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Yin H, Feng Y, Wang Y, Jiang Q, Zhang J, Zhao J, Chen Y, Wang Y, Peng R, Wang Y, Zhao T, Zheng C, Xu L, Gao X, Gao H, Li J, Wang Z, Zhang L. Genome-Wide Scans for Selection Signatures in Ningxia Angus Cattle Reveal Genetic Variants Associated with Economic and Adaptive Traits. Animals (Basel) 2024; 15:58. [PMID: 39795001 PMCID: PMC11718920 DOI: 10.3390/ani15010058] [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: 11/28/2024] [Revised: 12/26/2024] [Accepted: 12/27/2024] [Indexed: 01/13/2025] Open
Abstract
The genetic improvement of beef cattle breeds is crucial for the advancement of the beef cattle industry. Whole-genome resequencing technology has been widely applied in genetic breeding as well as research on selection signatures in beef cattle. In this study, 20× whole-genome resequencing was performed on 282 Angus cattle from the Ningxia region, and a high-quality dataset encompassing extensive genomic variations across the entire genome was constructed. The iHS test identified 495 selection signal regions, which included pregnancy-associated glycoprotein (PAG) family genes and immune-related genes such as UL16-binding protein 21 (ULBP21), CD1b molecule (CD1B), and tumor necrosis factor ligand superfamily member 11 (TNFSF11). A quantitative trait locus (QTL) enrichment analysis revealed that several economic traits, including longissimus muscle area, marbling score, carcass weight, average daily gain, and milk yield, were significantly enriched in cattle with these selection signatures. Although the enrichment of QTLs for health traits was low, immune-related genes may indirectly contribute to improvements in production performance. These findings show the genetic basis of economic and adaptive traits in Ningxia Angus cattle, providing a theoretical foundation and guidance for further genetic improvement and breeding strategies.
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Affiliation(s)
- Haiqi Yin
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Yuan Feng
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Yu Wang
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Qiufei Jiang
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Juan Zhang
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China;
| | - Jie Zhao
- Ningxia Autonomous Region Animal Husbandry Workstation, Yinchuan 750004, China; (Y.F.); (Y.W.); (Q.J.); (J.Z.)
| | - Yafei Chen
- Yinchuan Animal Husbandry Technology Extension Service Center, Yinchuan 750021, China;
| | - Yaxuan Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Ruiqi Peng
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Yahui Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Tong Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Caihong Zheng
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Lingyang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Xue Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Huijiang Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Junya Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Zezhao Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
| | - Lupei Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (Y.W.); (R.P.); (Y.W.); (T.Z.); (C.Z.); (L.X.); (X.G.); (H.G.); (J.L.)
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Casano AB, Menchetti L, Trabalza-Marinucci M, Riva F, De Matteis G, Brecchia G, Inglesi A, Rossi E, Signorelli F, Barile VL, Barbato O. Gene expression of pregnancy-associated glycoproteins-1 (PAG-1), interferon-tau (IFNt) and interferon stimulated genes (ISGs) as diagnostic and prognostic markers of maternal-fetal cellular interaction in buffalo cows. Theriogenology 2023; 209:89-97. [PMID: 37379587 DOI: 10.1016/j.theriogenology.2023.06.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
The aim of this study was to determine the presence of Pregnancy-associated glycoprotein -1 (PAG-1) mRNA expression in the maternal circulation of pregnant buffaloes during the early stage of pregnancy. Contemporaneously, the mRNA expression levels of Interferon-tau (IFNt) and some Interferon stimulated genes (ISGs) (interferon stimulated gene 15 ubiquitin-like modifier interferon, ISG15; Mixoviruses resistance 1 and 2, MX1 and MX2; 2',5'-oligoadenylate synthase 1,OAS1) were evaluated in order to expand our knowledge of the molecular processes involved in the early stages of pregnancy and to identify potential biomarkers of maternal-fetal cellular interaction in buffalo. The study was conducted on 38 synchronized and artificially inseminated buffalo cows (d 0), divided ex post into 3 groups: Pregnant (n = 17), Non-pregnant (n = 15) and Embryo mortality (n = 6). Blood samples were collected on d 14, 19, 28 and 40 after artificial insemination (AI) for peripheral blood mononuclear cells (PBMCs) isolation. Expression levels of mRNA of PAG-1, IFNt, ISG15. MX1, MX2 and OAS1 were measured using RT-qPCR. No significant changes were observed in IFNt and PAG gene expressions between groups, while significant differences (p < 0.001) were found for ISG15, MX1, MX2, and OAS1. Pairwise comparisons revealed that the differences between groups occurred on days 19 and 28 post-AI. ISG15 proved to have the best diagnostic performance for distinguishing between pregnant animals and animals that experienced embryo mortality with the ROC analysis. According to the results of the univariate analyses, day 19 was identified as the most indicative to discriminate between groups while the most reliable genes for this differentiation were ISG15, MX1 and MX2. MX2 proved to be the best gene for discriminating pregnant buffaloes using the discriminant analysis, while MX1 was the gene that best predicted embryo mortality. Our results showed that among PAG-1, IFNt and ISGs expression as diagnostic and prognostic markers of maternal-fetal cellular interaction in buffalo cows, ISGs proved to be the best peripheral biomarkers for predicting pregnancy and embryonic mortality during the peri-implantation period. These insights into the mechanisms behind maternal-fetal interaction and the development of a method for the early detection of embryo distress may enable us to implement effective strategies to support embryo survival.
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Affiliation(s)
- A B Casano
- Department of Veterinary Medicine, University of Perugia, 06126, Perugia, Italy
| | - L Menchetti
- School of Bioscience and Veterinary Medicine, University of Camerino, 62024, Matelica, MC, Italy
| | | | - F Riva
- Department of Veterinary Medicine and Animal Science, University of Milano, 26900, Lodi, Italy
| | - G De Matteis
- Research Centre for Animal Production and Aquaculture, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), 00015, Monterotondo, Roma, Italy
| | - G Brecchia
- Department of Veterinary Medicine and Animal Science, University of Milano, 26900, Lodi, Italy
| | - A Inglesi
- Department of Veterinary Medicine and Animal Science, University of Milano, 26900, Lodi, Italy
| | - E Rossi
- Research Centre for Animal Production and Aquaculture, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), 00015, Monterotondo, Roma, Italy
| | - F Signorelli
- Research Centre for Animal Production and Aquaculture, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), 00015, Monterotondo, Roma, Italy
| | - V L Barile
- Research Centre for Animal Production and Aquaculture, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), 00015, Monterotondo, Roma, Italy
| | - O Barbato
- Department of Veterinary Medicine, University of Perugia, 06126, Perugia, Italy.
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Interferon Tau (IFNt) and Interferon-Stimulated Genes (ISGs) Expression in Peripheral Blood Leukocytes and Correlation with Circulating Pregnancy-Associated Glycoproteins (PAGs) during Peri-Implantation and Early Pregnancy in Buffalo Cows. Animals (Basel) 2022; 12:ani12223068. [PMID: 36428296 PMCID: PMC9686730 DOI: 10.3390/ani12223068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
The objective of this study was to analyze interferon-stimulated genes (ISGs) and interferon tau (IFNt) gene expression in peripheral blood leukocytes during the peri-implantation period and until 40 days of pregnancy in buffalo cows. Relationships were also examined between the expression of ISGs and IFNt and pregnancy-associated glycoproteins (PAGs) peripheral plasma concentration. Buffalo cows were synchronized and artificially inseminated (d 0). Blood samples were collected on days 0, 18, 28 and 40 after artificial insemination (AI) for peripheral blood mononuclear cells (PBMCs) and polymorphonuclear leukocytes (PMNs) isolation and PAGs radioimmunoassay analysis. The study was carried out on 21 buffalo cows divided ex post into Pregnant (n = 12) and Non-pregnant (n = 9) groups. Steady state levels of OAS1, MX2, ISG15 and IFNt mRNA were measured by RT-qPCR and their estimated marginal means (p < 0.01 for all) were higher in pregnant than non-pregnant buffaloes, both in PBMCs and PMNs. In PBMCs, pairwise comparisons showed that OAS1 and MX2 expressions differed between pregnant and non-pregnant buffaloes on all the days of observation (p < 0.001), while significant differences in ISG15 and IFNt started from day 28 post-AI (p < 0.05). In PMNs, ISG15 expression differed between groups only at days 18 and 28 (p < 0.001), while comparisons were always significant for IFNt (p < 0.05). The expression of all genes, except ISG15 as determined in PMNs, was positively associated with PAGs plasma concentrations (p < 0.05). This work showed a significant increase in ISGs and IFNt expressions in PBMCs and PMNs in buffalo during the peri-implantation period and early pregnancy, and their correlation with PAGs plasma concentration.
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Barbato O, Menchetti L, Brecchia G, Barile VL. Using Pregnancy-Associated Glycoproteins (PAGs) to Improve Reproductive Management: From Dairy Cows to Other Dairy Livestock. Animals (Basel) 2022; 12:ani12162033. [PMID: 36009621 PMCID: PMC9404451 DOI: 10.3390/ani12162033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Pregnancy loss is a major cause of infertility in dairy animals, particularly in cattle, which affects the productivity and profitability of farms. Detecting these unsuccessful pregnancies could offer farmers the opportunity to reduce the economic damage caused by pregnancy loss. The determination of proteins secreted by the placenta and related to the presence of a viable conceptus called pregnancy-associated glycoproteins (PAGs) represents a diagnostic tool to identify pregnant or non-pregnant animals and to predict early pregnancy failures. This review describes the state of the art related to PAGs’ function, pregnancy profile, and use in reproductive management in bovine and other dairy livestock. Abstract Pregnancy success represents a major issue for the economic income of cattle breeders. Early detection of pregnant and non-pregnant animals, as well as the prediction of early pregnancy failure, can influence farm management decisions. Several diagnostic tools for pregnancy are currently available. Among these, pregnancy-associated glycoproteins (PAGs) have been shown to be useful for identifying the presence of vital embryos and for pregnancy follow-up monitoring. This review presents an overview of the PAGs’ functions, their pregnancy trends, and their use as a tool to improve reproductive management in bovine and other dairy livestock, such as small ruminants and buffalos.
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Affiliation(s)
- Olimpia Barbato
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
- Correspondence:
| | - Laura Menchetti
- Department of Veterinary Medicine, University of Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Gabriele Brecchia
- Department of Veterinary Medicine, University of Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Vittoria Lucia Barile
- Research Centre for Animal Production and Aquaculture, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Via Salaria 31, 00015 Monterotondo, Italy
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Approaches to Identify Pregnancy Failure in Buffalo Cows. Animals (Basel) 2021; 11:ani11020487. [PMID: 33673362 PMCID: PMC7917614 DOI: 10.3390/ani11020487] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Embryonic mortality and pregnancy failures still represent a major issue in domestic livestock production, particularly in dairy cattle. Despite the presence of extensive work in this research area, there is still no effective, accurate and practical method able to determine timing and viability of embryo specifically during early gestation. Indeed, technologies and techniques for predicting pregnancy success must continue to be developed. The aim of this work was to find the best strategy to diagnose pregnancy failures in buffalo cows in order to improve farm reproductive management. Among the methods compared in this study (ultrasonography, progesterone, PAGs), pregnancy-associated glycoproteins (PAGs) seem to be the best marker for predicting embryonic mortality between 25 and 40 days of gestation to be utilized as a diagnostic tool to improve reproductive management in buffalo farms. Abstract The aim of this work was to find the best strategy to diagnose pregnancy failures in buffalo. A total of 109 animals belonging to a buffalo herd subjected to a synchronization and artificial insemination (AI) program were enrolled in this study. Blood samples were collected at days 0, 14, 25, 28 and 40 after AI for the determination of progesterone (P4) and pregnancy-associated glycoproteins (PAGs) by the radioimmunoassay (RIA) method. Transrectal ultrasonography was performed on day 25, 28 and 40 after AI to monitor pregnancy. The animals included in the data analysis were assigned ex post in pregnant (n = 50) and mortality (n = 12) groups. By ultrasonography, the predictive sign of mortality was the heartbeat. At day 25, the PAGs concentration was significant in predicting embryonic mortality with respect to ultrasonography and P4, at the cut-off of 1.1 ng/mL. At day 28, either PAGs, at a cut-off of 2.2 ng/mL, or ultrasonography, with no detection of heartbeat, were highly predictive of embryonic mortality. PAGs were the best marker (p < 0.05) for predicting embryonic mortality between 25 and 40 days of gestation in buffalo. Its utilization as a diagnostic tool can influence management decisions in order to improve farm reproductive management.
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