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Hernández-Avilés C, Ramírez-Agámez L, Varner DD, Raudsepp T, Love CC. Spermatozoal acrosome dysfunction and its role in stallion subfertility. J Equine Vet Sci 2024; 143:105213. [PMID: 39490453 DOI: 10.1016/j.jevs.2024.105213] [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: 09/06/2024] [Revised: 10/23/2024] [Accepted: 10/24/2024] [Indexed: 11/05/2024]
Abstract
Cases of stallion subfertility due to acrosome dysfunction have been recognized since the 1990s. While some of these were observed in stallions with reduced sperm motility and morphology, a more severe form has been reported in stallions with normal-to-excellent sperm quality parameters, which is also uniquely observed in individuals of the Thoroughbred registry. These stallions carry a susceptibility genotype (A/A-A A in the gene FKBP6, exon 5) for Impaired Acrosomal Exocytosis (IAE). Current clinical observations from our group have identified a few highly subfertile stallions from other breed registries that also display a lower ability to undergo acrosomal exocytosis (AE) but do not carry the A/A-A/A genotype. This document provides a concise review of the role of acrosome dysfunction as a cause of stallion subfertility, including methods to estimate acrosome function and clinical descriptions of IAE in TB and non-TB stallions.
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Affiliation(s)
- Camilo Hernández-Avilés
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, College Station, Texas 77843-4457, United States.
| | - Luisa Ramírez-Agámez
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, College Station, Texas 77843-4457, United States
| | - Dickson D Varner
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, College Station, Texas 77843-4457, United States
| | - Terje Raudsepp
- Molecular Cytogenetics Laboratory, Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States
| | - Charles C Love
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, College Station, Texas 77843-4457, United States
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Khan MZ, Chen W, Naz S, Liu X, Liang H, Chen Y, Kou X, Liu Y, Ashraf I, Han Y, Peng Y, Wang C, Zahoor M. Determinant genetic markers of semen quality in livestock. Front Endocrinol (Lausanne) 2024; 15:1456305. [PMID: 39429738 PMCID: PMC11489916 DOI: 10.3389/fendo.2024.1456305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/09/2024] [Indexed: 10/22/2024] Open
Abstract
The reproductive efficiency of livestock is crucial for agricultural productivity and economic sustainability. One critical factor in successful fertilization and the viability of offspring is the quality of semen. Poor semen quality, especially in frozen-thawed semen used in artificial insemination (AI) have been shown to influence conception outcomes, resulting a negative impact on livestock production. Recent advancements in genetic research have identified specific markers linked to semen quality traits in various livestock species, such as cattle, sheep, goats, pigs, buffalo, and equines. These genetic markers are essential in screening males for breeding suitability, which in turn enhances selective breeding programs. Understanding these markers is crucial for improving reproductive performance and increasing productivity in livestock populations. This review offers a comprehensive overview of the genetic markers associated with semen quality in key livestock. It explores the underlying genetic mechanisms and their practical implications in animal breeding and management. The review underscores the importance of integrating genetic insights into breeding strategies to optimize reproductive efficiency and ensure the sustainable development of livestock industries.
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Affiliation(s)
- Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Wenting Chen
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Saima Naz
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, Pakistan
| | - Xiaotong Liu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Huili Liang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yinghui Chen
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Xiyan Kou
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yihong Liu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Iqra Ashraf
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, Pakistan
| | - Ying Han
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yongdong Peng
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Muhammad Zahoor
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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Hernández-Avilés C, Ramírez-Agámez L, Weintraub ST, Scoggin CF, Davis BW, Raudsepp T, Varner DD, Love CC. Proteomic analysis of sperm from fertile stallions and subfertile stallions due to impaired acrosomal exocytosis. Sci Rep 2024; 14:12446. [PMID: 38816557 PMCID: PMC11139894 DOI: 10.1038/s41598-024-63410-3] [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: 03/29/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Thoroughbred stallions that carry a double-homozygous genotype A/A-A/A for SNPs rs397316122 and rs69101140 in exon 5 of the FKBP6 gene (chr13; EquCab3.0) are uniquely subfertile due to impaired acrosomal exocytosis (IAE). In this study, the sperm proteome in frozen/thawed semen from subfertile Thoroughbred stallions was studied and compared to that of frozen/thawed sperm from fertile Thoroughbred stallions. A total of 2,220 proteins was identified, of which 140 proteins were found to be differentially abundant in sperm from the subfertile stallions compared to that of fertile stallions (83 less and 57 more abundant). Proteins of differential abundance in sperm from the subfertile stallions were mainly overrepresented in the "metabolism" and the "metabolism of lipids" pathways. One of these proteins, arylsulfatase F (ARSF), was studied by immunofluorescence. A lower proportion of sperm displaying ARSF signal at the acrosome region was observed in sperm from subfertile Thoroughbred stallions. In addition, heterologous zona pellucida binding assays revealed that sperm from subfertile Thoroughbred stallions bound at a lower proportion to zonae pellucidae than sperm from fertile Thoroughbred stallions. In conclusion, a group of differential abundance proteins, including some of acrosome origin, were identified in sperm from subfertile stallions with acrosome dysfunction.
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Affiliation(s)
- Camilo Hernández-Avilés
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA.
| | - Luisa Ramírez-Agámez
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Charles F Scoggin
- LeBlanc Reproduction Center, Rood & Riddle Equine Hospital, Lexington, KY, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Dickson D Varner
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA
| | - Charles C Love
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA
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Waqas MS, Arroyo E, Tibary A. Diagnostic Approach to Equine Testicular Disorders. Vet Sci 2024; 11:243. [PMID: 38921990 PMCID: PMC11209109 DOI: 10.3390/vetsci11060243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
Management of breeding stallions is crucial to equine reproduction. The longevity of the breeding career is the ultimate objective, whether the stallion is used for natural cover or for semen collection and artificial insemination. Stud farm veterinarians should be aware of the techniques used to evaluate testicular function and the diagnostic approach to testicular disorders in cases of emergency. This paper presents the clinical methods used to evaluate testicular health, including palpation, ultrasonography, biopsy, and fine-needle aspiration. The discussion of testicular disorders is broken down into four categories: congenital disorders (cryptorchidism, monorchidism, and testicular hypoplasia), differential diagnosis of scrotal enlargement, differential diagnosis of causes of progressive testicular enlargement, and differential diagnosis of testicular asymmetry or reduction in size with an emphasis on testicular degeneration. The sudden increase in testicular size is often accompanied by severe clinical signs and is a major cause for referral of stallion for surgery. Testicular disorders are illustrated with clinical cases seen by the authors.
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Affiliation(s)
- Muhammad-Salman Waqas
- Comparative Theriogenology, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Center for Reproductive Biology, Washington State University, Pullman, WA 99163, USA;
| | - Eduardo Arroyo
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Ahmed Tibary
- Comparative Theriogenology, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Center for Reproductive Biology, Washington State University, Pullman, WA 99163, USA;
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Vigolo V, Gautier C, Ertl R, Aurich C, Falomo ME. Protamine 2 and phospholipase C zeta 1 are possible biomarkers for the diagnosis of male subfertility in frozen-thawed stallion semen. Theriogenology 2024; 215:343-350. [PMID: 38142472 DOI: 10.1016/j.theriogenology.2023.12.012] [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: 09/25/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023]
Abstract
Subfertility is one of the main issues in horse breeding and the study of mRNAs in sperm might help in elucidating the reasons that lead to this diagnosis. The present study aims at assessing the differences in the expression of 10 potential candidate genes in stallions of different fertility. Frozen-thawed semen of 29 stallions was included. Each sample was classified into two groups according to pregnancy rates (PR) achieved with this semen: "good fertility" (GF; n = 17; PR ≥ 30 %) or "poor fertility" (PF; n = 12; PR <20 %). All stallions underwent a breeding soundness examination (BSE) before semen production and were only included into the semen cryopreservation program when raw semen characteristics at BSE met minimal requirements. Semen was cryopreserved following European Union regulations and all stallions met the respective health requirements. Each sample was assessed for concentration (NucleoCounter SP-100), motility (CASA), membrane functionality (SYBR-14/PI), mitochondrial membrane potential (JC-1), morphology (SpermacStain), acrosome integrity (SpermacStain), membrane integrity (HOS test) and chromatin integrity (Aniline blue). Sperm RNAs were extracted using the Direct-zol RNA Miniprep Kit (Zymo Research) and RT-qPCR was performed for each target gene. ACTB and RPL32 were included as reference genes (RGs) for normalization. For each variable of each group, mean, standard deviation and SEM were calculated. The difference in gene expression levels between the GF and PF group were analyzed using the Mann-Whitney U test and Spearman's rank correlation. Significant results were considered with p < 0.05. Sperm quality parameters did not differ significantly between the two groups except for concentration, that was significantly higher in GF (p = 0.043). In GF a positive correlation was identified for PRM1/PRM2 with r = +0.6, while PRM1/ACR (r = -0.495), PRM2/ZPBP (r = -0.645) and CRISP3/ACR (r = -0.551) were inversely correlated. In PF direct correlations were registered for PRM1/PRM2 (r = +0.629), PRM1/PRM3 (r = +0.657), PRM2/SPA17 (r = +0.685), SPA17/PLCZ1 (r = +0.786) and PRM3/ACR (r = +0.627). In the total sample (GF + PF), positive correlations were detected for PRM1/PRM2 (r = +0.625), PRM1/PRM3 (r = +0.368); PRM2/SPA17 (r = +0.465), SPA17/PLCZ1 (r = +0.637) and PLCZ1/ZAN (r = +0.587). Only two of the genes considered were differentially expressed in the 2 groups: PRM2 and PLCZ1, that were significantly (p < 0.05) overexpressed in the GF group. Stallions frozen-thawed semen with higher expression levels of PRM2 and PLCZ1 are more likely to belong to animals with a good pregnancy rate. Further studies are needed to investigate the role of sperm transcripts in male subfertility in stallions.
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Affiliation(s)
- Veronica Vigolo
- Department of Animal Medicine, Production and Health (MAPS), Università di Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy; Artificial Insemination and Embryo Transfer, Department for Small Animals and Horses, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Camille Gautier
- Artificial Insemination and Embryo Transfer, Department for Small Animals and Horses, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Christine Aurich
- Artificial Insemination and Embryo Transfer, Department for Small Animals and Horses, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Maria Elena Falomo
- Department of Animal Medicine, Production and Health (MAPS), Università di Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy
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Gonzalez-Castro RA, Carnevale EM. Phospholipase C Zeta 1 (PLCZ1): The Function and Potential for Fertility Assessment and In Vitro Embryo Production in Cattle and Horses. Vet Sci 2023; 10:698. [PMID: 38133249 PMCID: PMC10747197 DOI: 10.3390/vetsci10120698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Phospholipase C Zeta 1 (PLCZ1) is considered a major sperm-borne oocyte activation factor. After gamete fusion, PLCZ1 triggers calcium oscillations in the oocyte, resulting in oocyte activation. In assisted fertilization, oocyte activation failure is a major cause of low fertility. Most cases of oocyte activation failures in humans related to male infertility are associated with gene mutations and/or altered PLCZ1. Consequently, PLCZ1 evaluation could be an effective diagnostic marker and predictor of sperm fertilizing potential for in vivo and in vitro embryo production. The characterization of PLCZ1 has been principally investigated in men and mice, with less known about the PLCZ1 impact on assisted reproduction in other species, such as cattle and horses. In horses, sperm PLCZ1 varies among stallions, and sperm populations with high PLCZ1 are associated with cleavage after intracytoplasmic sperm injection (ICSI). In contrast, bull sperm is less able to initiate calcium oscillations and undergo nuclear remodeling, resulting in poor cleavage after ICSI. Advantageously, injections of PLCZ1 are able to rescue oocyte failure in mouse oocytes after ICSI, promoting full development and birth. However, further research is needed to optimize PLCZ1 diagnostic tests for consistent association with fertility and to determine whether PLCZ1 as an oocyte-activating treatment is a physiological, efficient, and safe method for improving assisted fertilization in cattle and horses.
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Affiliation(s)
| | - Elaine M. Carnevale
- Equine Reproduction Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA;
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Hernández-Avilés C, Ramírez-Agámez L, Varner DD, Love CC. Lactate-induced spontaneous acrosomal exocytosis as a method to study acrosome function in stallion sperm. Theriogenology 2023; 210:169-181. [PMID: 37517302 DOI: 10.1016/j.theriogenology.2023.07.024] [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: 05/31/2023] [Revised: 07/13/2023] [Accepted: 07/22/2023] [Indexed: 08/01/2023]
Abstract
Evaluation of acrosome function in stallion sperm is mostly based on the use of inducers of acrosomal exocytosis (AE), such as the calcium ionophore A23187 or progesterone. Recently, it has been reported that incubation of stallion sperm under presumed capacitating conditions (i.e., medium formulated with calcium, bicarbonate, and bovine serum albumin) using a lactate-only containing medium (Lac-MW) results in a high rate of spontaneous AE in viable sperm (AE/Viable). In the current study, we developed an alternative assay of acrosome function for stallion sperm following the incubation of sperm in a medium formulated only with lactate as an energy substrate (Lac-MW). In Experiment 1, freshly ejaculated stallion sperm was incubated with 10 μM A23187, Lac-MW, or Control, for up to 6 h under capacitating conditions. The percentages of motile sperm, viable sperm, total AE (Total AE), and AE in viable sperm (AE/Viable) were compared among treatment groups. Incubation in Lac-MW, but not with Control or A23187, resulted in a time-dependent increase in the percentage of AE/Viable, as determined by flow cytometry, particularly at 4 and 6 h of incubation (P < 0.05). In Experiment 2, freshly ejaculated sperm was incubated in Lac-MW for up to 6 h, and the occurrence of protein tyrosine phosphorylation and AE/Viable were determined. At 4h and 6h of incubation in Lac-MW, ∼40% of the sperm displayed a protein tyrosine phosphorylation immunofluorescence pattern that coincides with that recently associated with stallion sperm capacitation (i.e., immunofluorescence signal at the acrosome and midpiece). In Experiment 3, the rate of AE/Viable sperm was compared among freshly ejaculated, cool-stored, and frozen/thawed stallion sperm. Except at 2h incubation in Lac-MW, differences in mean AE/Viable among fresh, cool-stored, and frozen/thawed sperm were not observed (P > 0.05). In Experiment 4, the relationship between Total AE (A23187), or AE/Viable (Lac-MW), and in vivo fertility of 5 stallions was determined. A linear relationship was observed between mean AE/Viable and the per-cycle (r = 0.93; P < 0.05) and seasonal (r = 0.66; P < 0.05) pregnancy rates of five stallions used for artificial insemination with cool-stored semen. In Experiment 5, frozen/thawed sperm from subfertile Thoroughbred (TB) stallions, known to carry the susceptibility genotype for Impaired Acrosomal Exocytosis (IAE; FKBP6 A/A-A/A) was evaluated following incubation in Lac-MW. Sperm from subfertile TB stallions with IAE had lower mean AE/Viable, at both 4h and 6h incubation in Lac-MW, when compared to that of fertile control stallions (P < 0.05). Overall, the Lac-MW model validated in the current study may be a useful complementary assay to evaluate the ability of stallion sperm to physiologically undergo AE and to study stallion fertility potential. This acrosome function assay can be used to evaluate fresh, cool-stored, or frozen/thawed stallion sperm, and describes a strong linear relationship with in vivo-fertility of stallions used in artificial insemination programs.
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Affiliation(s)
- Camilo Hernández-Avilés
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4475, USA.
| | - Luisa Ramírez-Agámez
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4475, USA
| | - Dickson D Varner
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4475, USA
| | - Charles C Love
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4475, USA
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Bhardwaj A, Tandon G, Pal Y, Sharma NK, Nayan V, Soni S, Iquebal MA, Jaiswal S, Legha RA, Talluri TR, Bhattacharya TK, Kumar D, Rai A, Tripathi BN. Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds. Genes (Basel) 2023; 14:1623. [PMID: 37628674 PMCID: PMC10454598 DOI: 10.3390/genes14081623] [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: 03/28/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.
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Affiliation(s)
- Anuradha Bhardwaj
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | - Gitanjali Tandon
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Yash Pal
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | - Nitesh Kumar Sharma
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar 125001, India;
| | - Sonali Soni
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Ram Avatar Legha
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | | | | | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - B. N. Tripathi
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110001, India
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9
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Pausch H, Mapel XM. Review: Genetic mutations affecting bull fertility. Animal 2023; 17 Suppl 1:100742. [PMID: 37567657 DOI: 10.1016/j.animal.2023.100742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 08/13/2023] Open
Abstract
Cattle are a well-suited "model organism" to study the genetic underpinnings of variation in male reproductive performance. The adoption of artificial insemination and genomic prediction in many cattle breeds provide access to microarray-derived genotypes and repeated measurements for semen quality and insemination success in several thousand bulls. Similar-sized mapping cohorts with phenotypes for male fertility are not available for most other species precluding powerful association testing. The repeated measurements of the artificial insemination bulls' semen quality enable the differentiation between transient and biologically relevant trait fluctuations, and thus, are an ideal source of phenotypes for variance components estimation and genome-wide association testing. Genome-wide case-control association testing involving bulls with either aberrant sperm quality or low insemination success revealed several causal recessive loss-of-function alleles underpinning monogenic reproductive disorders. These variants are routinely monitored with customised genotyping arrays in the male selection candidates to avoid the use of subfertile or infertile bulls for artificial insemination and natural service. Genome-wide association studies with quantitative measurements of semen quality and insemination success revealed quantitative trait loci for male fertility, but the underlying causal variants remain largely unknown. Moreover, these loci explain only a small part of the heritability of male fertility. Integrating genome-wide association studies with gene expression and other omics data from male reproductive tissues is required for the fine-mapping of candidate causal variants underlying variation in male reproductive performance in cattle.
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Affiliation(s)
- Hubert Pausch
- Animal Genomics, Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland.
| | - Xena Marie Mapel
- Animal Genomics, Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
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10
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The stallion sperm acrosome: Considerations from a research and clinical perspective. Theriogenology 2023; 196:121-149. [PMID: 36413868 DOI: 10.1016/j.theriogenology.2022.11.012] [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: 08/30/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
During the fertilization process, the interaction between the sperm and the oocyte is mediated by a process known as acrosomal exocytosis (AE). Although the role of the sperm acrosome on fertilization has been studied extensively over the last 70 years, little is known about the molecular mechanisms that govern acrosomal function, particularly in species other than mice or humans. Even though subfertility due to acrosomal dysfunction is less common in large animals than in humans, the evaluation of sperm acrosomal function should be considered not only as a complementary but a routine test when individuals are selected for breeding potential. This certainly holds true for stallions, which might display lower levels of fertility in the face of "acceptable" sperm quality parameters determined by conventional sperm assays. Nowadays, the use of high throughput technologies such as flow cytometry or mass spectrometry-based proteomic analysis is commonplace in the research arena. Such techniques can also be implemented in clinical scenarios of males with "idiopathic" subfertility. The current review focuses on the sperm acrosome, with particular emphasis on the stallion. We aim to describe the physiological events that lead to the acrosome formation within the testis, the role of very specific acrosomal proteins during AE, the methods to study the occurrence of AE under in vitro conditions, and the potential use of molecular biology techniques to discover new markers of acrosomal function and subfertility associated with acrosomal dysfunction in stallions.
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11
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Nikitkina EV, Dementieva NV, Shcherbakov YS, Atroshchenko MM, Kudinov AA, Samoylov OI, Pozovnikova MV, Dysin AP, Krutikova AA, Musidray AA, Mitrofanova OV, Plemyashov KV, Griffin DK, Romanov MN. Genome-wide association study for frozen-thawed sperm motility in stallions across various horse breeds. Anim Biosci 2022; 35:1827-1838. [PMID: 35240017 PMCID: PMC9659452 DOI: 10.5713/ab.21.0504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/22/2022] [Accepted: 02/23/2022] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds. METHODS Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), progressive motility after freezing (FPM), and the difference between PM and FPM. The respective DNA samples from these stallions were genotyped using Axiom Equine Genotyping Array. RESULTS We performed a GWAS search for single nucleotide polymorphism (SNP) markers and potential genes related to motility properties of frozen-thawed semen in the stallions of various breeds. As a result of the GWAS analysis, two SNP markers, rs1141327473 and rs1149048772, were identified that were associated with preservation of the frozen-thawed stallion sperm motility, the relevant putative candidate genes being NME/NM23 family member 8 (NME8), olfactory receptor family 2 subfamily AP member 1 (OR2AP1), and olfactory receptor family 6 subfamily C member 4 (OR6C4). Potential implications of effects of these genes on sperm motility are herein discussed. CONCLUSION The GWAS results enabled us to localize novel SNPs and candidate genes for sperm motility in stallions. Implications of the study for horse breeding and genetics are a better understanding of genomic regions and candidate genes underlying stallion sperm quality, and improvement in horse reproduction and breeding techniques. The identified markers and genes for sperm cryotolerance and the respective genomic regions are promising candidates for further studying the biological processes in the formation and function of the stallion reproductive system.
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Affiliation(s)
- Elena V. Nikitkina
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Natalia V. Dementieva
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Yuri S. Shcherbakov
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Mikhail M. Atroshchenko
- All-Russian Research Institute for Horse Breeding, Rybnovsky District, Ryazan Oblast, 391105,
Russia
| | - Andrei A. Kudinov
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Oleg I. Samoylov
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Marina V. Pozovnikova
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Artem P. Dysin
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Anna A. Krutikova
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Artem A. Musidray
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Olga V. Mitrofanova
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
| | - Kirill V. Plemyashov
- Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, Tyarlevo, Pushkin, St. Petersburg, 196625,
Russia
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Hernández-Avilés C, Castaneda C, Raudsepp T, Varner DD, Love CC. The role of impaired acrosomal exocytosis (IAE) in stallion subfertility: A retrospective analysis of the clinical condition, and an update on its diagnosis by high throughput technologies. Theriogenology 2022; 186:40-49. [DOI: 10.1016/j.theriogenology.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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13
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Castaneda C, Juras R, Kjöllerström J, Hernandez Aviles C, Teague SR, Love CC, Cothran EG, Varner DD, Raudsepp T. Thoroughbred stallion fertility is significantly associated with FKBP6 genotype but not with inbreeding or the contribution of a leading sire. Anim Genet 2021; 52:813-823. [PMID: 34610162 DOI: 10.1111/age.13142] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/12/2022]
Abstract
This is a follow-up study to validate the previously detected association of the FKBP6 gene with stallion subfertility. Using a select cohort of 150 Thoroughbred stallions with detailed breeding records, we confirm significant association (P < 0.0001) between low per-cycle pregnancy rates (≤50%) and a combined A/A-A/A genotype of SNPs chr13:11 353 372G>A and chr13:11 353 436A>C in FKBP6 exon 5. We also show that stallion subfertility and the combined genotype A/A-A/A are not associated with the level of genetic diversity based on 12 autosomal microsatellite markers, or with pedigree-based inbreeding rate, or the extent of contribution of a leading Thoroughbred sire, Northern Dancer, in a stallion's pedigree. We develop a TaqMan allelic discrimination assay for the two SNPs to facilitate accurate and high-throughput genotyping. We determine allele, genotype and combined genotype frequencies of FKBP6 exon 5 SNPs in a global cohort of 518 Thoroughbreds (76% stallions or geldings and 24% mares) and show that the frequency of the A/A-A/A genotype is 4%. Because there is no similar association between the FKBP6 exon 5 genotype and stallion subfertility in Hanoverians, we suggest that the two SNPs are not causative but rather tagging a breed-specific haplotype with genetic variants unique to Thoroughbreds. Further WGS-based research is needed to identify the molecular causes underlying the observed genotype-phenotype association in Thoroughbred stallions.
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Affiliation(s)
- C Castaneda
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - R Juras
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - J Kjöllerström
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - C Hernandez Aviles
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - S R Teague
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - C C Love
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - E G Cothran
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - D D Varner
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
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14
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Laseca N, Anaya G, Peña Z, Pirosanto Y, Molina A, Demyda Peyrás S. Impaired Reproductive Function in Equines: From Genetics to Genomics. Animals (Basel) 2021; 11:393. [PMID: 33546520 PMCID: PMC7913728 DOI: 10.3390/ani11020393] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/15/2022] Open
Abstract
Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.
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Affiliation(s)
- Nora Laseca
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Gabriel Anaya
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Zahira Peña
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Yamila Pirosanto
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1900, Argentina;
- Consejo Superior de Investigaciones Científicas y Tecnológicas (CONICET), CCT-La Plata, La Plata 1900, Argentina
| | - Antonio Molina
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Sebastián Demyda Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1900, Argentina;
- Consejo Superior de Investigaciones Científicas y Tecnológicas (CONICET), CCT-La Plata, La Plata 1900, Argentina
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15
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Abstract
Reproductive disorders are genetically heterogeneous and complex; available genetic tests are limited to chromosome analysis and 1 susceptibility gene. Cytogenetic analysis should be the first test to confirm or rule out chromosomal aberrations. No causative genes/mutations are known. The only available genetic test for stallion subfertility is based on a susceptibility gene FKBP6. The ongoing progress in equine genomics will improve the status of genetic testing. However, because subfertile phenotypes do not facilitate collection of large numbers of samples or pedigrees, and clinical causes of many cases remain unknown, further progress requires constructive cross-talk between geneticists, clinicians, breeders, and owners.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Molecular Cytogenetics Laboratory, Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, Veterinary Research Building Room 306, 588 Raymond Stotzer Parkway, College Station, TX 77843-4458, USA.
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16
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Abstract
High-quality genomic tools have been integral in understanding genomic architecture and function in the modern-day horse. The equine genetics community has a long tradition of pooling resources to develop genomic tools. Since the equine genome was sequenced in 2006, several iterations of high throughput genotyping arrays have been developed and released, enabling rapid and cost-effective genotyping. This review highlights the design considerations of each iteration, focusing on data available during development and outlining considerations in selecting the genetic variants included on each array. Additionally, we outline recent applications of equine genotyping arrays as well as future prospects and applications.
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Affiliation(s)
- Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Avenue, St Paul, MN 55108, USA.
| | - Molly E McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Avenue, St Paul, MN 55108, USA. https://twitter.com/Molly_McCue_DVM
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17
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Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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18
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Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 2017; 18:565. [PMID: 28750625 PMCID: PMC5530493 DOI: 10.1186/s12864-017-3943-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 07/13/2017] [Indexed: 12/30/2022] Open
Abstract
Background To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Results Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. Conclusions Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3943-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ernest Bailey
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Danika L Bannasch
- School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Eric Barrey
- Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-Saclay, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, 76100, Rehovot, Israel
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Samantha A Brooks
- Department of Animal Science, University of Florida, Gainesville, FL, USA
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Hannover, Germany
| | - Ruedi Fries
- Lehrstuhl für Tierzucht der Technischen Universität München, Liesel-Beckmann-Strasse 1, 85354, Freising, Germany
| | - Carrie J Finno
- School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3001, Bern, Switzerland
| | - Bianca Haase
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney, Regimental Drive, B19-301 RMC Gunn, Sydney, NSW, 2006, Australia
| | | | - Ted Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001, Bern, Switzerland
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores, Angra do heroísmo, Portugal
| | - Núria Mach
- Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-Saclay, AgroParisTech, 78350, Jouy-en-Josas, France
| | | | - James N MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Annette McCoy
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Hannover, Germany
| | - Cecilia Penedo
- Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA
| | - Sagi Polani
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, 76100, Rehovot, Israel
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580, Avenches, Switzerland
| | - Imke Tammen
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney, Regimental Drive, B19-301 RMC Gunn, Sydney, NSW, 2006, Australia
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany.,Department of Animal Sciences, Functional Breeding Group, Georg-August University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany
| | - Andrea Verini-Supplizi
- Department of Veterinary Medicine - Sport Horse Research Centre, University of Perugia, Perugia, Italy
| | - Claire M Wade
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney, Regimental Drive, B19-301 RMC Gunn, Sydney, NSW, 2006, Australia
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Molly E McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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19
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Abstract
Stallion semen evaluation is an important part of the breeding soundness evaluation. The results of the semen evaluation cannot be interpreted without a thorough knowledge of the mare and management effects that may have played a role or may affect the potential fertility of the stallion evaluated. There are considerations and limitations that the clinician should understand about each test. Any sperm quality test must be interpreted with a clear understanding of how it relates to fertility.
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Affiliation(s)
- Charles C Love
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA.
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20
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Li B, Luo H, Weng Q, Wang S, Pan Z, Xie Z, Wu W, Liu H, Li Q. Differential DNA methylation of the meiosis-specific geneFKBP6in testes of yak and cattle-yak hybrids. Reprod Domest Anim 2016; 51:1030-1038. [DOI: 10.1111/rda.12794] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/17/2016] [Indexed: 12/15/2022]
Affiliation(s)
- B Li
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - H Luo
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Q Weng
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - S Wang
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Z Pan
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Z Xie
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - W Wu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - H Liu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Q Li
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
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21
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22
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Genome-wide association study for semen quality traits in German Warmblood stallions. Anim Reprod Sci 2016; 171:81-6. [DOI: 10.1016/j.anireprosci.2016.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 12/16/2022]
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23
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Kjöllerström HJ, do Mar Oom M, Chowdhary BP, Raudsepp T. Fertility Assessment in Sorraia Stallions by Sperm-Fish and Fkbp6 Genotyping. Reprod Domest Anim 2016; 51:351-9. [PMID: 27020485 DOI: 10.1111/rda.12686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 02/27/2016] [Indexed: 01/10/2023]
Abstract
The Sorraia, a critically endangered indigenous Iberian horse breed, is characterized by low genetic variability, high rate of inbreeding, bad sperm quality and subfertility. Here, we studied 11 phenotypically normal but subfertile Sorraia stallions by karyotyping, sex chromosome sperm-FISH and molecular analysis of FKBP6 - a susceptibility locus for impaired acrosome reaction (IAR). The stallions had normal sperm concentration (>300 million cells/ml), but the numbers of progressively motile sperm (21%) and morphologically normal sperm (28%) were invariably low. All stallions had a normal 64,XY karyotype. The majority of sperm (89%) had normal haploid sex chromosome content, although 11% of sperm carried various sex chromosome aneuploidies. No correlation was found between the percentage of sperm sex chromosome abnormalities and inbreeding, sperm morphology or stallion age. Direct sequencing of FKBP6 exon 4 for SNPs g.11040315G>A and g.11040379C>A revealed that none of the stallions had the susceptibility genotype (A/A-A/A) for IAR. Instead, all animals had a G/G-A/A genotype - a testimony of low genetic variability. The findings ruled out chromosomal abnormalities and genetic predisposition for IAR as contributing factors for subfertility. However, low fertility of the Sorraia stallions could be partly attributed to relatively higher rate of sex chromosome aneuploidies in the sperm.
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Affiliation(s)
- H J Kjöllerström
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - M do Mar Oom
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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Rode K, Sieme H, Otzen H, Schwennen C, Lüpke M, Richterich P, Schrimpf R, Distl O, Brehm R. Effects of Repeated Testicular Biopsies in Adult Warmblood Stallions and Their Diagnostic Potential. J Equine Vet Sci 2016. [DOI: 10.1016/j.jevs.2016.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Ni B, Lin Y, Sun L, Zhu M, Li Z, Wang H, Yu J, Guo X, Zuo X, Dong J, Xia Y, Wen Y, Wu H, Li H, Zhu Y, Ping P, Chen X, Dai J, Jiang Y, Xu P, Du Q, Yao B, Weng N, Lu H, Wang Z, Zhu X, Yang X, Xiong C, Ma H, Jin G, Xu J, Wang X, Zhou Z, Liu J, Zhang X, Conrad DF, Hu Z, Sha J. Low-frequency germline variants across 6p22.2-6p21.33 are associated with non-obstructive azoospermia in Han Chinese men. Hum Mol Genet 2015; 24:5628-5636. [PMID: 26199320 PMCID: PMC4902876 DOI: 10.1093/hmg/ddv257] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 07/01/2015] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified several common loci contributing to non-obstructive azoospermia (NOA). However, a substantial fraction of NOA heritability remains undefined, especially those low-frequency [defined here as having a minor allele frequency (MAF) between 0.5 and 5%] and rare (MAF below 0.5%) variants. Here, we performed a 3-stage exome-wide association study in Han Chinese men to evaluate the role of low-frequency or rare germline variants in NOA development. The discovery stage included 962 NOA cases and 1348 healthy male controls genotyped by exome chips and was followed by a 2-stage replication with an additional 2168 cases and 5248 controls. We identified three low-frequency variants located at 6p22.2 (rs2298090 in HIST1H1E encoding p.Lys152Arg: OR = 0.30, P = 2.40 × 10(-16)) and 6p21.33 (rs200847762 in FKBPL encoding p.Pro137Leu: OR = 0.11, P = 3.77 × 10(-16); rs11754464 in MSH5: OR = 1.78, P = 3.71 × 10(-7)) associated with NOA risk after Bonferroni correction. In summary, we report an instance of newly identified signals for NOA risk in genes previously undetected through GWAS on 6p22.2-6p21.33 in a Chinese population and highlight the role of low-frequency variants with a large effect in the process of spermatogenesis.
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Affiliation(s)
- Bixian Ni
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Yuan Lin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui 230022, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Zheng Li
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Hui Wang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Jun Yu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Histology and Embryology, Nanjing Medical University, Nanjing 210029, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Histology and Embryology, Nanjing Medical University, Nanjing 210029, China
| | - Xianbo Zuo
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui 230022, China
| | - Jing Dong
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Toxicology and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yang Wen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Hao Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Histology and Embryology, Nanjing Medical University, Nanjing 210029, China
| | - Honggang Li
- Family Planning Research Institute, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430032, China
| | - Yong Zhu
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Ping Ping
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xiangfeng Chen
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Yue Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Peng Xu
- Jinghua Hospital, Shenyang Dongfang Medical Group, Shenyang 110004, China
| | - Qiang Du
- Department of Reproduction, Shengjing Hospital, China Medical University, Shenyang 110004, China
| | - Bing Yao
- Department of Andrology, Nanjing Jinling Hospital, Nanjing 210029, China
| | - Ning Weng
- Jinghua Hospital, Shenyang Dongfang Medical Group, Shenyang 110004, China
| | - Hui Lu
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Zhuqing Wang
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xiaobin Zhu
- Shanghai Human Sperm Bank, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xiaoyu Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Chenliang Xiong
- Family Planning Research Institute, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430032, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and
| | - Jianfeng Xu
- Department of Urology, Huashan Hospital, Shanghai 200052, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Toxicology and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zuomin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Histology and Embryology, Nanjing Medical University, Nanjing 210029, China
| | - Jiayin Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui 230022, China
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA, Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200052, China,
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China, Department of Histology and Embryology, Nanjing Medical University, Nanjing 210029, China,
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26
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McQueen CM, Dindot SV, Foster MJ, Cohen ND. Genetic Susceptibility to Rhodococcus equi. J Vet Intern Med 2015; 29:1648-59. [PMID: 26340305 PMCID: PMC4895676 DOI: 10.1111/jvim.13616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023] Open
Abstract
Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).
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Affiliation(s)
- C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
| | - S V Dindot
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - M J Foster
- Medical Sciences Library, Texas A&M University, College Station, TX
| | - N D Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
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27
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Schrimpf R, Metzger J, Martinsson G, Sieme H, Distl O. Implication of FKBP6
for Male Fertility in Horses. Reprod Domest Anim 2014; 50:195-199. [DOI: 10.1111/rda.12467] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/16/2014] [Indexed: 11/29/2022]
Affiliation(s)
- R Schrimpf
- Institute for Animal Breeding and Genetics; University of Veterinary Medicine Hannover; Hannover Germany
| | - J Metzger
- Institute for Animal Breeding and Genetics; University of Veterinary Medicine Hannover; Hannover Germany
| | | | - H Sieme
- Clinic for Horses; Unit for Reproduction Medicine; University of Veterinary Medicine Hannover; Hannover Germany
| | - O Distl
- Institute for Animal Breeding and Genetics; University of Veterinary Medicine Hannover; Hannover Germany
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28
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Schrimpf R, Dierks C, Martinsson G, Sieme H, Distl O. Genome-wide association study identifies phospholipase C zeta 1 (PLCz1) as a stallion fertility locus in Hanoverian warmblood horses. PLoS One 2014; 9:e109675. [PMID: 25354211 PMCID: PMC4212906 DOI: 10.1371/journal.pone.0109675] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/02/2014] [Indexed: 12/13/2022] Open
Abstract
A consistently high level of stallion fertility plays an economically important role in modern horse breeding. We performed a genome-wide association study for estimated breeding values of the paternal component of the pregnancy rate per estrus cycle (EBV-PAT) in Hanoverian stallions. A total of 228 Hanoverian stallions were genotyped using the Equine SNP50 Beadchip. The most significant association was found on horse chromosome 6 for a single nucleotide polymorphism (SNP) within phospholipase C zeta 1 (PLCz1). In the close neighbourhood to PLCz1 is located CAPZA3 (capping protein (actin filament) muscle Z-line, alpha 3). The gene PLCz1 encodes a protein essential for spermatogenesis and oocyte activation through sperm induced Ca2+-oscillation during fertilization. We derived equine gene models for PLCz1 and CAPZA3 based on cDNA and genomic DNA sequences. The equine PLCz1 had four different transcripts of which two contained a premature termination codon. Sequencing all exons and their flanking sequences using genomic DNA samples from 19 Hanoverian stallions revealed 47 polymorphisms within PLCz1 and one SNP within CAPZA3. Validation of these 48 polymorphisms in 237 Hanoverian stallions identified three intronic SNPs within PLCz1 as significantly associated with EBV-PAT. Bioinformatic analysis suggested regulatory effects for these SNPs via transcription factor binding sites or microRNAs. In conclusion, non-coding polymorphisms within PLCz1 were identified as conferring stallion fertility and PLCz1 as candidate locus for male fertility in Hanoverian warmblood. CAPZA3 could be eliminated as candidate gene for fertility in Hanoverian stallions.
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Affiliation(s)
- Rahel Schrimpf
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Claudia Dierks
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Harald Sieme
- Clinic for Horses, Unit for Reproduction Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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29
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Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014; 9:e98710. [PMID: 24892408 PMCID: PMC4043894 DOI: 10.1371/journal.pone.0098710] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/04/2014] [Indexed: 11/30/2022] Open
Abstract
Pneumonia caused by Rhodococcus equi is a common cause of disease and death in foals. Although agent and environmental factors contribute to the incidence of this disease, the genetic factors influencing the clinical outcomes of R. equi pneumonia are ill-defined. Here, we performed independent single nucleotide polymorphism (SNP)- and copy number variant (CNV)-based genome-wide association studies to identify genomic loci associated with R. equi pneumonia in foals. Foals at a large Quarter Horse breeding farm were categorized into 3 groups: 1) foals with R. equi pneumonia (clinical group [N = 43]); 2) foals with ultrasonographic evidence of pulmonary lesions that never developed clinical signs of pneumonia (subclinical group [N = 156]); and, 3) foals without clinical signs or ultrasonographic evidence of pneumonia (unaffected group [N = 49]). From each group, 24 foals were randomly selected and used for independent SNP- and CNV-based genome-wide association studies (GWAS). The SNP-based GWAS identified a region on chromosome 26 that had moderate evidence of association with R. equi pneumonia when comparing clinical and subclinical foals. A joint analysis including all study foals revealed a 3- to 4-fold increase in odds of disease for a homozygous SNP within the associated region when comparing the clinical group with either of the other 2 groups of foals or their combination. The region contains the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) gene, which is involved in neutrophil function. No associations were identified in the CNV-based GWAS. Collectively, these data identify a region on chromosome 26 associated with R. equi pneumonia in foals, providing evidence that genetic factors may indeed contribute to this important disease of foals.
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