive analysis. The result showed that almost respondents knew about contests and they defined contests as a media to find good breeds as well as a media to find and/or improve networks. Main sources of information contests were the organization, family, and social media. Respondents had positive perception toward contests, and they actively participated in the different level of contests. The findings are important as social input for the management of animal genetic resources (AnGR) in Indonesia

Expression profile of the myoglobin gene in indigenous native chicken

In the present study, we quantified myoglobin (Mb) gene expression in two different indigenous chicken breeds, namely Ghagus and Aseel to discern tissue specific expression pattern in different age groups. Quantitative real-time PCR assay was developed for measurement of the Mb mRNA expression in different tissues in chickens of different age groups (day old and day 28). Overall, the Mb mRNA level displayed a significant difference among all the tissues investigated in the study. Results exhibited that, bursa and heart tissues relatively had the highest expression of Mb related to the other tissues (P less than 0.05). Further, in gizzard and bursa, a significant difference was found in the expression between both the breeds studied. It is concluded that the expression of Mb gene varied significantly among different tissues and between age groups in chicken.

Molecular characteristics of avian leukosis viruses isolated from indigenous chicken breeds in China.

To assess the status of avian leukosis virus (ALV) infection in indigenous chicken breeds in China, 121 plasma samples collected from various indigenous chicken breeds were tested for the presence of ALV from 2015 to 2016. A total of 14 ALV strains were isolated and identified, including two ALV-A strains, one ALV-B strain, eight ALV-J strains, and three ALV-K strains. To study the genome structure, biological characteristics, and the evolutionary relationships of the ALV-K strains with other known subgroup strains from infected chickens, we determined the complete genome sequence of the three ALV-K strains and performed comparative analysis using the whole genome sequence or selected sequence elements. The replication rates of the three ALV-K strains were markedly lower than the rates of other ALVs, and they shared a common mutation in the pol gene, which had not been previously observed. In addition, nine putative recombinant events were detected in the genomes of the three newly isolated ALV-K strains, with high statistical support. This was the first report of an ALV-K reorganization event, which has contributed to its genetic evolution. In summary, we established a robust classification system for ALV, especially for ALV-K, and revealed additional genomic diversity for the ALV strains in indigenous chicken breeds. Therefore additional works are warranted to explore ALV genomics and epidemiology.

Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight -A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds.

Body weight (BW) is one of the most important economic traits for animal production and breeding, and it has been studied extensively for its phenotype–genotype associations. While mapping studies have mostly aimed at finding as many loci as possible that contributed to the variation in BW, the role of other factors in its genetic architecture, including their frequencies in the population and their interactions, have been largely overlooked. To comprehensively characterized the genetic architecture of BW, we performed a genome-wide association study (GWAS) both at the single-marker and haplotype level on birds from four indigenous Chinese chicken breeds (Chahua, Silkie, Langshan, and Beard), rather than studying crosses between two founder lines. Additionally, samples from two more breeds (Red Junglefowl and Recessive White) were included to better reflect variable genetic characteristics across populations. Six loci were mapped in this study, revealing the polygenic basis underlying BW. Moreover, by further examining the frequencies of the significantly associated haplotypes in each subpopulation and their effect sizes, most of the loci were found to affect BW in the Beard chicken breed alone. Two loci in GGA9 and GGA27, however, had a common effect on BW across subpopulations, showing that different underlying genetic mechanisms contribute to the phenotypic variability. These findings, particularly the variable genetic architectures found in different loci, improve our understanding of the overall genetic contributions to the large variability in BW among Chinese indigenous chicken breeds. These findings thus will have important implications for future chicken breeding.