The Experts below are selected from a list of 4527 Experts worldwide ranked by ideXlab platform
Peng Zhao - One of the best experts on this subject based on the ideXlab platform.
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molecular characteristics of avian leukosis viruses isolated from indigenous Chicken Breeds in china
Poultry Science, 2018Co-Authors: Qi Su, Yang Li, Weihua Li, Sibao Tian, Peng Zhao, Shuang ChangAbstract:ABSTRACT 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.
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identification of a new subgroup of avian leukosis virus isolated from chinese indigenous Chicken Breeds
Chinese journal of virology, 2012Co-Authors: Xin Wang, Peng ZhaoAbstract:In order to clarify Avian leukosis virus (ALV) characteristics from Chinese native Chicken Breeds, three ALV JS11C1, JS11C2 and JS11C3 were isolated from Chinese native breed "luhua" by inoculation of DF1 cell culture and detection of p27 antigen. Using PCR amplification of env gene, the amplified gp85 genes were analyzed and compared to all six Chicken ALV subgroups reported. The gp85 genes of these three viruses were 1 005bp in length and encoded 335 amino acids, and the gp37 genes were 609bp and encoded 203 amino acids. The homology of gp85 among these three isolated strains was 91.9%-97.0%. Comparing to 18 stains of subgroup A, B, C, D, E published in GenBank, the homology was only in the range of 77.7%-84.6%, significantly lower than the gp85 homology observed within the common Chicken subgroups A (88.2%-98.5%), B (91.6%-98.8%), and E (97.9%-99.4%). The gp85 homology compared with subgroup J was only 34.2%-36.5%. These results suggested that three isolated strains from Chinese native breed "luhua" belong to a new subgroup different from all six known subgroups from Chickens, and thus designated as subgroup K.
Jianqiang Ye - One of the best experts on this subject based on the ideXlab platform.
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novel avian leukosis viruses from domestic Chicken Breeds in mainland china
Archives of Virology, 2017Co-Authors: Hongxia Shao, Lin Wang, Jianjun Sang, Tuofan Li, Kun Qian, Jianqiang YeAbstract:Two novel avian leukosis viruses (ALVs) were isolated from 1380 whole blood samples taken from domestic Chicken Breeds in China. The two ALVs were uniquely different from the env (Envelope) genes of ALV A-J and carried an LTR (long terminal repeat) cluster from ALV-E. Large scale sequence analysis further showed that these ALVs (with different env and LTRs) were recently endemic in domestic Chicken Breeds in both China and Japan. The emergence of these novel ALVs is challenging the current ALV eradication program, and as such novel ALVs should be monitored in a timely and careful manner to stop their transmission and further recombination in the future.
Weifang Yang - One of the best experts on this subject based on the ideXlab platform.
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Identification of candidate genomic regions for Chicken egg number traits based on genome-wide association study
'Springer Science and Business Media LLC', 2021Co-Authors: Xiurong Zhao, Changsheng Nie, Yu Chen, Jinxin Zhang, Liang Wang, Tao Zhu, Zi Guan, Weifang YangAbstract:Abstract Background Since the domestication of Chicken, various Breeds have been developed for food production, entertainment, and so on. Compared to indigenous Chicken Breeds which generally do not show elite production performance, commercial Breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic differences of egg number between commercial egg-type Chickens and indigenous Chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg number traits (57 significantly, 91 suggestively). Among them, 4 SNPs overlapped with previously reported quantitative trait loci (QTL), including 2 for egg production and 2 for reproductive traits. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2 (neural EGFL like 2), KITLG (KIT ligand), GHRHR (Growth hormone releasing hormone receptor), NCOA1 (Nuclear receptor coactivator 1), ITPR1 (inositol 1, 4, 5-trisphosphate receptor type 1), GAMT (guanidinoacetate N-methyltransferase), and CAMK4 (calcium/calmodulin-dependent protein kinase IV) deserve our attention and further study since they have been reported to be closely related to egg production, egg number and reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61–48.84 Mb on GGA5. In this region, we have repeatedly identified four genes, in which YY1 (YY1 transcription factor) and WDR25 (WD repeat domain 25) have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg number traits. Conclusion Our study utilized the genomic information from various Chicken Breeds or populations differed in the average annual egg number to understand the molecular genetic mechanisms involved in egg number traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with egg number, which could help us in developing the egg production trait in Chickens
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genome wide population genetic analysis of commercial indigenous game and wild Chickens using 600k snp microarray data
Frontiers in Genetics, 2020Co-Authors: Jinxin Zhang, Zhonghua Ning, Changsheng Nie, Yaxiong Jia, Yu Chen, Jianlin Han, Liang Wang, Weifang YangAbstract:Following Chicken domestication, diversified Chicken Breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making Chickens an ideal genetic research model. To better understand the genetic structure of Chicken Breeds under different selection pressures, we genotyped various Chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral Chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, Red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and run of homozygosity analyses. The gamecock Breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous Breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local Breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local Chickens had lower genetic variation than the Chinese local Breeds, which could be attributed to the shorter history of the European breed. ROH present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild Chickens). These ROH islands were involved in egg production, growth and silky feathers and so on. Moreover, we estimated the effective sex ratio of these Breeds to demonstrate the change in the ratio of the two sexes. We found that commercial Chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, Red junglefowl comprised a greater proportion of males than females. Our results show the population genetics of Chickens under selection pressures, and can aid in the development of better conservation strategies for different Chicken Breeds.
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genome wide population genetic analysis of commercial indigenous game and wild Chickens using 600k snp microarray data
Frontiers in Genetics, 2020Co-Authors: Jinxin Zhang, Zhonghua Ning, Changsheng Nie, Yaxiong Jia, Yu Chen, Jianlin Han, Liang Wang, Weifang YangAbstract:Following Chicken domestication, diversified Chicken Breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making Chickens an ideal genetic research model. To better understand the genetic structure of Chicken Breeds under different selection pressures, we genotyped various Chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral Chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and ROH analyses. The gamecock Breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous Breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local Breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local Chickens had lower genetic variation than the Chinese local Breeds, which could be attributed to the shorter history of the European breed. ROH were present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild Chickens). These ROH islands were involved in egg production, growth and silky feathers and other traits. Moreover, we estimated the effective sex ratio of these Breeds to demonstrate the change in the ratio of the two sexes. We found that commercial Chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, RJF comprised a greater proportion of males than females. Our results show the population genetics of Chickens under selection pressures, and can aid in the development of better conservation strategies for different Chicken Breeds.
Xin Wang - One of the best experts on this subject based on the ideXlab platform.
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identification of a new subgroup of avian leukosis virus isolated from chinese indigenous Chicken Breeds
Chinese journal of virology, 2012Co-Authors: Xin Wang, Peng ZhaoAbstract:In order to clarify Avian leukosis virus (ALV) characteristics from Chinese native Chicken Breeds, three ALV JS11C1, JS11C2 and JS11C3 were isolated from Chinese native breed "luhua" by inoculation of DF1 cell culture and detection of p27 antigen. Using PCR amplification of env gene, the amplified gp85 genes were analyzed and compared to all six Chicken ALV subgroups reported. The gp85 genes of these three viruses were 1 005bp in length and encoded 335 amino acids, and the gp37 genes were 609bp and encoded 203 amino acids. The homology of gp85 among these three isolated strains was 91.9%-97.0%. Comparing to 18 stains of subgroup A, B, C, D, E published in GenBank, the homology was only in the range of 77.7%-84.6%, significantly lower than the gp85 homology observed within the common Chicken subgroups A (88.2%-98.5%), B (91.6%-98.8%), and E (97.9%-99.4%). The gp85 homology compared with subgroup J was only 34.2%-36.5%. These results suggested that three isolated strains from Chinese native breed "luhua" belong to a new subgroup different from all six known subgroups from Chickens, and thus designated as subgroup K.
Xiangtao Kang - One of the best experts on this subject based on the ideXlab platform.
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breeding history and candidate genes responsible for black skin of xichuan black bone Chicken
BMC Genomics, 2020Co-Authors: Guirong Sun, Meng Zhang, Yanfang Cao, Chenxi Zhang, Ruirui Jiang, Ruili Han, Yanbin Wang, Yadong Tian, Xiaojun Liu, Xiangtao KangAbstract:Domesticated Chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other Chicken Breeds, Xichuan black-bone Chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. 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. 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. Fst analysis identified a selective sweep that contains genes related to melanogenesis. 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. 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.