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Chen S, Zhao M, Chen K, Xu J, Li H. A Network of Circular RNA and MicroRNA Sequencing Provides Insights into Pigment Deposition of Changshun Blue Eggshell Chickens. Genes (Basel) 2024; 15:812. [PMID: 38927747 PMCID: PMC11202489 DOI: 10.3390/genes15060812] [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: 05/24/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was used to analyse the uterine gland transcriptome (CircRNA and miRNA) of Changshun chicken blue-shell hens producing four different eggshell color eggs including dark blue PK(DB) and light blue (LB), dark brown and greenish (between blue and pink, DP) and pink (p). We found that miR-192-x, targeting SLC16a7, was expressed in DB, DP, and LB groups compared with the PK group, which indicates that miR-192-x may play a role in the blue eggshell color. KEGG and GO analyses showed that the "metabolic pathways" with targeted genes such BLVRA and HMOX1 were detected in dark and light blue color eggshell chickens, which confirms the different ratios of biliverdin and HO-1 involved in the deposition of blue color. As annotated by connectivity analysis, RASGRF1 and RASGRF2, belonging to the RASGRF family, are involved in the Ras signaling pathway, which plays an important role in cell growth, differentiation, metastasis and apoptosis. Our findings enrich the database of circRNA, miRNAs and genes for chicken uterine tissue, which will be useful in accelerating molecular selection for blue eggshell color layers.
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Affiliation(s)
| | | | | | | | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
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2
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Perini F, Cendron F, Lasagna E, Cassandro M, Penasa M. Genomic insights into shank and eggshell color in Italian local chickens. Poult Sci 2024; 103:103677. [PMID: 38593544 PMCID: PMC11004871 DOI: 10.1016/j.psj.2024.103677] [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: 12/20/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications.
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Affiliation(s)
- Francesco Perini
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
| | - Filippo Cendron
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy.
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia 06121, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
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Xu W, Mu R, Gegen T, Luo J, Xiao Y, Ou S, Wu Q, Zuo Y, Chen Z, Li F. Comparative analysis of hepatic transcriptomes and metabolomes of Changshun green-shell laying hens based on different green eggshell color intensities. Poult Sci 2024; 103:103220. [PMID: 37980748 PMCID: PMC10685025 DOI: 10.1016/j.psj.2023.103220] [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: 08/07/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023] Open
Abstract
The eggshell color of avian species is an important trait that is predominantly determined by the pigments biliverdin and protoporphyrin. Various factors affect eggshell pigment deposition and coloration; however, the underlying mechanisms remain unclear. We analyzed the hepatic transcriptomes and metabolomes of Changshun green-shell hens laying dark green and light green eggs to investigate the potential role of the liver in regulating the intensity of the green eggshell color. In total, 350 differentially expressed genes and 211 differentially altered metabolites were identified. Gene set enrichment analysis revealed that the enriched pathways and Gene Ontology (GO) terms were mainly associated with energy, immunity, and nutrient metabolism. Metabolite set enrichment analysis revealed that the enriched pathways were mainly associated with amino acid, vitamin, bile acid, and lipid metabolism. Moreover, gene-metabolite interaction network analysis revealed 1 subnetwork. Most genes and metabolites in this subnetwork were determined to be related to melanin metabolism and transport. In conclusion, our results suggest that hepatic melanin metabolism and transport are critical for eggshell coloration. Six candidate genes (CDKN2B, DDC, PYCR1, ABCG5, SLC3A1, and P2RX2) and 7 candidate metabolites (serotonin, 5-hydroxyindoleacetic acid, ornithine, acetylcholine, L-tryptophan, D-ornithine, and ADP) were suggested to play important roles in this process. Meanwhile, this study suggests that changes in hepatic energy metabolism, immune status, antioxidation activity, nutrient availability, and bile acid synthesis can impair eggshell coloration.
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Affiliation(s)
- Wenbin Xu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China; College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ren Mu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China.
| | - Tuya Gegen
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China; Library, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Jiaxiang Luo
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Yang Xiao
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Shunnian Ou
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Qi Wu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China
| | - Yongsong Zuo
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China
| | - Zhi Chen
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China
| | - Fangwei Li
- Guizhou Changshun Tiannong Green Shell Laying Hen Industrial Co. Ltd., Chang Shun 550700, China
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4
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Li L, Quan J, Gao C, Liu H, Yu H, Chen H, Xia C, Zhao S. Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks. Poult Sci 2023; 102:102748. [PMID: 37209656 DOI: 10.1016/j.psj.2023.102748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023] Open
Abstract
Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources.
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Affiliation(s)
- Lanlan Li
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China; College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
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Wang X, Li P, Cao X, Liu B, He S, Cao Z, Xing S, Liu L, Li ZH. Effects of ocean acidification and tralopyril on bivalve biomineralization and carbon cycling: A study of the Pacific Oyster (Crassostrea gigas). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120161. [PMID: 36100119 DOI: 10.1016/j.envpol.2022.120161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/21/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
The combined effects of emerging pollutants and ocean acidification (OA) on marine organisms and marine ecosystems have attracted increasing attention. However, the combined effects of tralopyril and OA on marine organisms and marine ecosystems remain unclear. In this study, Crassostrea gigas (C. gigas) were exposed to tralopyril (1 μg/L) and/or OA (PH = 7.7) for 21 days and a 14-day recovery acclimation. To investigate the stress response and potential molecular mechanisms of C. gigas to OA and tralopyril exposure alone or in combination, as well as the effects of OA and/or tralopyril on bivalve biomineralization and marine carbon cycling. The results showed that the combined toxicity was between that of acidification and tralopyril alone. Single or combined exposure activated the general stress defense responses of C. gigas mantle, affected energy metabolism and biomineralization of the organism and the carbon cycle of the marine ecosystem. Moreover, acidification-induced and tralopyril-induced toxicity showed potential recoverability at molecular and biochemical levels. This study provides a new perspective on the molecular mechanisms of tralopyril toxicity to bivalve shellfish and reveals the potential role of tralopyril and OA on marine carbon cycling.
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Affiliation(s)
- Xu Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Xuqian Cao
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Bin Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Shuwen He
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhihan Cao
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Shaoying Xing
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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Bello SF, Adeola AC, Nie Q. The study of candidate genes in the improvement of egg production in ducks – a review. Poult Sci 2022; 101:101850. [PMID: 35544958 PMCID: PMC9108513 DOI: 10.1016/j.psj.2022.101850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/01/2022] Open
Abstract
Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.
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Ren J, Yang Q, Tang Q, Liu R, Hu J, Li L, Bai L, Liu H. Metabonomics reveals the main small molecules differences between green and white egg shells in ducks. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2021.2024096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jia Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qinglan Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qian Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ruixin Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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8
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Liu H, Hu J, Guo Z, Fan W, Xu Y, Liang S, Liu D, Zhang Y, Xie M, Tang J, Huang W, Zhang Q, Xi Y, Li Y, Wang L, Ma S, Jiang Y, Feng Y, Wu Y, Cao J, Zhou Z, Hou S. A single nucleotide polymorphism variant located in the cis-regulatory region of the ABCG2 gene is associated with mallard egg colour. Mol Ecol 2021; 30:1477-1491. [PMID: 33372351 DOI: 10.1111/mec.15785] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population resulting from the mating of Pekin ducks (white-shelled eggs) and mallards (green-shelled eggs). We further narrowed the candidate region to a 30-kb interval by comparing genome divergence in seven indigenous duck populations. Among the genes located in the finely mapped region, only one transcript of the ABCG2 gene (XM_013093252.2) exhibited higher uterine expression in green-shelled individuals than in white-shelled individuals, as supported by transcriptome data from four populations. ABCG2 has been reported to encode a protein that functions as a membrane transporter for biliverdin. Sanger sequencing of the whole 30-kb candidate region (Chr4: 47.41-47.44 Mb) and a plasmid reporter assay helped to identify a single nucleotide polymorphism (Chr4: 47,418,074 G>A) located in a conserved predicted promoter region whose variation may alter ABCG2 transcription activity. We provide a useful molecular marker for duck breeding and contribute data to the research on ecological evolution based on egg colour patterns among birds.
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Affiliation(s)
- Hehe Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Hu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanbao Guo
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlei Fan
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaxi Xu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suyun Liang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dapeng Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsheng Zhang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Xie
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Tang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Huang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yong Jiang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulong Feng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongbao Wu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junting Cao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengkui Zhou
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Han GP, Kim JM, Kang HK, Kil DY. Transcriptomic analysis of the liver in aged laying hens with different intensity of brown eggshell color. Anim Biosci 2020; 34:811-823. [PMID: 33152221 PMCID: PMC8100479 DOI: 10.5713/ajas.20.0237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/22/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE Eggshell color is an important indicator of egg quality for consumers, especially for brown eggs. Various factors related to laying hens and their environment affect brown eggshell coloration. However, there have been no studies investigating hepatic functions of laying hens with variable intensity of brown eggshell color. Therefore, this study was aimed to identify potential factors affecting brown eggshell coloration in aged laying hens at the hepatic transcriptomic level. METHODS Five hundred 92-wk-old Hy-line Brown laying hens were screened to select laying hens with different intensity of brown eggshell color based on eggshell color fans. Based on eggshell color scores, hens with dark brown eggshells (DBE; eggshell color fan score = 14.8) and hens with light brown eggshells (LBE; eggshell color fan score = 9.7) were finally selected for the liver sampling. We performed RNA-seq analysis using the liver samples through the paired-end sequencing libraries. Differentially expressed genes (DEGs) profiling was carried out to identify their biological meaning by bioinformatics. RESULTS A total of 290 DEGs were identified with 196 being up-regulated and 94 being down-regulated in DBE groups as compared to LBE groups. The Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed that these DEGs belong to several biological pathways including herpes simplex infection (toll-like receptor 3 [TLR3], cyclin-dependent kinase 1, etc.) and influenza A (TLR3, radical S-adenosyl methionine domain containing 2, myxovirus [influenza virus] resistance 1, etc.). Genes related to stress response (ceremide kinase like) and nutrient metabolism (phosphoenolpyruvate carboxy-kinase 1, methylmalonic aciduria [cobalamin deficiency] cblB type, glycine receptor alpha 2, solute carrier family 7 member 11, etc.) were also identified to be differentially expressed. CONCLUSION The current results provide new insights regarding hepatic molecular functions related to different intensity of brown eggshell color in aged laying hens. These insights will contribute to future studies aiming to optimize brown eggshell coloration in aged laying hens.
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Affiliation(s)
- Gi Ppeum Han
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Hwan Ku Kang
- Poultry Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang 25342, Korea
| | - Dong Yong Kil
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
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10
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Morales J. Eggshell Biliverdin as an Antioxidant Maternal Effect. Bioessays 2020; 42:e2000010. [DOI: 10.1002/bies.202000010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/25/2020] [Indexed: 02/05/2023]
Affiliation(s)
- Judith Morales
- National Museum of Natural SciencesSpanish National Research Council (CSIC) c/ José Gutiérrez Abascal 2 Madrid 28006 Spain
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11
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Transcriptome analysis of genes related to gonad differentiation and development in Muscovy ducks. BMC Genomics 2020; 21:438. [PMID: 32590948 PMCID: PMC7318502 DOI: 10.1186/s12864-020-06852-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/19/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Sex-related genes play a crucial role in gonadal differentiation into testes or ovaries. However, the genetic control of gonadal differentiation in Muscovy ducks remains unknown. Therefore, the objective of our study was to screen new candidate genes associated with ovarian and testicular development. RESULTS In this study, 24 males before gonadal differentiation (MB), 24 females before gonadal differentiation (FB), 24 males after gonadal differentiation (MA) and 24 females after gonadal differentiation (FA) were selected from Putian Muscovy ducks, forming 4 groups. RNA-Seq revealed 101.76 Gb of clean reads and 2800 differentially expressed genes (DEGs), including 46 in MB vs FB, 609 in MA vs FA, 1027 in FA vs FB, and 1118 in MA vs MB. A total of 146 signalling pathways were enriched by KEGG analysis, among which 20, 108, 108 and 116 signalling pathways were obtained in MB vs FB, MA vs MB, MA vs FA and FA vs FB, respectively. In further GO and KEGG analyses, a total of 21 candidate genes related to gonad differentiation and development in Muscovy ducks were screened. Among these, 9 genes were involved in the differentiation and development of the testes, and 12 genes were involved in the differentiation and development of the ovaries. In addition, RNA-Seq data revealed 2744 novel genes. CONCLUSIONS RNA-Seq data revealed 21 genes related to gonadal differentiation and development in Muscovy ducks. We further identified 12 genes, namely, WNT5B, HTRA3, RSPO3, BMP3, HNRNPK, NIPBL, CREB3L4, DKK3, UBE2R2, UBPL3KCMF1, ANXA2, and OSR1, involved in the differentiation and development of ovaries. Moreover, 9 genes, namely, TTN, ATP5A1, DMRT1, DMRT3, AMH, MAP3K1, PIK3R1, AGT and ADAMTSL1, were related to the differentiation and development of testes. Moreover, after gonadal differentiation, DMRT3, AMH, PIK3R1, ADAMTSL1, AGT and TTN were specifically highly expressed in males. WNT5B, ANXA2 and OSR1 were specifically highly expressed in females. These results provide valuable information for studies on the sex control of Muscovy ducks and reveal novel candidate genes for the differentiation and development of testes and ovaries.
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12
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Javůrková VG, Pokorná M, Mikšík I, Tůmová E. Concentration of egg white antimicrobial and immunomodulatory proteins is related to eggshell pigmentation across traditional chicken breeds. Poult Sci 2019; 98:6931-6941. [PMID: 31420680 PMCID: PMC8913977 DOI: 10.3382/ps/pez472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/30/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Veronika Gvoždíková Javůrková
- Department of Animal Science, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague – Suchdol, Czech Republic
- Corresponding author
| | - Monika Pokorná
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Ivan Mikšík
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Eva Tůmová
- Department of Animal Science, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague – Suchdol, Czech Republic
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13
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Yin Z, Zhang F, Smith J, Kuo R, Hou ZC. Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. Sci Data 2019; 6:275. [PMID: 31754106 PMCID: PMC6872741 DOI: 10.1038/s41597-019-0293-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/31/2019] [Indexed: 01/05/2023] Open
Abstract
Duck (Anas platyrhynchos), one of the most economically important waterfowl, is an ideal model for studying the immune protection mechanism of birds. An incomplete duck reference genome and very limited availability of full-length cDNAs has hindered the identification of alternatively spliced transcripts and slowed down many basic studies in ducks. We applied PacBio Iso-Seq technologies to multiple tissues from duck for use in transcriptome sequencing. We obtained 199,993 full-length transcripts and comprehensively annotated these transcripts. 23,755 lncRNAs were predicted from all identified transcripts and 35,031 alternative splicing events, which divided into 5 models, were accurately predicted from 3,346 genes. Our data constitute a large increase in the known number of both lncRNA, and alternatively spliced transcripts of duck and plays an important role in improving current genome annotation. In addition, the data will be extremely useful for functional studies in other birds.
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Affiliation(s)
- ZhongTao Yin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Richard Kuo
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zhuo-Cheng Hou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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14
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Chen X, Zhu W, Du Y, Liu X, Geng Z. Genetic Parameters for Yolk Cholesterol and Transcriptional Evidence Indicate a Role of Lipoprotein Lipase in the Cholesterol Metabolism of the Chinese Wenchang Chicken. Front Genet 2019; 10:902. [PMID: 31632438 PMCID: PMC6786094 DOI: 10.3389/fgene.2019.00902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/26/2019] [Indexed: 11/13/2022] Open
Abstract
The yolk cholesterol has been reported to affect egg quality and breeding performance in chickens. However, the genetic parameters and molecular mechanisms regulating yolk cholesterol remain largely unknown. Here, we used the Wenchang chicken, a Chinese indigenous breed with a complete pedigree, as an experimental model, and we examined 24 sire families (24 males and 240 females) and their 362 daughters. First, egg quality and yolk cholesterol content were determined in 40-week-old chickens of two consecutive generations, and the heritability of these parameters was analyzed using the half-sib correlation method. Among first-generation individuals, the egg weight, egg shape index, shell strength, shell thickness, yolk weight, egg white height, Haugh unit, and cholesterol content were 45.36 ± 4.44 g, 0.81 ± 0.12, 3.07 ± 0.92 kg/cm2, 0.340 ± 0.032 mm, 15.57 ± 1.64 g, 3.36 ± 1.15 mm, 58.70 ± 12.33, and 274.3 ± 36.73 mg/egg, respectively. When these indexes were compared to those of the following generation, no statistically significant difference was detected. Although yolk cholesterol content was not associated with egg quality in females, an increase in yolk cholesterol content was correlated with increased yolk weight and albumin height in sire families (p < 0.05). Moreover, the heritability estimates for the yolk cholesterol content were 0.328 and 0.530 in female and sire families, respectively. Therefore, the yolk cholesterol content was more strongly associated with the sire family. Next, chickens with low and high yolk cholesterol contents were selected for follicular membrane collection. Total RNA was extracted from these samples and used as a template for transcriptional sequencing. In total, 375 down- and 578 upregulated genes were identified by comparing the RNA sequencing data of chickens with high and low yolk cholesterol contents. Furthermore, Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses indicated the involvement of energy metabolism and immune-related pathways in yolk cholesterol deposition. Several genes participating in the regulation of the yolk cholesterol content were located on the sex chromosome Z, among which lipoprotein lipase (LPL) was associated with the peroxisome proliferator-activated receptor signaling pathway and the Gene Ontology term cellular component. Collectively, our data suggested that the ovarian steroidogenesis pathway and the downregulation of LPL played critical roles in the regulation of yolk cholesterol content.
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Affiliation(s)
- Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Wenjun Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yeye Du
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xue Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
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15
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Zhang X, Cao C, Liu Y, Qi H, Zhang W, Hao C, Chen H, Zhang Q, Zhang W, Gao M, Wang J, Ma B. Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq. Vet Res 2018; 49:52. [PMID: 29925406 PMCID: PMC6011267 DOI: 10.1186/s13567-018-0545-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/23/2018] [Indexed: 01/18/2023] Open
Abstract
Duck hepatitis A virus 3 (DHAV-3), the only member of the novel genus Avihepatovirus, in the family Picornaviridae, can cause significant economic losses for duck farms in China. Reports on the pathogenicity and the antiviral molecular mechanisms of the lethal DHAV-3 strain in ducklings are inadequate and remain poorly understood. We conducted global gene expression profiling and screened differentially expressed genes (DEG) of duckling liver tissues infected with lethal DHAV-3. There were 1643 DEG and 8979 DEG when compared with mock ducklings at 12 hours post-infection (hpi) and at 48 hpi, respectively. Gene pathway analysis of DEG highlighted mainly biological processes involved in metabolic pathways, host immune responses, and viral invasion. The results may provide valuable information for us to explore the pathogenicity of the virulent DHAV-3 strain and to improve our understanding of host–virus interactions.
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Affiliation(s)
- Xuelian Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.,College of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong Province, China
| | - Chong Cao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Haihui Qi
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Wenjing Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Chunxue Hao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Haotian Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Qi Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Wenlong Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Mingchun Gao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Junwei Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China. .,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Northeast Agricultural University, Harbin, 150030, China.
| | - Bo Ma
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China. .,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Northeast Agricultural University, Harbin, 150030, China.
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