1
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Qiu M, Yu C, Zhu S, Hu C, Yang L, Song X, Xia B, Jiang X, Du H, Li Q, Zhang Z, Yang C. Characterization of circRNA expression profiles associated with non-Mendelian inheritance in feather growth of chickens. Br Poult Sci 2024; 65:371-377. [PMID: 38717938 DOI: 10.1080/00071668.2024.2339485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/05/2024] [Indexed: 07/27/2024]
Abstract
1. Non-coding RNAs, such as miRNAs, play a crucial role in chicken feather growth rate. However, circular RNA (circRNA) expression profiles in fast- and slow-feathering chickens that follow and do not follow Mendelian inheritance are unclear.2. The circRNA expression profiles was analysed by RNA sequencing of hair follicles of slow-feathering chickens that follow genetic rules and fast-feathering chickens that did not follow genetic rules. Differentially expressed circRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network was then constructed and the key factors and regulation mechanisms controlling feather growth rate were identified.3. The results revealed that 67 circRNAs were significantly differentially expressed in hens, including 22 up-regulated and 45 down-regulated circRNAs in non-Mendelian inheritance-mediated fast-feathering hens compared with Mendelian inheritance-mediated slow-feathering hens. In addition, 16 significantly differentially expressed circRNAs were identified in cockerels, including nine up-regulated and seven down-regulated circRNAs in non-Mendelian inheritance-mediated fast- compared with Mendelian inheritance-mediated slow-feathering cocks. Moreover, circRNA-mediated ceRNA regulation of hair follicle formation was particularly abundant in the Jak-STAT, Wnt and Toll-like receptor signalling pathways. Furthermore, circABI3BP was seen to be a crucial circRNA in regulating feather growth rate, by binding with gga-miR-1649-5p to regulate SSTR2 expression.4. In conclusion, this study analysed circRNA expression profiles in fast- and slow-feathering chickens that follow and do not follow Mendelian inheritance, which laid the foundation for understanding the role of circRNA in chicken feather growth rate.
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Affiliation(s)
- M Qiu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - C Yu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - S Zhu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - C Hu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - L Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - X Song
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - B Xia
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - X Jiang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - H Du
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Q Li
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Z Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - C Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
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2
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Banks CM, Trott JF, Hovey RC. The prolactin receptor: A cross-species comparison of gene structure, transcriptional regulation, tissue-specificity, and genetic variation. J Neuroendocrinol 2024; 36:e13385. [PMID: 38586906 DOI: 10.1111/jne.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/25/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024]
Abstract
The conserved and multifaceted functions of prolactin (PRL) are coordinated through varied distribution and expression of its cell-surface receptor (PRLR) across a range of tissues and physiological states. The resultant heterogeneous expression of PRLR mRNA and protein across different organs and cell types supports a wide range of PRL-regulated processes including reproduction, lactation, development, and homeostasis. Genetic variation within the PRLR gene also accounts for several phenotypes impacting agricultural production and human pathology. The goal of this review is to highlight the many elements that control differential expression of the PRLR across tissues, and the various phenotypes that exist across species due to variation in the PRLR gene.
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Affiliation(s)
- Carmen M Banks
- Department of Animal Science, University of California, Davis, Davis, California, USA
| | - Josephine F Trott
- Department of Animal Science, University of California, Davis, Davis, California, USA
| | - Russell C Hovey
- Department of Animal Science, University of California, Davis, Davis, California, USA
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3
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Recuerda M, Campagna L. How structural variants shape avian phenotypes: Lessons from model systems. Mol Ecol 2024; 33:e17364. [PMID: 38651830 DOI: 10.1111/mec.17364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.
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Affiliation(s)
- María Recuerda
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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4
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Shen Q, Li J, Bao H, Wu C. Identification of Duplication Genotypes of the Feathering Rate Gene in Chicken by a Multiplex PCR Following Electrophoresis and/or Sanger Sequencing. Animals (Basel) 2023; 13:ani13061091. [PMID: 36978632 PMCID: PMC10044632 DOI: 10.3390/ani13061091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/30/2023] Open
Abstract
Sex-linked phenotypes of late feathering (LF) and early feathering (EF) are controlled by a pair of alleles K and k+. Autosexing based on the feathering rate is widely used in poultry production. It is reported that a tandem duplication of 176,324 base pairs linked to the K locus is responsible for LF expression and could be used as a molecular marker to detect LF chicken. So far, there is no genotyping method that can accurately and stably identify the LF homozygote and heterozygote in all chicken breeds. In the present study, a multiplex PCR test was developed to identify EF, LF homozygote, and heterozygote according to electrophoretic bands and the relative height of the peaks by Sanger sequencing. We tested 413 chickens of six native Chinese breeds with this method. The identification was consistent with the sex and phenotype records of the chickens. Band density analysis was performed, and the results supported our genotyping using the new assay. In order to further verify the accuracy of this test in distinguishing homozygote and heterozygote males, 152 LF males were mated with EF females, and the results of the offspring's phenotypes were consistent with our expectations. Our results support tandem duplication as molecular markers of LF, and this new test is applicable to all LF chickens associated with tandem duplication.
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Affiliation(s)
- Qingmiao Shen
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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5
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Mo G, Wei P, Hu B, Nie Q, Zhang X. Advances on genetic and genomic studies of ALV resistance. J Anim Sci Biotechnol 2022; 13:123. [PMID: 36217167 PMCID: PMC9550310 DOI: 10.1186/s40104-022-00769-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/14/2022] [Indexed: 12/01/2022] Open
Abstract
Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.
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Affiliation(s)
- Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530001, Guangxi, China
| | - Bowen Hu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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6
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Mo G, Hu B, Wei P, Luo Q, Zhang X. The Role of Chicken Prolactin, Growth Hormone and Their Receptors in the Immune System. Front Microbiol 2022; 13:900041. [PMID: 35910654 PMCID: PMC9331192 DOI: 10.3389/fmicb.2022.900041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Prolactin (PRL) and growth hormone (GH) exhibit important roles in the immune system maintenance. In poultry, PRL mainly plays its roles in nesting, hatching, and reproduction, while GH is primarily responding to body weight, fat formation and feed conversion. In this review, we attempt to provide a critical overview of the relationship between PRL and GH, PRLR and GHR, and the immune response of poultry. We also propose a hypothesis that PRL, GH and their receptors might be used by viruses as viral receptors. This may provide new insights into the pathogenesis of viral infection and host immune response.
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Affiliation(s)
- Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Bowen Hu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Qingbin Luo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
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7
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Mo G, Hu B, Zhang Q, Ruan Z, Li W, Liang J, Shen Y, Mo Z, Zhang Z, Wu Z, Shi M, Zhang X. dPRLR causes differences in immune responses between early and late feathering chickens after ALV-J infection. Vet Res 2022; 53:1. [PMID: 34998433 PMCID: PMC8742939 DOI: 10.1186/s13567-021-01016-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/09/2021] [Indexed: 12/24/2022] Open
Abstract
To understand the differences in immune responses between early feathering (EF) and late feathering (LF) chickens after infection with avian leukosis virus, subgroup J (ALV-J), we monitored the levels of prolactin, growth hormone and the immunoglobulins IgG and IgM in the serum of LF and EF chickens for 8 weeks. Moreover, we analysed the expression of immune-related genes in the spleen and the expression of PRLR, SPEF2 and dPRLR in the immune organs and DF-1 cells by qRT–PCR. The results showed that ALV-J infection affected the expression of prolactin, growth hormone, IgG and IgM in the serum. Regardless of whether LF and EF chickens were infected with ALV-J, the serum levels of the two hormones and two immunoglobulins in EF chickens were higher than those in LF chickens (P < 0.05). However, the expression of immune-related genes in the spleen of positive LF chickens was higher than that in the spleen of positive EF chickens. In the four immune organs, PRLR and SPEF2 expression was also higher in LF chickens than in EF chickens. Furthermore, the dPRLR expression of positive LF chickens was higher than that of negative LF chickens. After infection with ALV-J, the expression of PRLR in DF-1 cells significantly increased. In addition, overexpression of PRLR or dPRLR in DF-1 cells promoted replication of ALV-J. These results suggested that the susceptibility of LF chickens to ALV-J might be induced by dPRLR.
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Affiliation(s)
- Guodong Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China.,Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530005, China
| | - Bowen Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Qihong Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Zhuohao Ruan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Jiaying Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Yizi Shen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Zhixin Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Zihao Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Zhuyue Wu
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530005, China
| | - Meiqing Shi
- Division of Immunology, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China.
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8
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Liu X, Wu Z, Li J, Bao H, Wu C. Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens. Front Genet 2021; 11:613078. [PMID: 33414812 PMCID: PMC7783405 DOI: 10.3389/fgene.2020.613078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/02/2020] [Indexed: 12/01/2022] Open
Abstract
The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0–13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene (SPEF2) and prolactin receptor (PRLR) gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that SPEF2 and PRLR are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.
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Affiliation(s)
- Xiayi Liu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhou Wu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Junying Li
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
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9
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Qiu M, Yang C, Du H, Li Q, Zhang Z, Xiong X, Yu C, Song X, Hu C, Xia B, Yang L, Peng H, Liu L, Jiang X. Whole-genome resequencing reveals aberrant autosomal SNPs affect chicken feathering rate. Anim Biotechnol 2020; 33:884-896. [PMID: 33342337 DOI: 10.1080/10495398.2020.1846545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Previous studies have shown that the feather growth rate of chicks is determined by two alleles located on the sex chromosome Z; however, in chicken production, feathering is usually not consistently controlled by the sex chromosome. To identify whether the feathering rate is related to autosomal inheritance, whole-genome resequencing was performed in eight chickens with slow- and fast-feathering rate. A total of 54,984 autosomal single nucleotide polymorphisms (SNPs) were identified, including 393 and 376 exonic SNPs in slow-feathering and fast-feathering chickens, respectively. Mutated genes were mainly involved in response to stimuli and growth and reproduction processes. Mutated genes related to slow-feathering rate were mainly involved in wingless-type MMTV integration site signaling pathway and mitogen-activated protein kinase signaling pathway, whereas mutated genes associated with fast-feathering rate were primarily enriched in autophagy, calcium signaling pathway, extracellular matrix-receptor interaction, and Focal adhesion processes. Importantly, two SNPs, involved in feather development, were found in the exonic regions of Wnt signaling genes. These results shed new light on the relationship between genetic mutation and feather growth rate from the perspective of autosomal inheritance and may have economic significance in chicken breeding.
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Affiliation(s)
- Mohan Qiu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Huarui Du
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Qingyun Li
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Zengrong Zhang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Xia Xiong
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Chunlin Yu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaoyan Song
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Chenming Hu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Bo Xia
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Li Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Han Peng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Lan Liu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaosong Jiang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
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10
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Wang Y, Buyse J, Courousse N, Tesseraud S, Métayer-Coustard S, Berri C, Schallier S, Everaert N, Collin A. Effects of sex and fasting/refeeding on hepatic AMPK signaling in chickens (Gallus gallus). Comp Biochem Physiol A Mol Integr Physiol 2019; 240:110606. [PMID: 31676410 DOI: 10.1016/j.cbpa.2019.110606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/10/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
Abstract
The alpha-1 isoform of chicken AMPK situates on the Z-chromosome, in contrast, the other isoforms in birds and the mammalian AMPKα1 are located on the autosomes. The present study aimed to investigate the role of hepatic AMPK signaling in adaptation to nutritional status and the potential sex-specific response in chickens. Hepatic genes and proteins were compared between the two sexes immediately after hatching. From 20d of age, chicks from each sex received feed treatments: Control was fed ad libitum; Fasted was starved for 24 h; Refed was fed for 4 h after a 24 h fasting. As a result, hepatic AMPKα1 mRNA level in males was significantly higher at both ages compared to females, due to the presence of Z-chromosomes. However, this did not make this kinase "male-bias" as it was eventually compensated at a translational level, which was not reported in previous studies. The protein levels and activation of AMPKα were even lower in newly-hatched male compared to female chicks, accompanied with a higher FAS and SREBP-1 gene expressions. Accordingly, hepatic G6PC2 mRNA levels in males were significantly lower associated with lower plasma glucose levels after hatching. Fasting activated hepatic AMPK, which in turn inhibited gene expression of GS, FAS and SREBP-1, and stimulated the downstream G6PC2 in both sexes. These changes recovered after refeeding. In conclusion, AMPK plays a role in adaptation to nutritional environment for both sexes. The Z-linked AMPK did not exert a sex-specific signaling, due to a "translational compensation" of AMPKα1.
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Affiliation(s)
- Yufeng Wang
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Johan Buyse
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium.
| | | | | | | | - Cécile Berri
- BOA, INRA, Université de Tours, 37380 Nouzilly, France
| | - Seline Schallier
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Nadia Everaert
- Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Anne Collin
- BOA, INRA, Université de Tours, 37380 Nouzilly, France
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11
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Okamura A, Masumoto A, Takenouchi A, Kudo T, Aizawa S, Ogoshi M, Takahashi S, Tsudzuki M, Takeuchi S. Changes in prolactin receptor homodimer availability may cause late feathering in chickens. Gen Comp Endocrinol 2019; 272:109-116. [PMID: 30594591 DOI: 10.1016/j.ygcen.2018.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 01/04/2023]
Abstract
Chicken early (EF) and late feathering (LF) are sex-linked phenotypes conferred by wild-type k+ and dominant K alleles on chromosome Z, respectively. Besides prolactin (PRL) receptor (PRLR) and sperm flagellar 2 (SPEF2) genes, the K allele contains a fusion gene in which partially duplicated PRLR (dPRLR) and SPEF2 (dSPEF2) genes are linked in a tail-to-tail manner. The causative dPRLR gene encodes a C-terminal truncated receptor. LF chickens have short or no primaries at hatching; however, their feather growth rate is higher than that of EF chickens. This study aimed to elucidate the molecular basis of the K allele's biphasic effect on feather development. By 3'RACE and RT-PCR analyses, we demonstrated that dSPEF2 gene transcription occurred beyond all coding exons of the dPRLR gene on the opposite strand and that dPRLR mRNA was less abundant than PRLR mRNA. In addition, a 5'UTR splice variant (SPV) of PRL receptor mRNAs was increased in LF chickens. In vitro expression analysis of 5'UTR linked to the luciferase reporter gene revealed higher translation efficiency of SPV. RT-qPCR showed that the dPRLR mRNA level was higher in embryos; conversely, SPV was higher in hatched chickens, as was dSPEF2 mRNA. These findings suggest that the K allele inhibits feather development at the fetal stage by expressing dPRLR to attenuate PRLR function and promotes feather growth after hatching by increasing PRLR through dSPEF2 mRNA expression. Increased SPV may cause greater feather growth than that in EF chickens by increasing the availability of PRLR homodimers and enhancing PRL signaling.
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Affiliation(s)
- Ayako Okamura
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan
| | - Ayane Masumoto
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan
| | - Atsushi Takenouchi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan; Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Toshiyuki Kudo
- Department of Pharmaceutical Sciences, School of Pharmacy, Shujitsu University, 1-6-1 Nakaku, Nishikawara, Okayama 703-8516, Japan
| | - Sayaka Aizawa
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan
| | - Maho Ogoshi
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan
| | - Sumio Takahashi
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan
| | - Masaoki Tsudzuki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan; Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Sakae Takeuchi
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Kitaku, Tsushimanaka, Okayama 700-8530, Japan.
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12
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Zhang X, Wang H, Zhang L, Wang Q, Du X, Ge L, Zhou R, Li L, Li X. Analysis of a genetic factors contributing to feathering phenotype in chickens. Poult Sci 2018; 97:3405-3413. [PMID: 29924355 DOI: 10.3382/ps/pey231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 06/08/2018] [Indexed: 12/21/2022] Open
Abstract
In the current study, we sought to determine whether or not the endogenous retroviral ev21 influences feathering type of chickens, and if one mutation locus in the unoccupied repeat (UR) region can be used to predict the corresponding feathering type and genotype. The distribution of ev21 as well as the mutation locus in UR and occupied site (OR) regions was detected in HY-line gray progenitor (HYGP) 4 lines, HY-line brown (HYB) and Taihang chickens (TH). Furthermore, a detection method for the genotype resulting in late feathering (LF) phenotype was developed by double PCR using C line of HYGP, C line of Dawu progenitor, commercial line of HY-line gray (HYG) males, LF males of TH and Bashang long-tail chickens (BS). Results indicated that a product of 7590 bp from the long fragment amplification was observed to be a partial segment of ev21, and was linked with the LF phenotype in HYGP but not in HYB and TH chickens. A total of 2 of 35 males and 10 of 29 females of TH LF chickens were found to be ev21 negative. HaeIII RFLP mutations of 1450 bp of UR, 1440 bp of OR, and 538 bp in the UR and OR common region were analyzed, and genotypic features at the locus correlated with the feathering type phenotype in HYGP, but exhibited no significant effects in HYB and TH chickens. The cut-off of relative intensity of 857 and 1305 bp from the double PCR for distinction between homozygous and heterozygous LF males was 1.37. In conclusion, ev21 and the HaeIII RFLP patterns within the locus in UR cannot be used for prediction of feathering type phenotypes in Chinese heritage chickens. However, the partial duplication of PRLR and SPEF2 were able to predict the LF phenotype. Therefore, the double PCR detecting products of 857 and 1305 bp described herein could be used for the accurate identification of genotypes influencing feathering type.
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Affiliation(s)
- Xiuling Zhang
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China.,Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Han Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lechao Zhang
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Qi Wang
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Xiaolong Du
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Linhan Ge
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Rongyan Zhou
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Lanhui Li
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Xianglong Li
- Hebei Normal University of Science & Technology, Qinhuangdao, Hebei 066600, China
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13
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Fang G, Jia X, Li H, Tan S, Nie Q, Yu H, Yang Y. Characterization of microRNA and mRNA expression profiles in skin tissue between early-feathering and late-feathering chickens. BMC Genomics 2018; 19:399. [PMID: 29801437 PMCID: PMC5970437 DOI: 10.1186/s12864-018-4773-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/09/2018] [Indexed: 01/05/2023] Open
Abstract
Background Early feathering and late feathering in chickens are sex-linked phenotypes, which have commercial application in the poultry industry for sexing chicks at hatch and have important impacts on performance traits. However, the genetic mechanism controlling feather development and feathering patterns is unclear. Here, miRNA and mRNA expression profiles in chicken wing skin tissues were analysed through high-throughput transcriptomic sequencing, aiming to understand the biological process of follicle development and the formation of different feathering phenotypes. Results Compared to the N1 group with no primary feathers extending out, 2893 genes and 31 miRNAs displayed significantly different expression in the F1 group with primary feathers longer than primary-covert feathers, and 1802 genes and 11 miRNAs in the L2 group displayed primary feathers shorter than primary-covert feathers. Only 201 altered genes and 3 altered miRNAs were identified between the N1 and L2 groups (fold change > 2, q value < 0.01). Both sequencing and qPCR tests revealed that PRLR was significantly decreased in the F1 and L2 groups compared to the N1 group, whereas SPEF2 was significantly decreased in the F1 group compared to the N1 or L2 group. Functional analysis revealed that the altered genes or targets of altered miRNAs were involved in multiple biological processes and pathways related to feather growth and development, such as the Wnt signalling pathway, the TGF-beta signalling pathway, the MAPK signalling pathway, epithelial cell differentiation, and limb development. Integrated analysis of miRNA and mRNA showed that 14 pairs of miRNA-mRNA negatively interacted in the process of feather formation. Conclusions Transcriptomic sequencing of wing skin tissues revealed large changes in F1 vs. N1 and L2 vs. N1, but few changes in F1 vs. L2 for both miRNA and mRNA expression. PRLR might only contribute to follicle development, while SPEF2 was highly related to the growth rate of primary feathers or primary-covert feathers and could be responsible for early and late feather formation. Interactions between miR-1574-5p/NR2F, miR-365-5p/JAK3 and miR-365-5p/CDK6 played important roles in hair or feather formation. In all, our results provide novel evidence to understand the molecular regulation of follicle development and feathering phenotype. Electronic supplementary material The online version of this article (10.1186/s12864-018-4773-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guijun Fang
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China.,College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xinzheng Jia
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China.,College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Hua Li
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China. .,Guangdong Tinoo's Foods Limited Company, Qingyuan, 511827, Guangdong, China.
| | - Shuwen Tan
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China.,Guangdong Tinoo's Foods Limited Company, Qingyuan, 511827, Guangdong, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Hui Yu
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China.,Guangdong Tinoo's Foods Limited Company, Qingyuan, 511827, Guangdong, China
| | - Ying Yang
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China
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14
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Bhanuprakash V, Chhotaray S, Pruthviraj DR, Rawat C, Karthikeyan A, Panigrahi M. Copy number variation in livestock: A mini review. Vet World 2018; 11:535-541. [PMID: 29805222 PMCID: PMC5960796 DOI: 10.14202/vetworld.2018.535-541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/31/2018] [Indexed: 01/22/2023] Open
Abstract
Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.
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Affiliation(s)
- V Bhanuprakash
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Supriya Chhotaray
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - D R Pruthviraj
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Chandrakanta Rawat
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - A Karthikeyan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
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15
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Derks MFL, Herrero-Medrano JM, Crooijmans RPMA, Vereijken A, Long JA, Megens HJ, Groenen MAM. Early and late feathering in turkey and chicken: same gene but different mutations. Genet Sel Evol 2018; 50:7. [PMID: 29566646 PMCID: PMC5863816 DOI: 10.1186/s12711-018-0380-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/15/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Sex-linked slow (SF) and fast (FF) feathering rates at hatch have been widely used in poultry breeding for autosexing at hatch. In chicken, the sex-linked K (SF) and k+ (FF) alleles are responsible for the feathering rate phenotype. Allele K is dominant and a partial duplication of the prolactin receptor gene has been identified as the causal mutation. Interestingly, some domesticated turkey lines exhibit similar slow- and fast-feathering phenotypes, but the underlying genetic components and causal mutation have never been investigated. In this study, our aim was to investigate the molecular basis of feathering rate at hatch in domestic turkey. RESULTS We performed a sequence-based case-control association study and detected a genomic region on chromosome Z, which is statistically associated with rate of feathering at hatch in turkey. We identified a 5-bp frameshift deletion in the prolactin receptor (PRLR) gene that is responsible for slow feathering at hatch. All female cases (SF turkeys) were hemizygous for this deletion, while 188 controls (FF turkeys) were hemizygous or homozygous for the reference allele. This frameshift mutation introduces a premature stop codon and six novel amino acids (AA), which results in a truncated PRLR protein that lacks 98 C-terminal AA. CONCLUSIONS We present the causal mutation for feathering rate in turkey that causes a partial C-terminal loss of the prolactin receptor, and this truncated PRLR protein is strikingly similar to the protein encoded by the slow feathering K allele in chicken.
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Affiliation(s)
- Martijn F L Derks
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Juan M Herrero-Medrano
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Richard P M A Crooijmans
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Addie Vereijken
- Hendrix Genetics Turkeys, Technolgy and Service B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Julie A Long
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Hendrik-Jan Megens
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Martien A M Groenen
- Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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16
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Zhao J, Yao J, Li F, Yang Z, Sun Z, Qu L, Wang K, Su Y, Zhang A, Montgomery SA, Geng T, Cui H. Identification of candidate genes for chicken early- and late-feathering. Poult Sci 2016; 95:1498-1503. [PMID: 27081197 DOI: 10.3382/ps/pew131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/25/2016] [Indexed: 11/20/2022] Open
Abstract
Previous studies suggest that prolactin receptor (Prlr) is a potential causative gene for chicken early- (EF) and late-feathering (LF) phenotypes. In this study, we evaluated candidate genes for this trait and determined the expression of 3 genes, including Prlr, sperm flagellar protein 2 (Spef2), and their fusion gene, in the skins of one-day-old EF and LF chicks using RT-qPCR. Data indicated that Prlr expression in the skin did not show significant difference between EF and LF chicks, suggesting Prlr may not be a suitable candidate gene. In contrast, Spef2 expression in the skin displayed a significant difference between EF and LF chicks (P < 0.01), suggesting that Spef2 may be a good candidate gene for chicken feathering. Moreover, dPrlr/dSpef2, the fusion gene, was also a good candidate gene as it was expressed only in LF chicks. However, the expression of the fusion gene was much lower than that of Prlr Additionally, using strand-specific primers, we found that the fusion gene was transcribed in 2 directions (one from dPrlr promoter, another from dSpef2 promoter), which could result in the formation of a double strand RNA. In conclusion, both Spef2 and the fusion gene are good candidate genes for chicken feathering, but Prlr is not. The research on the function and regulation of the candidate genes will help elucidate the molecular basis of the chicken feathering trait.
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Affiliation(s)
- J Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - J Yao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - F Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Z Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Z Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - L Qu
- Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, Jiangsu 225125, China
| | - K Wang
- Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, Jiangsu 225125, China
| | - Y Su
- Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, Jiangsu 225125, China
| | - A Zhang
- Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, Jiangsu 225125, China
| | - S A Montgomery
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - T Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - H Cui
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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17
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Chen CF, Foley J, Tang PC, Li A, Jiang TX, Wu P, Widelitz RB, Chuong CM. Development, regeneration, and evolution of feathers. Annu Rev Anim Biosci 2014; 3:169-95. [PMID: 25387232 PMCID: PMC5662002 DOI: 10.1146/annurev-animal-022513-114127] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The feather is a complex ectodermal organ with hierarchical branching patterns. It provides functions in endothermy, communication, and flight. Studies of feather growth, cycling, and health are of fundamental importance to avian biology and poultry science. In addition, feathers are an excellent model for morphogenesis studies because of their accessibility, and their distinct patterns can be used to assay the roles of specific molecular pathways. Here we review the progress in aspects of development, regeneration, and evolution during the past three decades. We cover the development of feather buds in chicken embryos, regenerative cycling of feather follicle stem cells, formation of barb branching patterns, emergence of intrafeather pigmentation patterns, interplay of hormones and feather growth, and the genetic identification of several feather variants. The discovery of feathered dinosaurs redefines the relationship between feathers and birds. Inspiration from biomaterials and flight research further fuels biomimetic potential of feathers as a multidisciplinary research focal point.
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Affiliation(s)
- Chih-Feng Chen
- Center for the Integrative and Evolutionary Galliformes Genomics, Taichung, Taiwan
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18
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Copy Number Variation in Chickens: A Review and Future Prospects. MICROARRAYS 2014; 3:24-38. [PMID: 27605028 PMCID: PMC5003453 DOI: 10.3390/microarrays3010024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/19/2022]
Abstract
DNA sequence variations include nucleotide substitution, deletion, insertion, translocation and inversion. Deletion or insertion of a large DNA segment in the genome, referred to as copy number variation (CNV), has caught the attention of many researchers recently. It is believed that CNVs contribute significantly to genome variability, and thus contribute to phenotypic variability. In chickens, genome-wide surveys with array comparative genome hybridization (aCGH), SNP chip detection or whole genome sequencing have revealed a large number of CNVs. A large portion of chicken CNVs involves protein coding or regulatory sequences. A few CNVs have been demonstrated to be the determinant factors for single gene traits, such as late-feathering, pea-comb and dermal hyperpigmentation. The phenotypic effects of the majority of chicken CNVs are to be delineated.
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19
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Bu G, Huang G, Fu H, Li J, Huang S, Wang Y. Characterization of the novel duplicated PRLR gene at the late-feathering K locus in Lohmann chickens. J Mol Endocrinol 2013; 51:261-76. [PMID: 23940279 DOI: 10.1530/jme-13-0068] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A partial duplication of the prolactin (PRL) receptor gene (designated as dPRLR) has been identified at the late-feathering (LF) K locus on chromosome Z of some chicken strains recently, implying that dPRLR is probably a candidate gene associated with LF development in chickens. However, little is known about the structure, functionality, and spatiotemporal expression of the dPRLR gene in chickens. In this study, using 3'-RACE and RT-PCR, the full-length cDNA of the dPRLR obtained from the kidneys of male Lohmann layer chickens carrying a K allele was cloned. The cloned dPRLR is predicted to encode a membrane-spanning receptor of 683 amino acids, which is nearly identical to the original PRLR, except for its lack of a 149-amino acid C-terminal tail. Using a 5× STAT5-Luciferase reporter system and western blot analysis, we demonstrated that dPRLR expressed in HepG2 cells could be potently activated by chicken PRL and functionally coupled to the intracellular STAT5 signaling pathway, suggesting that dPRLR may function as a novel receptor for PRL. RT-PCR assays revealed that similar to the original PRLR gene, dPRLR mRNA is widely expressed in all embryonic and adult tissues examined including the skin of male Lohmann chickens with a K allele. These findings, together with the expression of PRL mRNA detected in the skin of embryos at embryonic day 20 and 1-week-old chicks, suggest that skin-expressed dPRLR and PRLR, together with plasma and skin-derived PRL, may be involved in the control of the LF development of chicks at hatching. Moreover, the wide tissue expression of dPRLR implies that dPRLR may regulate other physiological processes of chickens carrying the K allele.
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Affiliation(s)
- Guixian Bu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, People's Republic of China
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