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Zhuang Z, Zhang C, Tan Y, Zhang J, Zhong C. ELF4 was a prognostic biomarker and related to immune infiltrates in glioma. J Cancer 2024; 15:5101-5117. [PMID: 39132148 PMCID: PMC11310870 DOI: 10.7150/jca.96886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/18/2024] [Indexed: 08/13/2024] Open
Abstract
ELF4 (E74-like factor 4) is a transcription factor, dysregulation of which has been associated with carcinogenesis and cancer development. Nevertheless, the precise role of ELF4 in glioma pathology and its impact on clinical outcomes remains to be investigated. In the present research, comprehensive analyses demonstrated that elevated expression of ELF4 in glioma tissues correlates with malignant phenotypes and adverse clinical outcomes. Multivariate Cox regression analysis determined that ELF4 expression could serve as a reliable predictor of glioma outcomes. (CGGA, hazard ratio [HR]: 1.21, 95% confidence interval [CI]: 1.09-1.34, p<0.001; TCGA, HR: 1.19, 95%CI: 1.01-1.41, p=0.043; and Gravendeel, HR: 1.44, 95%CI: 1.15-1.80, p=0.002). Knockdown of ELF4 reduced the cell viability and migration capacity of glioma cells in vitro. In addition to the tumor invasive role, enrichment analysis revealed the overexpressed ELF4 was involved in the immune regulation, characterized by the elevated activity of Il6/Jak/Stat3 signaling, interferon alpha (IFN-α) response, and IL2/Stat5 signaling. Single-cell RNA sequencing (scRNA)-seq and spatial transcriptome (ST)-seq analyses revealed that ELF4 could induce reprogramming of tumor-associated monocytes/macrophages (TAMMs). Molecular docking analysis revealed ELF4 might be targeted by drugs/compounds, including Veliparib (ABT-888), Motesanib (AMG 706), and EHT 1864. Genomic analysis revealed that, in LGG, in the low ELF4 expression subgroup, IDH1 demonstrated a higher mutation rate, and TP53 and ATRX Chromatin Remodeler (ATRX) displayed the lower mutation rates, than the high ELF4 expression group. Conclusion: Our research suggests that ELF4 may contribute to the prognostic assessment of glioma and personalized medicine.
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Affiliation(s)
- Zhongwei Zhuang
- Department of Neurosurgery, Shanghai East Hospital, Nanjing Medical University, Nanjing, China
| | - Chunyu Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yinqiu Tan
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute for Advanced Study, Tongji University, Shanghai, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, Nanjing Medical University, Nanjing, China
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Lotfizadeh F, Masoudi AA, Vaez Torshizi R, Emrani H. Genome-wide association study of copy number variations with shank traits in a F 2 crossbred chicken population. Anim Genet 2024; 55:559-574. [PMID: 38764135 DOI: 10.1111/age.13447] [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: 10/02/2023] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
Copy number variations (CNVs) are large-scale changes in the DNA sequence that can affect the genetic structure and phenotype of an organism. The purpose of this study was to investigate the existing CNVs and their associations with the shank diameter (ShD) and shank length (ShL) traits using data from an F2 crossbred chicken population. To carry out the study, 312 chickens were genotyped using the Illumina 60k SNP Beadchip. The shank traits of the birds were measured from day 1 to 12 weeks of age. penncnv and cnvruler tools were used to find copy numbers and regions with copy number changes (CNVR), respectively. The CNVRanger package was used to perform a genome-wide association study between shank traits and CNVs. Gene ontology research in CNVRs was carried out using the david database. In this investigation, 966 CNVs and 606 regions with copy number changes were discovered. The copy number states and variations were randomly distributed along the length of the autosomal chromosomes. Weeks 1-4, 9 and 12 of growth revealed a significant association of copy number variations with shank traits, false discovery rate (FDR-corrected p-value < 0.01), and the majority of CNVs that were statistically significant were found on chromosomes 1-3. These CNV segments are nearby genes such as KCNJ12, FGF6 and MYF5, which are fundamental to growth and development. In addition, gene set analyses revealed terms related to muscle physiology, regulation of cellular processes and potassium channels.
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Affiliation(s)
- Fateme Lotfizadeh
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Hossein Emrani
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
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3
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Yang S, Ning C, Yang C, Li W, Zhang Q, Wang D, Tang H. Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study. Vet Sci 2024; 11:76. [PMID: 38393094 PMCID: PMC10892766 DOI: 10.3390/vetsci11020076] [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: 12/18/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Copy number variation (CNV), as an essential source of genetic variation, can have an impact on gene expression, genetic diversity, disease susceptibility, and species evolution in animals. To better understand the weight and egg quality traits of chickens, this paper aimed to detect CNVs in Wenshui green shell-laying chickens and conduct a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) to identify variants and candidate genes associated with their weight and egg quality traits to support related breeding efforts. In our paper, we identified 11,035 CNVRs in Wenshui green shell-laying chickens, which collectively spanned a length of 13.1 Mb, representing approximately 1.4% of its autosomal genome. Out of these CNVRs, there were 10,446 loss types, 491 gain types, and 98 mixed types. Notably, two CNVRs showed significant correlations with egg quality, while four CNVRs exhibited significant associations with body weight. These significant CNVRs are located on chromosome 4. Further analysis identified potential candidate genes that influence weight and egg quality traits, including FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. In this paper, the CNV map of the Wenshui green shell-laying chicken genome was constructed for the first time through population genotyping. Additionally, CNVRs can be employed as molecular markers to genetically improve chickens' weight and egg quality traits.
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Affiliation(s)
- Suozhou Yang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Chao Ning
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Cheng Yang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Wenqiang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
- College of Animal Science and Technology, China Agricultural University, Beijing 100083, China
| | - Dan Wang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Hui Tang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
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Davoudi P, Do DN, Colombo S, Rathgeber B, Sargolzaei M, Plastow G, Wang Z, Hu G, Valipour S, Miar Y. Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 2024; 14:24. [PMID: 38167844 PMCID: PMC10762091 DOI: 10.1038/s41598-023-50497-3] [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: 10/04/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Mielczarek M, Frąszczak M, Zielak-Steciwko AE, Nowak B, Hofman B, Pierścińska J, Kruszyński W, Szyda J. An effect of large-scale deletions and duplications on transcript expression. Funct Integr Genomics 2022; 23:19. [PMID: 36564645 PMCID: PMC9789009 DOI: 10.1007/s10142-022-00946-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022]
Abstract
Since copy number variants (CNVs) have been recognized as an important source of genetic and transcriptomic variation, we aimed to characterize the impact of CNVs located within coding, intergenic, upstream, and downstream gene regions on the expression of transcripts. Regions in which deletions occurred most often were introns, while duplications in coding regions. The transcript expression was lower for deleted coding (P = 0.008) and intronic regions (P = 1.355 × 10-10), but it was not changed in the case of upstream and downstream gene regions (P = 0.085). Moreover, the expression was decreased if duplication occurred in the coding region (P = 8.318 × 10-5). Furthermore, a negative correlation (r = - 0.27) between transcript length and its expression was observed. The correlation between the percent of deleted/duplicated transcript and transcript expression level was not significant for all concerned genomic regions in five out of six animals. The exceptions were deletions in coding regions (P = 0.004) and duplications in introns (P = 0.01) in one individual. CNVs in coding (deletions, duplications) and intronic (deletions) regions are important modulators of transcripts by reducing their expression level. We hypothesize that deletions imply severe consequences by interrupting genes. The negative correlation between the size of the transcript and its expression level found in this study is consistent with the hypothesis that selection favours shorter introns and a moderate number of exons in highly expressed genes. This may explain the transcript expression reduction by duplications. We did not find the correlation between the size of deletions/duplications and transcript expression level suggesting that expression is modulated by CNVs regardless of their size.
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Affiliation(s)
- Magda Mielczarek
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland.
| | - Magdalena Frąszczak
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Anna E Zielak-Steciwko
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Błażej Nowak
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Bartłomiej Hofman
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Jagoda Pierścińska
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Wojciech Kruszyński
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Joanna Szyda
- Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
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6
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Ahmad SF, Singh A, Panda S, Malla WA, Kumar A, Dutt T. Genome-wide elucidation of CNV regions and their association with production and reproduction traits in composite Vrindavani cattle. Gene 2022; 830:146510. [PMID: 35447249 DOI: 10.1016/j.gene.2022.146510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/23/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022]
Abstract
The present study was aimed to analyze the genome-wide copy number variations (CNVs) in Vrindavani composite cattle and concatenate them into CNV regions (CNVRs), and finally test the association of CNVRs with different production and reproduction traits. Genotypic data, generated on BovineSNP50 Beadchip (v3) array for 96 Vrindavani animals, was used to elucidate the CNVs at the genome level. Intensity data covering over 53,218 SNP genotypes on bovine genome was used. Algorithm based on Hidden Markov Model was employed in PennCNV program to detect, normalize and filter CNVs across the genome. 252 putative CNVs, detected via PennCNV program, in different individuals were concatenated into 71 CNV regions (CNVRs) using CNVRuler program. Association of CNVRs with important (re)production traits in Vrindavani animals was assessed using linear regression. Five CNVRs were found to be significantly associated with ten important (re)production traits. The genes harbored in these regions provided useful insights into the association of CNVRs with genes and ultimately the variation at phenotype level. Important genes that overlapped with CNVRs included WASHC4, HS6ST3, MBNL2, TOLLIP, PIDD1 and TSPAN4. Furthermore, the CNVRs were found to overlap with important QTLs available in AnimalQTL database which affect milk yield and composition along with reproduction and immune function traits. The copy number states of three enes were validated using digital droplet PCR technique. The results from the present study significantly enhance the understanding about CNVs in Vrindavani cattle and should help establish its CNV map. The study will also enable further investigation on association of these variants with important traits of economic interest including disease incidence.
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Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Akansha Singh
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Snehasmita Panda
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
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Guerra D, Morcia C, Badeck F, Rizza F, Delbono S, Francia E, Milc JA, Monostori I, Galiba G, Cattivelli L, Tondelli A. Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:553-569. [PMID: 34757472 PMCID: PMC8866391 DOI: 10.1007/s00122-021-03985-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.
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Affiliation(s)
- Davide Guerra
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy.
| | - Caterina Morcia
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Franz Badeck
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Fulvia Rizza
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Justyna Anna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Istvan Monostori
- Centre for Agricultural Research, Agricultural Institute, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
| | - Gabor Galiba
- Centre for Agricultural Research, Agricultural Institute, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Department of Environmental Sustainability, Festetics Doctoral School, IES, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, 8360, Hungary
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics - Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda , PC, Italy
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Sin SYW, Cloutier A, Nevitt G, Edwards SV. Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. Genetics 2021; 220:6458329. [PMID: 34888634 DOI: 10.1093/genetics/iyab210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that ORs genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.
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Affiliation(s)
- Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gabrielle Nevitt
- Department of Neurobiology, Physiology and Behavior and the Graduate Group in Ecology, University of California, Davis, CA 95616, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Basilicata MF, Keller Valsecchi CI. The good, the bad, and the ugly: Evolutionary and pathological aspects of gene dosage alterations. PLoS Genet 2021; 17:e1009906. [PMID: 34882671 PMCID: PMC8659298 DOI: 10.1371/journal.pgen.1009906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Diploid organisms contain a maternal and a paternal genome complement that is thought to provide robustness and allow developmental progression despite genetic perturbations that occur in heterozygosity. However, changes affecting gene dosage from the chromosome down to the individual gene level possess a significant pathological potential and can lead to developmental disorders (DDs). This indicates that expression from a balanced gene complement is highly relevant for proper cellular and organismal function in eukaryotes. Paradoxically, gene and whole chromosome duplications are a principal driver of evolution, while heteromorphic sex chromosomes (XY and ZW) are naturally occurring aneuploidies important for sex determination. Here, we provide an overview of the biology of gene dosage at the crossroads between evolutionary benefit and pathogenicity during disease. We describe the buffering mechanisms and cellular responses to alterations, which could provide a common ground for the understanding of DDs caused by copy number alterations.
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Fernandes AC, da Silva VH, Goes CP, Moreira GCM, Godoy TF, Ibelli AMG, Peixoto JDO, Cantão ME, Ledur MC, de Rezende FM, Coutinho LL. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics 2021; 22:354. [PMID: 34001004 PMCID: PMC8130382 DOI: 10.1186/s12864-021-07676-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07676-1.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.
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11
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Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle. Sci Rep 2020; 10:19466. [PMID: 33173134 PMCID: PMC7655849 DOI: 10.1038/s41598-020-76576-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistics and 92 outlier markers based on Bayescan test. The 13 outlier windows detected by at least two approaches, harboured genes (e.g. GH1, ACE, ASIC3, HSPH1, MVD, BCL2, HIGD2A, CBFA2T3) that may be involved in physiological adaptations required to cope with environmental stressors that are typical of the North African area such as infectious diseases, extended drought periods, scarce food supply, oxygen scarcity in the mountainous areas and high-intensity solar radiation. Our data also point to candidate genes involved in transcriptional regulation suggesting that regulatory elements had also a prominent role in North African cattle response to environmental constraints. Our study yields novel insights into the unique adaptive capacity in these endangered populations emphasizing the need for the use of whole genome sequence data to gain a better understanding of the underlying molecular mechanisms.
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12
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da Silva VH, Laine VN, Bosse M, Spurgin LG, Derks MFL, van Oers K, Dibbits B, Slate J, Crooijmans RPMA, Visser ME, Groenen MAM. The Genomic Complexity of a Large Inversion in Great Tits. Genome Biol Evol 2020; 11:1870-1881. [PMID: 31114855 PMCID: PMC6609730 DOI: 10.1093/gbe/evz106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 12/11/2022] Open
Abstract
Chromosome inversions have clear effects on genome evolution and have been associated with speciation, adaptation, and the evolution of the sex chromosomes. In birds, these inversions may play an important role in hybridization of species and disassortative mating. We identified a large (≈64 Mb) inversion polymorphism in the great tit (Parus major) that encompasses almost 1,000 genes and more than 90% of Chromosome 1A. The inversion occurs at a low frequency in a set of over 2,300 genotyped great tits in the Netherlands with only 5% of the birds being heterozygous for the inversion. In an additional analysis of 29 resequenced birds from across Europe, we found two heterozygotes. The likely inversion breakpoints show considerable genomic complexity, including multiple copy number variable segments. We identified different haplotypes for the inversion, which differ in the degree of recombination in the center of the chromosome. Overall, this remarkable genetic variant is widespread among distinct great tit populations and future studies of the inversion haplotype, including how it affects the fitness of carriers, may help to understand the mechanisms that maintain it.
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Affiliation(s)
- Vinicius H da Silva
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Veronika N Laine
- Department of Molecular and Cellular Biology, Harvard University
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park University of East Anglia, Norwich, United Kingdom
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jon Slate
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom
| | | | - Marcel E Visser
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
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13
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Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome. Animals (Basel) 2019; 9:ani9100809. [PMID: 31618984 PMCID: PMC6826909 DOI: 10.3390/ani9100809] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Chickens have been bred for meat and egg production as a source of animal protein. With the increase of productivity as the main purpose of domestication, factors such as metabolism and immunity were boosted, which are detectable signs of selection on the genome. This study focused on copy number variation (CNV) to find evidence of domestication on the genome. CNV was detected from whole-genome sequencing of 65 chickens including Red Jungle Fowl, broilers, and layers. After that, CNV region, the overlapping region of CNV between individuals, was made to identify which genomic regions showed copy number differentiation. The 663 domesticated-specific CNV regions were associated with various functions such as metabolism and organ development. Also, by performing population differentiation analyses such as clustering analysis and ANOVA test, we found that there are a lot of genomic regions with different copy number patterns between broilers and layers. This result indicates that different genetic variations can be found, depending on the purpose of artificial selection and provides considerations for future animal breeding. Abstract Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.
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14
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da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, Geistlinger L. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics 2019; 36:972-973. [PMID: 31392308 PMCID: PMC9887538 DOI: 10.1093/bioinformatics/btz632] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/17/2019] [Accepted: 08/06/2019] [Indexed: 02/02/2023] Open
Abstract
SUMMARY Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes. AVAILABILITY AND IMPLEMENTATION http://bioconductor.org/packages/CNVRanger.
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Affiliation(s)
- Vinicius da Silva
- Department of Animal Breeding and Genomics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Marcel Ramos
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA
| | - Martien Groenen
- Department of Animal Breeding and Genomics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Richard Crooijmans
- Department of Animal Breeding and Genomics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Anna Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | | | - Luiz Coutinho
- Department of Animal Science, University of São Paulo, 13418-900 Piracicaba, Brazil
| | - Ralf Zimmer
- Department of Bioinformatics, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA
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15
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Corbi-Botto CM, Morales-Durand H, Zappa ME, Sadaba SA, Peral-García P, Giovambattista G, Díaz S. Genomic structural diversity in Criollo Argentino horses: Analysis of copy number variations. Gene 2019; 695:26-31. [DOI: 10.1016/j.gene.2018.12.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/04/2018] [Accepted: 12/27/2018] [Indexed: 12/11/2022]
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16
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Diniz WJS, Mazzoni G, Coutinho LL, Banerjee P, Geistlinger L, Cesar ASM, Bertolini F, Afonso J, de Oliveira PSN, Tizioto PC, Kadarmideen HN, Regitano LCA. Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle. Front Genet 2019; 10:210. [PMID: 30930938 PMCID: PMC6424907 DOI: 10.3389/fgene.2019.00210] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected.
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Affiliation(s)
- Wellison J S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.,Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Priyanka Banerjee
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ludwig Geistlinger
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil.,Graduate School of Public Health and Health Policy, The City University of New York, New York, NY, United States
| | - Aline S M Cesar
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Francesca Bertolini
- Department of Aquaculture, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Juliana Afonso
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Haja N Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
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