1
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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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2
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Wu S, Dou T, Wang K, Yuan S, Yan S, Xu Z, Liu Y, Jian Z, Zhao J, Zhao R, Wu H, Gu D, Liu L, Li Q, Wu DD, Ge C, Su Z, Jia J. Artificial selection footprints in indigenous and commercial chicken genomes. BMC Genomics 2024; 25:428. [PMID: 38689225 PMCID: PMC11061962 DOI: 10.1186/s12864-024-10291-5] [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: 12/22/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China. RESULTS We found 30 million non-redundant single nucleotide variants and small indels (< 50 bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (~ 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds. CONCLUSION We identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs.
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Affiliation(s)
- Siwen Wu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sisi Yuan
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zonghui Jian
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rouhan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dahai Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Qihua Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
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3
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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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4
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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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5
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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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6
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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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7
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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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8
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Takenouchi A, Toshishige M, Ito N, Tsudzuki M. Endogenous viral gene ev21 is not responsible for the expression of late feathering in chickens. Poult Sci 2018; 97:403-411. [PMID: 29253229 DOI: 10.3382/ps/pex345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/17/2017] [Indexed: 11/20/2022] Open
Abstract
The late-feathering (LF) gene K on the Z chromosome is an important gene in the chicken industry, which is frequently utilized for the feather sexing, a type of autosexing, of neonatal chicks. The K gene is closely associated with the endogenous ev21 gene from an avian leukosis virus and the incomplete duplication (ID) of prolactin receptor (PRLR) and sperm flagellar protein 2 (SPEF2) genes, and ev21 has been used as a molecular marker to detect LF birds. In the present study, a comprehensive survey for the presence or absence of ev21 and ID across 1,994 birds from 52 chicken breeds, three commercial hybrid groups, and the Red Jungle Fowl revealed that almost all LF breeds have both ev21 and ID. However, only one LF breed (Ingie) has only ID and no ev21. Moreover, this study revealed that almost all early (normal)-feathering (EF) breeds lack both ev21 and ID, but only one breed (White Plymouth Rock) included EF birds with ev21 but no ID. Therefore, regarding LF expression, the results indicated that ID is responsible, but ev21 is not required. Henceforth, ID should be used as a molecular marker to detect LF birds instead of ev21. Because ev21 contains the full genome of an avian leukosis virus, there is a risk of disease development in breeds with this gene. Therefore, the Ingie breed, which has no ev21 at the K locus, represents excellent material for the establishment of new LF stocks.
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Affiliation(s)
- A Takenouchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - M Toshishige
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - N Ito
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Yamaguchi Prefectural Agriculture and Forestry General Technology Center, Mine, Yamaguchi 759-2221, Japan
| | - M Tsudzuki
- Laboratory of Animal Breeding and Genetics, 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
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9
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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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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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