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Ahmed Z, Xiang W, Wang F, Nawaz M, Kuthu ZH, Lei C, Xu D. Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle. Anim Genet 2024; 55:511-526. [PMID: 38726735 DOI: 10.1111/age.13434] [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: 04/02/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 07/04/2024]
Abstract
Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.
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Affiliation(s)
- Zulfiqar Ahmed
- College of Animal Science and Technology, Huazhong Agriculture University, Wuhan, China
- NCLBG&G, Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Weixuan Xiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mohsin Nawaz
- NCLBG&G, Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Zulfiqar Hussan Kuthu
- NCLBG&G, Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Dequan Xu
- College of Animal Science and Technology, Huazhong Agriculture University, Wuhan, China
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Kyselová J, Tichý L, Sztankóová Z, Marková J, Kavanová K, Beinhauerová M, Mušková M. Comparative Characterization of Immune Response in Sheep with Caseous Lymphadenitis through Analysis of the Whole Blood Transcriptome. Animals (Basel) 2023; 13:2144. [PMID: 37443943 DOI: 10.3390/ani13132144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Caseous lymphadenitis (CL) is a chronic contagious disease that affects small ruminants and is characterized by the formation of pyogranulomas in lymph nodes and other organs. However, the pathogenesis of this disease and the response of the host genome to infection are not yet fully understood. This study aimed to investigate the whole blood transcriptome and evaluate differential gene expression during the later stages of CL in naturally infected ewes. The study included diseased, serologically positive (EP), exposed, serologically negative (EN) ewes from the same infected flock and healthy ewes (CN) from a different flock. RNA sequencing was performed using the Illumina NextSeq system, and differential gene expression was estimated using DESeq2 and Edge R approaches. The analysis identified 191 annotated differentially expressed genes (DEGs) in the EP group (102 upregulated and 89 downregulated) and 256 DEGs in the EN group (106 upregulated and 150 downregulated) compared to the CN group. Numerous immunoregulatory interactions between lymphoid and nonlymphoid cells were influenced in both EP and EN ewes. Immune DEGs were preferentially assigned to antigen presentation through the MHC complex, T lymphocyte-mediated immunity, and extracellular matrix interactions. Furthermore, the EP group showed altered regulation of cytokine and chemokine signaling and activation and recombination of B-cell receptors. Conversely, NF-kappa B signaling, apoptosis, and stress response were the main processes influenced in the EN group. In addition, statistically significant enrichment of the essential immune pathways of binding and uptake of ligands by scavenger receptors in EP and p53 signaling in the EN group was found. In conclusion, this study provides new insights into the disease course and host-pathogen interaction in naturally CL-infected sheep by investigating the blood transcriptome.
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Affiliation(s)
- Jitka Kyselová
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic
| | - Ladislav Tichý
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Zuzana Sztankóová
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic
| | - Jiřina Marková
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Kateřina Kavanová
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Monika Beinhauerová
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Michala Mušková
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic
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Minozzi G, De Iorio MG, Palazzo F, Gandini G, Biffani S, Paolillo G, Ciani E, Di Marco Lo Presti V, Stella A, Williams JL. Genome-wide association study for antibody response to Mycobacterium avium ssp. paratubeculosis in goats. Anim Genet 2023; 54:78-81. [PMID: 36321295 DOI: 10.1111/age.13271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 07/14/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP), causes Johne's disease (JD), or paratuberculosis, a chronic enteritis of ruminants, which in goats is characterized by ileal lesions. The work described here is a case-control association study using the Illumina Caprine SNP50 BeadChip to unravel the genes involved in susceptibility of goats to JD. Goats in herds with a high occurrence of Johne's disease were classified as healthy or infected based on the level of serum antibodies against MAP, and 331 animals were selected for the association study. Goats belonged to the Jonica (157) and Siriana breeds (174). Whole-genome association analysis identified one region suggestive of significance associated with an antibody response to MAP on chromosome 7 (p-value = 1.23 × 10-5 ). These results provide evidence for genetic loci involved in the antibody response to MAP in goats.
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Affiliation(s)
- Giulietta Minozzi
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Maria Grazia De Iorio
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Fiorentina Palazzo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, Università degli Studi di Teramo, Teramo, Italy
| | - Gustavo Gandini
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology, National Research Council, Milano, Milano, Italia
| | - Gianluigi Paolillo
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Vincenzo Di Marco Lo Presti
- Istituto Zooprofilattico Sperimentale della Sicilia 'A. Mirri', Area Territoriale Barcellona Pozzo di Gotto, Messina, Italy
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council, Milano, Milano, Italia
| | - John L Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Adelaide, South Australia, Australia
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Curti N, Levi G, Giampieri E, Castellani G, Remondini D. A network approach for low dimensional signatures from high throughput data. Sci Rep 2022; 12:22253. [PMID: 36564421 PMCID: PMC9789141 DOI: 10.1038/s41598-022-25549-9] [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: 06/14/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
One of the main objectives of high-throughput genomics studies is to obtain a low-dimensional set of observables-a signature-for sample classification purposes (diagnosis, prognosis, stratification). Biological data, such as gene or protein expression, are commonly characterized by an up/down regulation behavior, for which discriminant-based methods could perform with high accuracy and easy interpretability. To obtain the most out of these methods features selection is even more critical, but it is known to be a NP-hard problem, and thus most feature selection approaches focuses on one feature at the time (k-best, Sequential Feature Selection, recursive feature elimination). We propose DNetPRO, Discriminant Analysis with Network PROcessing, a supervised network-based signature identification method. This method implements a network-based heuristic to generate one or more signatures out of the best performing feature pairs. The algorithm is easily scalable, allowing efficient computing for high number of observables ([Formula: see text]-[Formula: see text]). We show applications on real high-throughput genomic datasets in which our method outperforms existing results, or is compatible with them but with a smaller number of selected features. Moreover, the geometrical simplicity of the resulting class-separation surfaces allows a clearer interpretation of the obtained signatures in comparison to nonlinear classification models.
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Affiliation(s)
- Nico Curti
- grid.6292.f0000 0004 1757 1758Department of Physics and Astronomy, University of Bologna, Bologna, Italy ,grid.470193.80000 0004 8343 7610INFN Bologna, Bologna, Italy
| | - Giuseppe Levi
- grid.6292.f0000 0004 1757 1758Department of Physics and Astronomy, University of Bologna, Bologna, Italy ,grid.470193.80000 0004 8343 7610INFN Bologna, Bologna, Italy
| | - Enrico Giampieri
- grid.470193.80000 0004 8343 7610INFN Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- grid.470193.80000 0004 8343 7610INFN Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Daniel Remondini
- grid.6292.f0000 0004 1757 1758Department of Physics and Astronomy, University of Bologna, Bologna, Italy ,grid.470193.80000 0004 8343 7610INFN Bologna, Bologna, Italy
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Using Omics Approaches in the Discovery of Biomarkers for Early Diagnosis of Johne's Disease in Sheep and Goats. Animals (Basel) 2021; 11:ani11071912. [PMID: 34199073 PMCID: PMC8300312 DOI: 10.3390/ani11071912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection. Abstract Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock; therefore, its control and prevention is a priority to reduce economic losses and health risks. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection. As JD has a long incubation period before the disease becomes evident, early diagnosis is important to control the spread of the disease.
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