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Zhao X, Qiu Y, Meng F, Zhuang Z, Ruan D, Wu J, Ma F, Zheng E, Cai G, Yang J, Yang M, Wu Z. Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs. Anim Genet 2024; 55:134-139. [PMID: 38098441 DOI: 10.1111/age.13386] [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: 09/24/2022] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 01/04/2024]
Abstract
This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated with LMA, LMD and BFT, respectively, and searched genes within the 1 Mb region near the significant SNPs with relevant functions as candidate genes. Consequently, we identified one (DOCK5), three (PID1, PITX2, ELOVL6) and three (CCR1, PARP14, CASR) promising candidate genes for LMA, LMD and BFT, respectively. Moreover, the multi-trait GWAS identified four significant SNPs associated with the three traits. In conclusion, the GWAS analysis of LMA, LMD and BFT in a DLY pig population identified several associated SNPs and candidate genes, further deepening our understanding of the genetic basis of these traits, and they may be useful for marker-assisted selection to improve the three traits in DLY pigs.
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Affiliation(s)
- Xiang Zhao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fanming Meng
- State Key Laboratory of Livestock and Poultry Breeding/Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fucai Ma
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ming Yang
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
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Zhao Q, Cheng J, Gao A, Wang J, Lu H, Jiang S, Li X, Ni J, Dong W, Lai S, Gong J, Zhu H, Liang Y. Duodenal-Jejunal bypass improves metabolism and re-models extra cellular matrix through modulating ceRNA network. Genomics 2023; 115:110744. [PMID: 37972907 DOI: 10.1016/j.ygeno.2023.110744] [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: 05/19/2023] [Revised: 09/29/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Bariatric surgery (BS) is an effective approach in treating obesity and ameliorating T2DM with obesity. Our previous studies demonstrated that duodenal-jejunal bypass (DJB) altered long non-coding RNAs (lncRNAs) in the gastrointestinal system, which is associated with modulation of lipid metabolism, and glycemic control through entero-pancreatic axis and gut-brain axis. The adipose non-coding RNA expression profile and the underlying competing endogenous RNA (ceRNA) regulatory network pattern post DJB needs further research and investigation. RESULTS In this study, we compared the lncRNAs, circular RNAs (circRNAs) and messenger RNAs (mRNAs) expression in adipose tissues between the sham group and the DJB group. 2219 differentially expressed mRNAs (DEmRNAs), 722 differential expression of lncRNAs (DElncRNAs) and 425 differential expression of circRNAs (DEcircRNAs) were identified. GO terms and KEGG pathways analysis of the DEmRNAs implied that the dysregulated adipose mRNAs were associated with lipid, amino acid metabolism, insulin resistance, and extra cellular matrix (ECM)-related pathways. Moreover, via analyzing ceRNA regulatory networks of DElncRNAs and DEcircRNAs, 31 hub DE mRNAs, especially Mpp7, 9330159F19Rik, Trhde. Trdn, Sorbs2, were found on these pathways. CONCLUSIONS The role of DJB in adipose tends to remodel ECM and improve the energy metabolism through the ceRNA regulatory network.
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Affiliation(s)
- Qingnan Zhao
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China; Shanghai Key Laboratory of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Jiaxin Cheng
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China; Department of Pharmacy, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Aimei Gao
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Jianqiao Wang
- School of pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Huiping Lu
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Shan Jiang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiaojing Li
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Jiahao Ni
- Xuhui Health Management and Development Center,50 yongchuan Road, Xuhui, Shanghai 200030, China
| | - Wenmin Dong
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Shenjin Lai
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Jingru Gong
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China.
| | - Han Zhu
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China; Fudan Zhangjiang Institute, Shanghai 201203, China.
| | - Yongjun Liang
- Fudan Zhangjiang Institute, Shanghai 201203, China; Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 201399 Shanghai, China; Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, Shanghai 201399, China.
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3
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Zhang L, Zhang S, Zhan F, Song M, Shang P, Zhu F, Li J, Yang F, Li X, Qiao R, Han X, Li X, Liu G, Wang K. Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions. Animals (Basel) 2023; 13:ani13081396. [PMID: 37106959 PMCID: PMC10135051 DOI: 10.3390/ani13081396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs.
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Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Fangxian Zhu
- National Animal Husbandry Service, Beijing 100193, China
| | - Jiang Li
- National Supercomputing Center in Zhengzhou, Zhengzhou 450001, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
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Kong Y, Liu C, Zhang X, Liu X, Li W, Li F, Wang X, Yue X. Characterization of fatty acid compositions in longissimus thoracis muscle and identification of candidate gene and SNPs related to polyunsaturated fatty acid in Hu sheep. J Anim Sci 2023; 101:skac382. [PMID: 36394948 PMCID: PMC9833039 DOI: 10.1093/jas/skac382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Fatty acid (FA) composition contributes greatly to the quality and nutritional value of lamb meat. In the present study, FA was measured in longissimus thoracis (LT) muscles of 1,085 Hu sheep using gas chromatography. Comparative transcriptomic analysis was conducted in LT muscles to identify differentially expressed genes (DEGs) between six individuals with high polyunsaturated fatty acids (H-PUFA, 15.27% ± 0.42%) and six with low PUFA (L-PUFA, 5.22% ± 0.25%). Subsequently, the single nucleotide polymorphisms (SNPs) in a candidate gene PLIN2 were correlated with FA traits. The results showed a total of 29 FA compositions and 8 FA groups were identified, with the highest content of monounsaturated fatty acids (MUFA, 46.54%, mainly C18:1n9c), followed by saturated fatty acids (SFA, 44.32%, mainly C16:0), and PUFA (8.72%, mainly C18:2n6c), and significant correlations were observed among the most of FA traits. Transcriptomic analyses identified 110 upregulated and 302 downregulated DEGs between H-PUFA and L-PUFA groups. The functional enrichment analysis revealed three significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 17 gene ontology (GO) terms, in which regulation of lipolysis in adipocytes, the AMPK signaling pathway, and the PPAR signaling pathway may play important roles in FA metabolism and biosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified 37 module genes associated with PUFA-related traits. In general, PLIN1, LIPE, FABP4, LEP, ACACA, ADIPOQ, SCD, PCK2, FASN, PLIN2, LPL, FABP3, THRSP, and ACADVL may have a great impact on PUFA metabolism and lipid deposition. Four SNPs within PLIN2 were significantly associated with FA. Of those, SNP1 (g.287 G>A) was significantly associated with C18:1n9c and MUFA, and SNP4 (g.7807 T>C) was significantly correlated with PUFA (C18:3n3). In addition, the combined genotype of SNP1 (g.287 G>A), SNP3 (g.7664 T>C), and SNP4 (g.7807 T>C) were significantly correlated with C16:1, C17:0, C18:1C6, PUFA (C18:3n3, C22:6n3), and n-6/n-3 PUFA. These results contribute to the knowledge of the biological mechanisms and genetic markers involved in the composition of FA in Hu sheep.
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Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chongyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xueying Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xing Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wenqiao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xinji Wang
- Extension Station of Animal Husbandry and Veterinary Medicine in Minqin, Minqin County 733300, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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Manaig YJY, Criado-Mesas L, Esteve-Codina A, Mármol-Sánchez E, Castelló A, Sánchez A, Folch JM. Identifying miRNA-mRNA regulatory networks on extreme n-6/n-3 polyunsaturated fatty acid ratio expression profiles in porcine skeletal muscle. PLoS One 2023; 18:e0283231. [PMID: 37141193 PMCID: PMC10159129 DOI: 10.1371/journal.pone.0283231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/06/2023] [Indexed: 05/05/2023] Open
Abstract
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids with antagonistic inflammatory functions that play vital roles in metabolic health and immune response. Current commercial swine diets tend to over-supplement with n-6 PUFAs, which may increase the likelihood of developing inflammatory diseases and affect the overall well-being of the animals. However, it is still poorly understood how n-6/n-3 PUFA ratios affect the porcine transcriptome expression and how messenger RNAs (mRNAs) and microRNAs (miRNAs) might regulate biological processes related to PUFA metabolism. On account of this, we selected a total of 20 Iberian × Duroc crossbred pigs with extreme values for n-6/n-3 FA ratio (10 high vs 10 low), and longissimus dorsi muscle samples were used to identify differentially expressed mRNAs and miRNAs. The observed differentially expressed mRNAs were associated to biological pathways related to muscle growth and immunomodulation, while the differentially expressed microRNAs (ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-15b and ssc-miR-7142-3p) were correlated to adipogenesis and immunity. Relevant miRNA-to-mRNA regulatory networks were also predicted (i.e., mir15b to ARRDC3; mir-7142-3p to METTL21C), and linked to lipolysis, obesity, myogenesis, and protein degradation. The n-6/n-3 PUFA ratio differences in pig skeletal muscle revealed genes, miRNAs and enriched pathways involved in lipid metabolism, cell proliferation and inflammation.
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Affiliation(s)
- Yron Joseph Yabut Manaig
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Lourdes Criado-Mesas
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Emilio Mármol-Sánchez
- Department of Molecular Biosciences, Science for Life Laboratory, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Anna Castelló
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
| | - Armand Sánchez
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
| | - Josep M Folch
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
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Chessari G, Criscione A, Tolone M, Bordonaro S, Rizzuto I, Riggio S, Macaluso V, Moscarelli A, Portolano B, Sardina MT, Mastrangelo S. High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context. Front Vet Sci 2023; 10:1127354. [PMID: 37205231 PMCID: PMC10185747 DOI: 10.3389/fvets.2023.1127354] [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: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Bordonaro
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Ilaria Rizzuto
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Vito Macaluso
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
- *Correspondence: Salvatore Mastrangelo,
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7
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UBE3D Regulates mRNA 3'-End Processing and Maintains Adipogenic Potential in 3T3-L1 Cells. Mol Cell Biol 2022; 42:e0017422. [PMID: 36519931 PMCID: PMC9753722 DOI: 10.1128/mcb.00174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have previously described the role of an essential Saccharomyces cerevisiae gene, important for cleavage and polyadenylation 1 (IPA1), in the regulation of gene expression through its interaction with Ysh1, the endonuclease subunit of the mRNA 3'-end processing complex. Through a similar mechanism, the mammalian homolog ubiquitin protein ligase E3D (UBE3D) promotes the migratory and invasive potential of breast cancer cells, but its role in the regulation of gene expression during normal cellular differentiation has not previously been described. In this study, we show that CRISPR/Cas9-mediated knockout of Ube3d in 3T3-L1 cells blocks their ability to differentiate into mature adipocytes. Consistent with previous studies in other cell types, Ube3d knockout leads to decreased levels of CPSF73 and global changes in cellular mRNAs indicative of a loss of 3'-end processing capacity. Ube3d knockout cells also display decreased expression of known preadipogenic markers. Overexpression of either UBE3D or CPSF73 rescues the differentiation defect and partially restores protein levels of these markers. These results support a model in which UBE3D is necessary for the maintenance of the adipocyte-committed state via its regulation of the mRNA 3'-end processing machinery.
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8
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Liu H, Heller-Trulli D, Moore CL. Targeting the mRNA endonuclease CPSF73 inhibits breast cancer cell migration, invasion, and self-renewal. iScience 2022; 25:104804. [PMID: 35992060 PMCID: PMC9385686 DOI: 10.1016/j.isci.2022.104804] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/26/2022] [Accepted: 07/15/2022] [Indexed: 12/02/2022] Open
Abstract
Cleavage by the endonuclease CPSF73 and polyadenylation of nascent RNA is an essential step in co-transcriptional mRNA maturation. Recent work has surprisingly identified CPSF73 as a promising drug target for inhibiting the growth of specific cancers, triggering further studies on understanding CPSF73 regulation and functions in cells. Here, we report that a HECT-like E3 ligase, UBE3D, participates in stabilizing CPFS73 protein by preventing its ubiquitin-mediated degradation by the proteasome. Depletion of UBE3D leads to CPSF73 downregulation, a pre-mRNA cleavage defect, and dysregulated gene expression in cells. UBE3D dysfunction or chemical inactivation of CPSF73 inhibited migration and invasion as well as stem cell renewal phenotypes in vitro in triple-negative breast cancer cells. In addition, genetic overexpression of CPSF73 promoted breast cancer stemness and knocking down CPSF73 inhibited stem cell renewal properties. Together, our findings indicate that targeting the pre-mRNA processing nuclease CPSF73 has potential for breast cancer therapy.
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Affiliation(s)
- Huiyun Liu
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Daniel Heller-Trulli
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Claire L. Moore
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
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9
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Li J, Yang Y, Tang C, Yue S, Zhao Q, Li F, Zhang J. Changes in lipids and aroma compounds in intramuscular fat from Hu sheep. Food Chem 2022; 383:132611. [PMID: 35413762 DOI: 10.1016/j.foodchem.2022.132611] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/04/2022]
Abstract
Intramuscular fat (IMF) content is associated with lamb flavor and largely varies between individuals of the same breed. However, studies investigating the effects of IMF variations on lipid profiles and aroma compounds are limited. Here, we performed lipidomic and volatilomic profiling of high-IMF and low-IMF Hu lambs. Triglycerides and diglycerides in the high-IMF group were significantly higher than those in the low-IMF group (p < 0.05). Seventy-nine of 842 lipids identified were significantly different between the groups under positive and negative ion modes (variable importance in projection > 1, p < 0.05). Volatilomic analyses revealed that the aroma profiles also differed between the groups. Fifteen aroma compounds, mainly originating from lipid oxidation, could be responsible for this difference. Thus, our findings provide a comprehensive understanding of the increases in IMF content that drive consumers' satisfaction and also provide a basis for underpinning breeding value for IMF.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Youyou Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chaohua Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shengnan Yue
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qingyu Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Junmin Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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10
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Liu Y, Cheng H, Wang S, Luo X, Ma X, Sun L, Chen N, Zhang J, Qu K, Wang M, Liu J, Huang B, Lei C. Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou. Front Genet 2022; 13:848951. [PMID: 35873486 PMCID: PMC9301131 DOI: 10.3389/fgene.2022.848951] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Weining cattle is a Chinese indigenous breed influenced by complex breeding and geographical background. The multi-ethnic breeding culture makes Weining cattle require more attention as livestock resources for its genetic diversity. Here, we used 10 Weining cattle (five newly sequenced and five downloaded) and downloaded another 48 genome data to understand the aspects of Weining cattle: genetic diversity, population structure, and cold-adapted performance. In the current study, a high level of genetic diversity was found in Weining cattle, and its breed comprised two potential ancestries, which were Bos taurus and Bos indicus. The positive selective sweep analysis in Weining cattle was analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 203 overlapped genes. In addition, we studied the cold adaptation of Weining cattle by comparing with other Chinese cattle (Wannan and Wenshan cattle) by three methods (FST, θπ-ratio, and XP-EHH). Of the top 1% gene list, UBE3D and ZNF668 were analyzed, and these genes may be associated with fat metabolism and blood pressure regulation in cold adaptation. Our findings have provided invaluable information for the development and conservation of cattle genetic resources, especially in southwest China.
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Affiliation(s)
- Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyv Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohui Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Mingjin Wang
- Bijie Animal Husbandry and Veterinary Science Institute, Bijie, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
- *Correspondence: Bizhi Huang, ; Chuzhao Lei,
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- *Correspondence: Bizhi Huang, ; Chuzhao Lei,
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11
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Bezerra AS, dos Santos MAS, Lourenço-Júnior JDB. Technologies Used in Production Systems for Santa Inês Sheep: A Systematic Review. Front Vet Sci 2022; 9:896241. [PMID: 35711795 PMCID: PMC9195131 DOI: 10.3389/fvets.2022.896241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
This study identifies the number of publications that presented technologies used in the production systems of Santa Inês sheep in the last 5 years (2017–2021) carried out in Brazil. Therefore, the objective was to identify where we are in terms of knowledge about technologies in different fields (health, reproduction, animal breeding, behavior and welfare, nutrition and feeding, forage and pasture, carcass and meat quality, and economics and management of livestock systems). After rigorous selection, 114 studies were appointed and classified by knowledge field, and the main approaches within each theme were evaluated, pointing out research gaps. Most technologies have been in northeastern states. However, government agencies should develop public policies to disseminate techniques in rural areas because the production system in this region is still subsistence. This study highlighted the need for works that present management practices and tools that impact the improvement of animal welfare. Agro-industrial by-products have been widely used as an alternative for sheep feeding. However, economic feasibility analyses are recommended with these foodstuffs to substantiate their use as an option to reduce production costs. There is a lack of research allusive to the management of production systems, especially those related to estimates of economic feasibility indicators.
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Affiliation(s)
- Andréia Santana Bezerra
- Institute of Veterinary Medicine, Postgraduate Program in Animal Science (PPGCAN), Federal University of Para (UFPA), Federal University of the Amazon (UFRA), Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal, Brazil
- *Correspondence: Andréia Santana Bezerra
| | | | - José de Brito Lourenço-Júnior
- Institute of Veterinary Medicine, Postgraduate Program in Animal Science (PPGCAN), Federal University of Para (UFPA), Federal University of the Amazon (UFRA), Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal, Brazil
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12
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Mohammadi H, Farahani AHK, Moradi MH, Mastrangelo S, Di Gerlando R, Sardina MT, Scatassa ML, Portolano B, Tolone M. Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep. Animals (Basel) 2022; 12:ani12091155. [PMID: 35565582 PMCID: PMC9104502 DOI: 10.3390/ani12091155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/05/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Milk production is the most economically crucial dairy sheep trait and constitutes the major genetic enhancement purpose via selective breeding. Also, mastitis is one of the most frequently encountered diseases, having a significant impact on animal welfare, milk yield, and quality. The aim of this study was to identify genomic region(s) associated with the milk production traits and somatic cell score (SCS) in Valle del Belice sheep using single-step genome-wide association (ssGWA) and genotyping data from medium density SNP panels. We identified several genomic regions (OAR1, OAR2, OAR3, OAR4, OAR6, OAR9, and OAR25) and candidate genes implicated in milk production traits and SCS. Our findings offer new insights into the genetic basis of milk production traits and SCS in dairy sheep. Abstract The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a 50 K single nucleotide polymorphism (SNP) array. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. The results showed that top ranked genomic windows (1 Mb windows) explained 3.49, 4.04, 5.37, 4.09, 3.80, and 5.24% of the genetic variances for MY, FY, FAT%, PY, PROT%, and total SCS, respectively. Among the candidate genes found, some known associations were confirmed, while several novel candidate genes were also revealed, including PPARGC1A, LYPLA1, LEP, and MYH9 for MY; CACNA1C, PTPN1, ROBO2, CHRM3, and ERCC6 for FY and FAT%; PCSK5 and ANGPT1 for PY and PROT%; and IL26, IFNG, PEX26, NEGR1, LAP3, and MED28 for SCS. These findings increase our understanding of the genetic architecture of six examined traits and provide guidance for subsequent genetic improvement through genome selection.
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Affiliation(s)
- Hossein Mohammadi
- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran; (A.H.K.F.); (M.H.M.)
- Correspondence: ; Tel.: +98-9127584572
| | - Amir Hossein Khaltabadi Farahani
- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran; (A.H.K.F.); (M.H.M.)
| | - Mohammad Hossein Moradi
- Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran; (A.H.K.F.); (M.H.M.)
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Maria Luisa Scatassa
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, 90129 Palermo, Italy;
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy; (S.M.); (R.D.G.); (M.T.S.); (B.P.); (M.T.)
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13
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Ladeira GC, Pilonetto F, Fernandes AC, Bóscollo PP, Dauria BD, Titto CG, Coutinho LL, E Silva FF, Pinto LFB, Mourão GB. CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep. J Anim Breed Genet 2022; 139:476-487. [PMID: 35218589 DOI: 10.1111/jbg.12671] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/04/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022]
Abstract
Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV-based genome-wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV-based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non-redundant CNV, ranging from 21.8 to 861.9 kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (pFDR -value<0.05) in OAR3 was associated with CY, while another significant CNV in OAR6 was associated with RFI. Additionally, another 5 CNV segments were considered relevant for investigation in the future studies. The significant segments overlapped 4 QTLs and spanned 8 genes, including the SPAST, TGFA and ADGRL3 genes, involved in cell differentiation and energy metabolism. Therefore, the results of the present study increase knowledge about CNV in sheep, their possible impacts on productive traits, and provide information for future investigations, being especially useful for those interested in structural variations in the sheep genome.
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Affiliation(s)
- Giovanni Coelho Ladeira
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Fabrício Pilonetto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Anna Carolina Fernandes
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Paola Pérez Bóscollo
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Brayan Dias Dauria
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Cristiane Gonçalves Titto
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Pirassununga, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | | | - Luís Fernando Batista Pinto
- Department of Animal Science, College of Veterinary Medicine and Animal Science, Federal University of Bahia, Salvador, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
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Nudda A, Bee G, Correddu F, Lunesu MF, Cesarani A, Rassu SPG, Pulina G, Battacone G. Linseed supplementation during uterine and early post-natal life markedly affects fatty acid profiles of brain, liver and muscle of lambs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2038039] [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)
- Anna Nudda
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Giuseppe Bee
- Agroscope, Institute for Livestock Sciences ILS, Posieux, 1725, Switzerland
| | - Fabio Correddu
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Mondina Francesca Lunesu
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Salvatore Pier Giacomo Rassu
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Giuseppe Pulina
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Gianni Battacone
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
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Cavedon M, vonHoldt B, Hebblewhite M, Hegel T, Heppenheimer E, Hervieux D, Mariani S, Schwantje H, Steenweg R, Theoret J, Watters M, Musiani M. Genomic legacy of migration in endangered caribou. PLoS Genet 2022; 18:e1009974. [PMID: 35143486 PMCID: PMC8830729 DOI: 10.1371/journal.pgen.1009974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
Wide-ranging animals, including migratory species, are significantly threatened by the effects of habitat fragmentation and habitat loss. In the case of terrestrial mammals, this results in nearly a quarter of species being at risk of extinction. Caribou are one such example of a wide-ranging, migratory, terrestrial, and endangered mammal. In populations of caribou, the proportion of individuals considered as "migrants" can vary dramatically. There is therefore a possibility that, under the condition that migratory behavior is genetically determined, those individuals or populations that are migratory will be further impacted by humans, and this impact could result in the permanent loss of the migratory trait in some populations. However, genetic determination of migration has not previously been studied in an endangered terrestrial mammal. We examined migratory behavior of 139 GPS-collared endangered caribou in western North America and carried out genomic scans for the same individuals. Here we determine a genetic subdivision of caribou into a Northern and a Southern genetic cluster. We also detect >50 SNPs associated with migratory behavior, which are in genes with hypothesized roles in determining migration in other organisms. Furthermore, we determine that propensity to migrate depends upon the proportion of ancestry in individual caribou, and thus on the evolutionary history of its migratory and sedentary subspecies. If, as we report, migratory behavior is influenced by genes, caribou could be further impacted by the loss of the migratory trait in some isolated populations already at low numbers. Our results indicating an ancestral genetic component also suggest that the migratory trait and their associated genetic mutations could not be easily re-established when lost in a population.
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Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Canada
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, Alberta, Canada
| | - Stefano Mariani
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Nanaimo, British Columbia, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Jessica Theoret
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Megan Watters
- Land and Resource Specialist, Fort St. John, British Columbia, Canada
| | - Marco Musiani
- Department of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, Alberta, Canada
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16
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Blay C, Haffray P, D'Ambrosio J, Prado E, Dechamp N, Nazabal V, Bugeon J, Enez F, Causeur D, Eklouh-Molinier C, Petit V, Phocas F, Corraze G, Dupont-Nivet M. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout. BMC Genomics 2021; 22:788. [PMID: 34732127 PMCID: PMC8564959 DOI: 10.1186/s12864-021-08062-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023] Open
Abstract
Background In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection. Results Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait. Conclusion This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08062-7.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Jonathan D'Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Enora Prado
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Virginie Nazabal
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | | | | | - David Causeur
- Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, Rennes, France
| | | | | | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR1419 NuMéA, St Pée sur, Nivelle, France
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17
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Sutera AM, Moscarelli A, Mastrangelo S, Sardina MT, Di Gerlando R, Portolano B, Tolone M. Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep. Front Genet 2021; 12:643531. [PMID: 33828586 PMCID: PMC8019815 DOI: 10.3389/fgene.2021.643531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
In the Mediterranean basin countries, the dairy sheep production is usually based on local breeds, which are very well-adapted to their production systems and environments and can indeed guarantee income, employment, and economic viability in areas where production alternatives are scarce or non-existent. Mastitis is still one of the greatest problems affecting commercial milk production. However, genetic evaluation of mastitis is particularly difficult because of its low heritability and the categorical nature of the trait. The aim of this study was to identify genomic regions putatively associated with somatic cells count (SCC) in the local economically important Valle del Belice sheep breed using of deregressed breeding values (DEBV) as response variables. All the samples were genotyped using the Illumina OvineSNP50K BeadChip. Genome-wide association analysis was carried out based on regression of DEBV. A total of eight markers were found to be significantly associated with log-transformed SCC. Several candidate genes associated with SCC were identified related to immunity system and udder conformation. The results can help improving the competitiveness of the local Valle del Belìce breed. Further studies considering a higher sample size or independent population will be needed to confirm our results.
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Affiliation(s)
- Anna Maria Sutera
- Dipartimento Scienze Veterinarie, University of Messina, Messina, Italy
| | - Angelo Moscarelli
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Marco Tolone
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
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18
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Ghoreishifar SM, Rochus CM, Moghaddaszadeh-Ahrabi S, Davoudi P, Salek Ardestani S, Zinovieva NA, Deniskova TE, Johansson AM. Shared Ancestry and Signatures of Recent Selection in Gotland Sheep. Genes (Basel) 2021; 12:genes12030433. [PMID: 33802939 PMCID: PMC8002741 DOI: 10.3390/genes12030433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation FST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the FST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran;
| | - Christina Marie Rochus
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands;
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz 5157944533, Iran;
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.D.); (S.S.A.)
| | - Siavash Salek Ardestani
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.D.); (S.S.A.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (N.A.Z.); (T.E.D.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (N.A.Z.); (T.E.D.)
| | - Anna M. Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
- Correspondence:
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19
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Yuan Z, Sunduimijid B, Xiang R, Behrendt R, Knight MI, Mason BA, Reich CM, Prowse-Wilkins C, Vander Jagt CJ, Chamberlain AJ, MacLeod IM, Li F, Yue X, Daetwyler HD. Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits. Genet Sel Evol 2021; 53:8. [PMID: 33461502 PMCID: PMC7812657 DOI: 10.1186/s12711-021-00602-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. Conclusions We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.
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Affiliation(s)
- Zehu Yuan
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture & Agri-Product Safety), Yangzhou University, Yangzhou, 225000, People's Republic of China
| | - Bolormaa Sunduimijid
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ralph Behrendt
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Matthew I Knight
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Brett A Mason
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Claire Prowse-Wilkins
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
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20
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Krivoruchko AY, Yatsyk OA, Safaryan EY. Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed. Vavilovskii Zhurnal Genet Selektsii 2020; 24:836-843. [PMID: 35087996 PMCID: PMC8763718 DOI: 10.18699/vj20.681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study
of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class.
The aim of this study was to identify new candidate genes for economically valuable traits based on the search for
single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals
belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6,
10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the
region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation
Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex
of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA,
EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and
DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development
of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can
influence the formation of exterior features and productive qualities of sheep. However, further research is needed
to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.
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Affiliation(s)
- A. Y. Krivoruchko
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - O. A. Yatsyk
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - E. Y. Safaryan
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
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21
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Pewan SB, Otto JR, Huerlimann R, Budd AM, Mwangi FW, Edmunds RC, Holman BWB, Henry MLE, Kinobe RT, Adegboye OA, Malau-Aduli AEO. Genetics of Omega-3 Long-Chain Polyunsaturated Fatty Acid Metabolism and Meat Eating Quality in Tattykeel Australian White Lambs. Genes (Basel) 2020; 11:E587. [PMID: 32466330 PMCID: PMC7288343 DOI: 10.3390/genes11050587] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022] Open
Abstract
Meat eating quality with a healthy composition hinges on intramuscular fat (IMF), fat melting point (FMP), tenderness, juiciness, flavour and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) content. These health-beneficial n-3 LC-PUFA play significant roles in optimal cardiovascular, retinal, maternal and childhood brain functions, and include alpha linolenic (ALA), eicosapentaenoic (EPA), docosahexaenoic (DHA) and docosapentaenoic (DPA) acids. The primary objective of this review was to access, retrieve, synthesise and critically appraise the published literature on the synthesis, metabolism and genetics of n-3 LC-PUFA and meat eating quality. Studies on IMF content, FMP and fatty acid composition were reviewed to identify knowledge gaps that can inform future research with Tattykeel Australian White (TAW) lambs. The TAW is a new sheep breed exclusive to MARGRA brand of lamb with an outstanding low fat melting point (28-39°C), high n-3 LC-PUFA EPA+DHA content (33-69mg/100g), marbling (3.4-8.2%), tenderness (20.0-38.5N) and overall consumer liking (7.9-8.5). However, correlations between n-3 LC-PUFA profile, stearoyl-CoA desaturase (SCD), fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), other lipogenic genes and meat quality traits present major knowledge gaps. The review also identified research opportunities in nutrition-genetics interactions aimed at a greater understanding of the genetics of n-3 LC-PUFA, feedlot finishing performance, carcass traits and eating quality in the TAW sheep. It was concluded that studies on IMF, FMP and n-3 LC-PUFA profiles in parental and progeny generations of TAW sheep will be foundational for the genetic selection of healthy lamb eating qualities and provide useful insights into their correlations with SCD, FASN and FABP4 genes.
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Affiliation(s)
- Shedrach Benjamin Pewan
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- National Veterinary Research Institute, Private Mail Bag 01, Vom, Plateau State, Nigeria
| | - John Roger Otto
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Roger Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia; (R.H.); (A.M.B.)
| | - Alyssa Maree Budd
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia; (R.H.); (A.M.B.)
| | - Felista Waithira Mwangi
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Richard Crawford Edmunds
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | | | - Michelle Lauren Elizabeth Henry
- Gundagai Meat Processors, 2916 Gocup Road, South Gundagai, New South Wales 2722, Australia;
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robert Tumwesigye Kinobe
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Oyelola Abdulwasiu Adegboye
- Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia;
| | - Aduli Enoch Othniel Malau-Aduli
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
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22
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Palombo V, Gaspa G, Conte G, Pilla F, Macciotta N, Mele M, D'Andrea M. Combined multivariate factor analysis and GWAS for milk fatty acids trait in Comisana sheep breed. Anim Genet 2020; 51:630-631. [PMID: 32394441 DOI: 10.1111/age.12948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Valentino Palombo
- Dipartimento, Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, 86100, Italy
| | - Giustino Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, 10095, Italy.,Dipartimento di Agraria, Sezione Scienze Zootecniche, Università degli Studi di Sassari, Sassari, 07100, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Pisa, 56124, Italy
| | - Fabio Pilla
- Dipartimento, Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, 86100, Italy
| | - Nicola Macciotta
- Dipartimento di Agraria, Sezione Scienze Zootecniche, Università degli Studi di Sassari, Sassari, 07100, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Pisa, 56124, Italy
| | - Mariasilvia D'Andrea
- Dipartimento, Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, 86100, Italy
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23
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Genome-Wide Association Study Using Fix-Length Haplotypes and Network Analysis Revealed New Candidate Genes for Nematode Resistance and Body Weight in Blackface Lambs. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The objectives of this study were to identify genomic regions by Bayesian methods (BayesA, BayesB, or BayesN) that fit fixed-length haplotypes or SNPs using GenSel. Covariates for haplo-type alleles of five lengths (125, 250, 500 kb, 1 or 2 Mb) were generated, and rare haplotypes were removed at three thresholds (1, 5, or 10%). Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same across traits. Genotypes at 41,034 SNPs that were common on OvineSNP50 panel were phased for 751 Scottish Blackface (SBF) lambs. This is the first study to quantify the proportion of genetic variance using haplotypes across the whole genome in an SBF population. The genetic variance explained of haplotype-based GWAS was higher than that of SNP-based GWAS in across traits studied. In this population, fitting 500kb haplotypes with a 1% frequency threshold resulted in the highest proportion of genetic variance explained for nematode resistance and fitting 2Mb haplotypes with a 10% frequency threshold improved genetic variance explained for body weight comparable to fitting SNPs by BayesB. Candidate genes, including CXCR4, STAT4, CCL1, CCL2, CCL3, CCL5, CCL8, CCL16, CCL18, CARMIL2, and HSPA14 were identified for nematode resistance and ADH5, PPP3CA, and FABP4 for body weight traits. Network analysis provided annotation results linking to all identified candidate genes. This study supported previous results from GWAS of nematode resistance and body weight and revealed additional regions in the ovine genome associated with these economically important traits. These results suggest that network analysis can provide new information regarding biological mechanisms and genes leading to complex phenotypes, like nematode resistance and body weight of lamb.
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24
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Lee SD, Liu HY, Graber JH, Heller-Trulli D, Kaczmarek Michaels K, Cerezo JF, Moore CL. Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation. RNA Biol 2020; 17:689-702. [PMID: 32009536 PMCID: PMC7237158 DOI: 10.1080/15476286.2020.1724717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Mutation of the essential yeast protein Ipa1 has previously been demonstrated to cause defects in pre-mRNA 3' end processing and growth, but the mechanism underlying these defects was not clear. In this study, we show that the ipa1-1 mutation causes a striking depletion of Ysh1, the evolutionarily conserved endonuclease subunit of the 19-subunit mRNA Cleavage/Polyadenylation (C/P) complex, but does not decrease other C/P subunits. YSH1 overexpression rescues both the growth and 3' end processing defects of the ipa1-1 mutant. YSH1 mRNA level is unchanged in ipa1-1 cells, and proteasome inactivation prevents Ysh1 loss and causes accumulation of ubiquitinated Ysh1. Ysh1 ubiquitination is mediated by the Ubc4 ubiquitin-conjugating enzyme and Mpe1, which in addition to its function in C/P, is also a RING ubiquitin ligase. In summary, Ipa1 affects mRNA processing by controlling the availability of the C/P endonuclease and may represent a regulatory mechanism that could be rapidly deployed to facilitate reprogramming of cellular responses.
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Affiliation(s)
- Susan D. Lee
- Department of Developmental, Molecular, and Chemical Biology and Tufts School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Hui-Yun Liu
- Department of Developmental, Molecular, and Chemical Biology and Tufts School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Joel H. Graber
- Computational Biology and Bioinformatics Core, Mount Desert Island Biological Laboratory, Bar Harbor, ME, USA
| | - Daniel Heller-Trulli
- Department of Developmental, Molecular, and Chemical Biology and Tufts School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Katarzyna Kaczmarek Michaels
- Department of Developmental, Molecular, and Chemical Biology and Tufts School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | | | - Claire L. Moore
- Department of Developmental, Molecular, and Chemical Biology and Tufts School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
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25
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Riley D, Mantilla-Rojas C, Miller R, Nicholson K, Gill C, Herring A, Riggs P, Sawyer J, Savell J, Sanders J. Genome association of carcass and palatability traits from Bos indicus-Bos taurus crossbred steers within electrical stimulation status and correspondence with steer temperament 3. Aroma and flavor attributes of cooked steaks. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Coltell O, Sorlí JV, Asensio EM, Barragán R, González JI, Giménez-Alba IM, Zanón-Moreno V, Estruch R, Ramírez-Sabio JB, Pascual EC, Ortega-Azorín C, Ordovas JM, Corella D. Genome-Wide Association Study for Serum Omega-3 and Omega-6 Polyunsaturated Fatty Acids: Exploratory Analysis of the Sex-Specific Effects and Dietary Modulation in Mediterranean Subjects with Metabolic Syndrome. Nutrients 2020; 12:E310. [PMID: 31991592 PMCID: PMC7071282 DOI: 10.3390/nu12020310] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Many early studies presented beneficial effects of polyunsaturated fatty acids (PUFA) on cardiovascular risk factors and disease. However, results from recent meta-analyses indicate that this effect would be very low or nil. One of the factors that may contribute to the inconsistency of the results is that, in most studies, genetic factors have not been taken into consideration. It is known that fatty acid desaturase (FADS) gene cluster in chromosome 11 is a very important determinant of plasma PUFA, and that the prevalence of the single nucleotide polymorphisms (SNPs) varies greatly between populations and may constitute a bias in meta-analyses. Previous genome-wide association studies (GWAS) have been carried out in other populations and none of them have investigated sex and Mediterranean dietary pattern interactions at the genome-wide level. Our aims were to undertake a GWAS to discover the genes most associated with serum PUFA concentrations (omega-3, omega-6, and some fatty acids) in a scarcely studied Mediterranean population with metabolic syndrome, and to explore sex and adherence to Mediterranean diet (MedDiet) interactions at the genome-wide level. Serum PUFA were determined by NMR spectroscopy. We found strong robust associations between various SNPs in the FADS cluster and omega-3 concentrations (top-ranked in the adjusted model: FADS1-rs174547, p = 3.34 × 10-14; FADS1-rs174550, p = 5.35 × 10-14; FADS2-rs1535, p = 5.85 × 10-14; FADS1-rs174546, p = 6.72 × 10-14; FADS2-rs174546, p = 9.75 × 10-14; FADS2- rs174576, p = 1.17 × 10-13; FADS2-rs174577, p = 1.12 × 10-12, among others). We also detected a genome-wide significant association with other genes in chromosome 11: MYRF (myelin regulatory factor)-rs174535, p = 1.49 × 10-12; TMEM258 (transmembrane protein 258)-rs102275, p = 2.43 × 10-12; FEN1 (flap structure-specific endonuclease 1)-rs174538, p = 1.96 × 10-11). Similar genome-wide statistically significant results were found for docosahexaenoic fatty acid (DHA). However, no such associations were detected for omega-6 PUFAs or linoleic acid (LA). For total PUFA, we observed a consistent gene*sex interaction with the DNTTIP2 (deoxynucleotidyl transferase terminal interacting protein 2)-rs3747965 p = 1.36 × 10-8. For adherence to MedDiet, we obtained a relevant interaction with the ME1 (malic enzyme 1) gene (a gene strongly regulated by fat) in determining serum omega-3. The top-ranked SNP for this interaction was ME1-rs3798890 (p = 2.15 × 10-7). In the regional-wide association study, specifically focused on the FADS1/FASD2/FADS3 and ELOVL (fatty acid elongase) 2/ELOVL 5 regions, we detected several statistically significant associations at p < 0.05. In conclusion, our results confirm a robust role of the FADS cluster on serum PUFA in this population, but the associations vary depending on the PUFA. Moreover, the detection of some sex and diet interactions underlines the need for these associations/interactions to be studied in all specific populations so as to better understand the complex metabolism of PUFA.
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Affiliation(s)
- Oscar Coltell
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain;
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
| | - Jose V. Sorlí
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Eva M. Asensio
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Rocío Barragán
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - José I. González
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Ignacio M. Giménez-Alba
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Vicente Zanón-Moreno
- Area of Health Sciences, Valencian International University, 46002 Valencia, Spain;
- Red Temática de Investigación Cooperativa en Patología Ocular (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Ophthalmology Research Unit “Santiago Grisolia”, Dr. Peset University Hospital, 46017 Valencia, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | | | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
- Assisted Reproduction Unit of the University Hospital of Valencia, 46010 Valencia, Spain
| | - Carolina Ortega-Azorín
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Jose M. Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111 USA;
- Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- IMDEA Alimentación, 28049 Madrid, Spain
| | - Dolores Corella
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
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Cesarani A, Gaspa G, Correddu F, Cellesi M, Dimauro C, Macciotta N. Genomic selection of milk fatty acid composition in Sarda dairy sheep: Effect of different phenotypes and relationship matrices on heritability and breeding value accuracy. J Dairy Sci 2019; 102:3189-3203. [DOI: 10.3168/jds.2018-15333] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/13/2018] [Indexed: 01/21/2023]
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