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Yue L, Lu Z, Guo T, Liu J, Yang B, Yuan C. Key genes and metabolites that regulate wool fibre diameter identified by combined transcriptome and metabolome analysis. Genomics 2024; 116:110886. [PMID: 38880312 DOI: 10.1016/j.ygeno.2024.110886] [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: 04/15/2024] [Revised: 06/02/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Fibre diameter is an important economic trait of wool fibre. As the fibre diameter decreases, the economic value of wool increases. Therefore, understanding the mechanism of wool fibre diameter regulation is important in improving the value of wool. RESULTS In this study, we used non-targeted metabolome and reference transcriptome data to detect differences in metabolites and genes in groups of Alpine Merino sheep with different wool fibre diameter gradients, and integrated metabolome and transcriptome data to identify key genes and metabolites that regulate wool fibre diameter. We found 464 differentially abundant metabolites (DAMs) and 901 differentially expressed genes (DEGs) in four comparisons of groups with different wool fibre diameters. Approximately 25% of the differentially abundant metabolites were lipid and lipid-like molecules. These molecules were predicted to be associated with skin development and keratin filament by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Key genes, including COL5A2, COL5A3, CREB3L4, COL1A1, and SFRP4, were identified by gene set enrichment analysis. CONCLUSIONS Key genes regulating wool fibre diameter were identified, the effects of lipid molecules on wool performance were investigated, and potential synergies between genes and metabolites were postulated, providing a theoretical framework for fine wool sheep breeding.
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Affiliation(s)
- Lin Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
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Yue L, Lu Z, Guo T, Liu J, Yang B, Yuan C. Proteome Analysis of Alpine Merino Sheep Skin Reveals New Insights into the Mechanisms Involved in Regulating Wool Fiber Diameter. Int J Mol Sci 2023; 24:15227. [PMID: 37894908 PMCID: PMC10607505 DOI: 10.3390/ijms242015227] [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: 09/12/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
Wool fiber is a textile material that is highly valued based on its diameter, which is crucial in determining its economic value. To analyze the molecular mechanisms regulating wool fiber diameter, we used a Data-independent acquisition-based quantitative proteomics approach to analyze the skin proteome of Alpine Merino sheep with four fiber diameter ranges. From three contrasts of defined groups, we identified 275, 229, and 190 differentially expressed proteins (DEPs). Further analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that pathways associated with cyclic adenosine monophosphate and peroxisome proliferator-activated receptor signaling are relevant to wool fiber diameter. Using the K-means method, we investigated the DEP expression patterns across wool diameter ranges. Using weighted gene co-expression network analysis, we identified seven key proteins (CIDEA, CRYM, MLX, TPST2, GPD1, GOPC, and CAMK2G) that may be involved in regulating wool fiber diameter. Our findings provide a theoretical foundation for identifying DEPs and pathways associated with wool fiber diameter in Alpine Merino sheep to enable a better understanding of the molecular mechanisms underlying the genetic regulation of wool fiber quality.
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Affiliation(s)
- Lin Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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3
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Wang D, Xie K, Wang Y, Hu J, Li W, Yang A, Zhang Q, Ning C, Fan X. Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing. Genet Sel Evol 2022; 54:75. [PMCID: PMC9673297 DOI: 10.1186/s12711-022-00766-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Background Rabbit wool traits are important in fiber production and for model organism research on hair growth, but their genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a breed well-known for the quality of its wool. Considering the cost to generate population-scale sequence data and the biased detection of variants using chip data, developing an effective genotyping strategy using low-coverage whole-genome sequencing (LCS) data is necessary to conduct genetic analyses. Results Different genotype imputation strategies (BaseVar + STITCH, Bcftools + Beagle4, and GATK + Beagle5), sequencing coverages (0.1X, 0.5X, 1.0X, 1.5X, and 2.0X), and sample sizes (100, 200, 300, 400, 500, and 600) were compared. Our results showed that using BaseVar + STITCH at a sequencing depth of 1.0X with a sample size larger than 300 resulted in the highest genotyping accuracy, with a genotype concordance higher than 98.8% and genotype accuracy higher than 0.97. We performed multivariate genome-wide association studies (GWAS), followed by conditional GWAS and estimation of the confidence intervals of quantitative trait loci (QTL) to investigate the genetic architecture of wool traits. Six QTL were detected, which explained 0.4 to 7.5% of the phenotypic variation. Gene-level mapping identified the fibroblast growth factor 10 (FGF10) gene as associated with fiber growth and diameter, which agrees with previous results from functional data analyses on the FGF gene family in other species, and is relevant for wool rabbit breeding. Conclusions We suggest that LCS followed by imputation can be a cost-effective alternative to array and high-depth sequencing for assessing common variants. GWAS combined with LCS can identify new QTL and candidate genes that are associated with quantitative traits. This study provides a cost-effective and powerful method for investigating the genetic architecture of complex traits, which will be useful for genomic breeding applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00766-y.
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Affiliation(s)
- Dan Wang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Kerui Xie
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Yanyan Wang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Jiaqing Hu
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Wenqiang Li
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Aiguo Yang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Qin Zhang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Chao Ning
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Xinzhong Fan
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
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4
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Zhang C, Qin Q, Liu Z, Xu X, Lan M, Xie Y, Wang Z, Li J, Liu Z. Identification of the key proteins associated with different hair types in sheep and goats. Front Genet 2022; 13:993192. [PMID: 36212123 PMCID: PMC9539809 DOI: 10.3389/fgene.2022.993192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Animal-derived fiber has the characteristics of being light, soft, strong, elastic and a good thermal insulator, and it is widely used in many industries and traditional products, so it plays an important role in the economy of some countries. Variations in phenotypes of wool fibers among different species and breeds are important for industry. We found that the mean fiber diameter of cashmere was significantly smaller than that of sheep wool (p < 0.01), and sheep wool was significantly smaller than goat wool (p < 0.01). Compared with traditional proteomics technology, we analyzed cashmere, guard hair, and wool by Laber-free proteomics technology and detected 159, 204, and 70 proteins, respectively. Through the sequential windowed acquisition of all theoretical fragmentations (SWATH), 41 and 54 differentially expressed proteins were successfully detected in the cashmere vs. wool group and guard hair vs. wool group. Protein‒protein interaction network analysis of differentially expressed proteins revealed many strong interactions related to KRT85, KRTAP15-1 and KRTAP3-1. The final analysis showed that the proportion of KRT85, KRTAP15-1 and KRTAP3-1 might be the key to the difference in fiber diameter and could be used as a potential molecular marker for distinguishing different fiber types.
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Affiliation(s)
- Chongyan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Qin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhichen Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolong Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingxi Lan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuchun Xie
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding of Ministry of Agriculture, Hohhot, China
- The Inner Mongolia Autonomous Region Goat Genetics and Breeding Engineering Technology Research Center, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding of Ministry of Agriculture, Hohhot, China
- The Inner Mongolia Autonomous Region Goat Genetics and Breeding Engineering Technology Research Center, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding of Ministry of Agriculture, Hohhot, China
- The Inner Mongolia Autonomous Region Goat Genetics and Breeding Engineering Technology Research Center, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China
- *Correspondence: Zhihong Liu,
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5
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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6
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Liu Y, Ding Y, Liu Z, Chen Q, Li X, Xue X, Pu Y, Ma Y, Zhao Q. Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending. Front Cell Dev Biol 2022; 10:836913. [PMID: 35433706 PMCID: PMC9011194 DOI: 10.3389/fcell.2022.836913] [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: 12/16/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
Zhongwei goat is a unique Chinese native goat breed for excellent lamb fur. The pattern of flower spikes of the lamb fur was significantly reduced due to the reduction of the bending of the hair strands with growth. In order to explore the molecular mechanism underlying hair bending with growth, we performed the comprehensive analysis of transcriptome and proteome of skins from 45-days, 108-days and 365-days goat based on TMT-based quantitative proteomics and RNA-seq methods. In the three comparison groups, 356, 592 and 282 differentially expressed proteins (DEPs) were screened, respectively. KEGG pathway analysis indicated that DEPs were significantly enriched in a set of signaling pathways related to wool growth and bending, such as ECM-receptor interaction, PI3K-Akt signaling pathway, PPAR signaling pathway, protein digestion and absorption, and metabolic pathways. In addition, 20 DEPs abundance of goat skin at three development stages were examined by PRM method, which validated the reliability of proteomic data. Among them, KRT and collagen alpha family may play an important role in the development of goat hair follicle and wool bending. COL6A1, COL6A2, CRNN, TNC and LOC102178129 were identified as candidate genes based on combined analysis of transcriptome and proteome data and PRM quantification. Our results identify the differential expressed proteins as well as pathways related to the wool bending of Zhongwei goats and provide a theoretical basis for further revealing the molecular mechanism underlying wool bending of goats.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yangyang Ding
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhanfa Liu
- The Ningxia Hui Autonomous Region Breeding Ground of Zhongwei Goat, Zhongwei, China
| | - Qian Chen
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiaobo Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xianglan Xue
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yabin Pu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuehui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- *Correspondence: Qianjun Zhao, ; Yuehui Ma,
| | - Qianjun Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affffairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- *Correspondence: Qianjun Zhao, ; Yuehui Ma,
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7
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Miller I, de Almeida AM, Eckersall PD. Across the great divide: Proteomics becoming an essential tool for animal and veterinary sciences. J Proteomics 2021; 241:104225. [PMID: 33857699 DOI: 10.1016/j.jprot.2021.104225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ingrid Miller
- University of Veterinary Medicine Vienna, Vienna, Austria.
| | - André M de Almeida
- LEAF, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - P David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
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8
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Almeida AM, Ali SA, Ceciliani F, Eckersall PD, Hernández-Castellano LE, Han R, Hodnik JJ, Jaswal S, Lippolis JD, McLaughlin M, Miller I, Mohanty AK, Mrljak V, Nally JE, Nanni P, Plowman JE, Poleti MD, Ribeiro DM, Rodrigues P, Roschitzki B, Schlapbach R, Starič J, Yang Y, Zachut M. Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis. J Proteomics 2021; 241:104220. [PMID: 33838350 DOI: 10.1016/j.jprot.2021.104220] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/01/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.
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Affiliation(s)
- André M Almeida
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal.
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Fabrizio Ceciliani
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milano, Italy
| | - P David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Lorenzo E Hernández-Castellano
- Department of Animal Science, AU-Foulum, Aarhus University, 8830 Tjele, Denmark; Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Rongwei Han
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Jaka J Hodnik
- Veterinary Faculty, Clinic for Reproduction and Large Animals - Section for Ruminants, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Shalini Jaswal
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - John D Lippolis
- Ruminant Diseases and Immunology Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa 50010, United States
| | - Mark McLaughlin
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Ingrid Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Ashok Kumar Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Vladimir Mrljak
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Jarlath E Nally
- Ruminant Diseases and Immunology Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa 50010, United States
| | - Paolo Nanni
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | | | - Mirele D Poleti
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - David M Ribeiro
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Pedro Rodrigues
- CCMAR - Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Jože Starič
- Veterinary Faculty, Clinic for Reproduction and Large Animals - Section for Ruminants, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Yongxin Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Maya Zachut
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization/Volcani Center, Rishon Lezion 7505101, Israel
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