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Sievers J, Distl O. Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse. Genes (Basel) 2025; 16:327. [PMID: 40149478 PMCID: PMC11942601 DOI: 10.3390/genes16030327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2025] [Revised: 03/01/2025] [Accepted: 03/03/2025] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND/OBJECTIVES The Rhenish German draught horse is an endangered German horse breed, originally used as working horse in agriculture. Therefore, the objective of this study was to evaluate the breed's genetic diversity using pedigree and genomic data in order to analyze classical and ancestral pedigree-based inbreeding, runs of homozygosity, ROH islands, and consensus ROH. METHODS We studied the genome-wide genotype data of 675 Rhenish German draught horses and collated pedigree-based inbreeding coefficients for these horses. The final dataset contained 64,737 autosomal SNPs. RESULTS The average number of ROH per individual was 43.17 ± 9.459 with an average ROH length of 5.087 Mb ± 1.03 Mb. The average genomic inbreeding coefficient FROH was 0.099 ± 0.03, the pedigree-based classical inbreeding coefficient FPED 0.016 ± 0.021, and ancestral inbreeding coefficients ranged from 0.03 (Fa_Kal) to 0.51 (Ahc). Most ROH (55.85%) were classified into the length category of 2-4 Mb, and the minority (0.43%) into the length category of >32 Mb. The effective population size (Ne) decreased in the last seven generations (~65 years) from 189.43 to 58.55. Consensus ROH shared by 45% of the horses were located on equine chromosomes 3 and 7, while ROH islands exceeding the 99th percentile threshold were identified on chromosomes 2, 3, 5, 7, 9, 10, and 11. These ROH islands contained genes associated with morphological development (HOXB cluster), fertility (AURKC, NLRP5, and DLX3), muscle growth, and skin physiology (ZNF gene cluster). CONCLUSIONS This study highlights how important it is to monitor genetic diversity in endangered populations with genomic data. The results of this study will help to develop breeding strategies to ensure the conservation of the German Rhenish draught horse population and show whether favorable alleles from the overrepresented candidate genes within ROH were transmitted to the next generation.
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Affiliation(s)
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
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Yu W, Peng X, Cai X, Xu H, Wang C, Liu F, Luo D, Tang S, Wang Y, Du X, Gao Y, Tian T, Liang S, Chen C, Kim NH, Yuan B, Zhang J, Jiang H. Transcriptome analysis of porcine oocytes during postovulatory aging. Theriogenology 2024; 226:387-399. [PMID: 38821784 DOI: 10.1016/j.theriogenology.2024.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Decreased oocyte quality is a significant contributor to the decline in female fertility that accompanies aging in mammals. Oocytes rely on mRNA stores to support their survival and integrity during the protracted period of transcriptional dormancy as they await ovulation. However, the changes in mRNA levels and interactions that occur during porcine oocyte maturation and aging remain unclear. In this study, the mRNA expression profiles of porcine oocytes during the GV, MII, and aging (24 h after the MII stage) stages were explored by transcriptome sequencing to identify the key genes and pathways that affect oocyte maturation and postovulatory aging. The results showed that 10,929 genes were coexpressed in porcine oocytes during the GV stage, MII stage, and aging stage. In addition, 3037 genes were expressed only in the GV stage, 535 genes were expressed only in the MII stage, and 120 genes were expressed only in the aging stage. The correlation index between the GV and MII stages (0.535) was markedly lower than that between the MII and aging stages (0.942). A total of 3237 genes, which included 1408 upregulated and 1829 downregulated genes, were differentially expressed during porcine oocyte postovulatory aging (aging stage vs. MII stage). Key functional genes, including ATP2A1, ATP2A3, ATP2B2, NDUFS1, NDUFA2, NDUFAF3, SREBF1, CYP11A1, CYP3A29, GPx4, CCP110, STMN1, SPC25, Sirt2, SYCP3, Fascin1/2, PFN1, Cofilin, Tmod3, FLNA, LRKK2, CHEK1/2, DDB1/2, DDIT4L, and TONSL, and key molecular pathways, such as the calcium signaling pathway, MAPK signaling pathway, TGF-β signaling pathway, PI3K/Akt signaling pathway, FoxO signaling pathway, gap junctions, and thermogenesis, were found in abundance during porcine postovulatory aging. These genes are mainly involved in the regulation of many biological processes, such as oxidative stress, calcium homeostasis, mitochondrial function, and lipid peroxidation, during porcine oocyte postovulatory aging. These results contribute to a more in-depth understanding of the biological changes, key regulatory genes and related biological pathways that are involved in oocyte aging and provide a theoretical basis for improving the efficiency of porcine embryo production in vitro and in vivo.
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Affiliation(s)
- Wenjie Yu
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Xinyue Peng
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Xiaoshi Cai
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Hong Xu
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Chen Wang
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Fengjiao Liu
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Dan Luo
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Shuhan Tang
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Yue Wang
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Xiaoxue Du
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Yan Gao
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Tian Tian
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China; Center of Reproductive Medicine & Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130062, Jilin, China
| | - Shuang Liang
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Chengzhen Chen
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Nam-Hyung Kim
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Bao Yuan
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Jiabao Zhang
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China
| | - Hao Jiang
- College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, China.
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Cortez JV, Hardwicke K, Cuervo-Arango J, Grupen CG. Cloning horses by somatic cell nuclear transfer: Effects of oocyte source on development to foaling. Theriogenology 2023; 203:99-108. [PMID: 37011429 DOI: 10.1016/j.theriogenology.2023.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
The cloning of horses is a commercial reality, yet the availability of oocytes for cloned embryo production remains a major limitation. Immature oocytes collected from abattoir-sourced ovaries or from live mares by ovum pick-up (OPU) have both been used to generate cloned foals. However, the reported cloning efficiencies are difficult to compare due to the different somatic cell nuclear transfer (SCNT) techniques and conditions used. The objective of this retrospective study was to compare the in vitro and in vivo development of equine SCNT embryos produced using oocytes recovered from abattoir-sourced ovaries and from live mares by OPU. A total of 1,128 oocytes were obtained, of which 668 were abattoir-derived and 460 were OPU-derived. The methods used for in vitro maturation and SCNT were identical for both oocyte groups, and the embryos were cultured in Dulbecco's Modified Eagle's Medium/Nutrient Mixture F-12 Ham medium supplemented with 10% fetal calf serum. Embryo development in vitro was assessed, and Day 7 blastocysts were transferred to recipient mares. The embryos were transferred fresh when possible, and a cohort of vitrified-thawed OPU-derived blastocysts was also transferred. Pregnancy outcomes were recorded at Days 14, 42 and 90 of gestation and at foaling. The rates of cleavage (68.7 ± 3.9% vs 62.4 ± 4.7%) and development to the blastocyst stage (34.6 ± 3.3% vs 25.6 ± 2.0%) were superior for OPU-derived embryos compared with abattoir-derived embryos (P < 0.05). Following transfer of Day 7 blastocysts to a total of 77 recipient mares, the pregnancy rates at Days 14 and 42 of gestation were 37.7% and 27.3%, respectively. Beyond Day 42, the percentages of recipient mares that still had a viable conceptus at Day 90 (84.6% vs 37.5%) and gave birth to a healthy foal (61.5% vs 12.5%) were greater for the OPU group compared with the abattoir group (P < 0.05). Surprisingly, more favourable pregnancy outcomes were achieved when blastocysts were vitrified for later transfer, probably because the uterine receptivity of the recipient mares was more ideal. A total of 12 cloned foals were born, 9 of which were viable. Given the differences observed between the two oocyte groups, the use of OPU-harvested oocytes for generating cloned foals is clearly advantageous. Continued research is essential to better understand the oocyte deficiencies and increase the efficiency of equine cloning.
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Derisoud E, Jouneau L, Dubois C, Archilla C, Jaszczyszyn Y, Legendre R, Daniel N, Peynot N, Dahirel M, Auclair-Ronzaud J, Wimel L, Duranthon V, Chavatte-Palmer P. Maternal age affects equine day 8 embryo gene expression both in trophoblast and inner cell mass. BMC Genomics 2022; 23:443. [PMID: 35705916 PMCID: PMC9199136 DOI: 10.1186/s12864-022-08593-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Breeding a mare until she is not fertile or even until her death is common in equine industry but the fertility decreases as the mare age increases. Embryo loss due to reduced embryo quality is partly accountable for this observation. Here, the effect of mare's age on blastocysts' gene expression was explored. Day 8 post-ovulation embryos were collected from multiparous young (YM, 6-year-old, N = 5) and older (OM, > 10-year-old, N = 6) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure or inner cell mass (ICM) enriched trophoblast, obtained by embryo bisection, were RNA sequenced. Deconvolution algorithm was used to discriminate gene expression in the ICM from that in the trophoblast. Differential expression was analyzed with embryo sex and diameter as cofactors. Functional annotation and classification of differentially expressed genes and gene set enrichment analysis were also performed. RESULTS Maternal aging did not affect embryo recovery rate, embryo diameter nor total RNA quantity. In both compartments, the expression of genes involved in mitochondria and protein metabolism were disturbed by maternal age, although more genes were affected in the ICM. Mitosis, signaling and adhesion pathways and embryo development were decreased in the ICM of embryos from old mares. In trophoblast, ion movement pathways were affected. CONCLUSIONS This is the first study showing that maternal age affects gene expression in the equine blastocyst, demonstrating significant effects as early as 10 years of age. These perturbations may affect further embryo development and contribute to decreased fertility due to aging.
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Affiliation(s)
- Emilie Derisoud
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.
| | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Cédric Dubois
- IFCE, Plateau technique de Chamberet, 19370, Chamberet, France
| | - Catherine Archilla
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Paris-Sud University F-91198, Gif-sur-Yvette, France
| | - Rachel Legendre
- Institut Pasteur-Bioinformatics and Biostatistics Hub-Department of Computational Biology, Paris, France
| | - Nathalie Daniel
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Michèle Dahirel
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | | | - Laurence Wimel
- IFCE, Plateau technique de Chamberet, 19370, Chamberet, France
| | - Véronique Duranthon
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.
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Derisoud E, Auclair-Ronzaud J, Palmer E, Robles M, Chavatte-Palmer P. Female age and parity in horses: how and why does it matter? Reprod Fertil Dev 2021; 34:52-116. [PMID: 35231230 DOI: 10.1071/rd21267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Although puberty can occur as early as 14-15months of age, depending on breed and use, the reproductive career of mares may continue to advanced ages. Once mares are used as broodmares, they will usually produce foals once a year until they become unfertile, and their productivity can be enhanced and/or prolonged through embryo technologies. There is a general consensus that old mares are less fertile, but maternal age and parity are confounding factors because nulliparous mares are usually younger and older mares are multiparous in most studies. This review shows that age critically affects cyclicity, folliculogenesis, oocyte and embryo quality as well as presence of oviductal masses and uterine tract function. Maternal parity has a non-linear effect. Primiparity has a major influence on placental and foal development, with smaller foals at the first gestation that remain smaller postnatally. After the first gestation, endometrial quality and uterine clearance capacities decline progressively with increasing parity and age, whilst placental and foal birthweight and milk production increase. These combined effects should be carefully balanced when breeding mares, in particular when choosing and caring for recipients and their foals.
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Affiliation(s)
- Emilie Derisoud
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; and Ecole Nationale Vétérinaire d'Alfort, BREED, 94700 Maisons-Alfort, France
| | | | - Eric Palmer
- Académie d'Agriculture de France, 75007 Paris, France
| | - Morgane Robles
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; and Ecole Nationale Vétérinaire d'Alfort, BREED, 94700 Maisons-Alfort, France; and INRS Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, H7V 1B7 Laval, QC, Canada
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; and Ecole Nationale Vétérinaire d'Alfort, BREED, 94700 Maisons-Alfort, France
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Orsolini MF, Meyers SA, Dini P. An Update on Semen Physiology, Technologies, and Selection Techniques for the Advancement of In Vitro Equine Embryo Production: Section II. Animals (Basel) 2021; 11:ani11113319. [PMID: 34828049 PMCID: PMC8614388 DOI: 10.3390/ani11113319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary In order to improve fertilization and pregnancy rates within artificial insemination or in vitro fertilization techniques in horses, producers may choose to select the best sperm within an ejaculate. In this paper, we review conventional and novel methods of sperm selection. Abstract As the use of assisted reproductive technologies (ART) and in vitro embryo production (IVP) expand in the equine industry, it has become necessary to further our understanding of available semen selection techniques. This segment of our two-section review will focus on the selection of spermatozoa based on quality and sex for equine intracytoplasmic sperm injection (ICSI), as well as current and future developments in sperm sorting technologies. Ultimately, novel methods of semen selection will be assessed based on their efficacy in other species and their relevance and future application towards ARTs in the horse.
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Affiliation(s)
- Morgan F. Orsolini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Stuart A. Meyers
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
- Correspondence:
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Benammar A, Derisoud E, Vialard F, Palmer E, Ayoubi JM, Poulain M, Chavatte-Palmer P. The Mare: A Pertinent Model for Human Assisted Reproductive Technologies? Animals (Basel) 2021; 11:2304. [PMID: 34438761 PMCID: PMC8388489 DOI: 10.3390/ani11082304] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/28/2021] [Accepted: 08/01/2021] [Indexed: 12/12/2022] Open
Abstract
Although there are large differences between horses and humans for reproductive anatomy, follicular dynamics, mono-ovulation, and embryo development kinetics until the blastocyst stage are similar. In contrast to humans, however, horses are seasonal animals and do not have a menstrual cycle. Moreover, horse implantation takes place 30 days later than in humans. In terms of artificial reproduction techniques (ART), oocytes are generally matured in vitro in horses because ovarian stimulation remains inefficient. This allows the collection of oocytes without hormonal treatments. In humans, in vivo matured oocytes are collected after ovarian stimulation. Subsequently, only intra-cytoplasmic sperm injection (ICSI) is performed in horses to produce embryos, whereas both in vitro fertilization and ICSI are applied in humans. Embryos are transferred only as blastocysts in horses. In contrast, four cells to blastocyst stage embryos are transferred in humans. Embryo and oocyte cryopreservation has been mastered in humans, but not completely in horses. Finally, both species share infertility concerns due to ageing and obesity. Thus, reciprocal knowledge could be gained through the comparative study of ART and infertility treatments both in woman and mare, even though the horse could not be used as a single model for human ART.
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Affiliation(s)
- Achraf Benammar
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; (A.B.); (E.D.); (F.V.); (J.M.A.); (M.P.)
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
- Department of Gynaecology and Obstetrics, Foch Hospital, 92150 Suresnes, France
| | - Emilie Derisoud
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; (A.B.); (E.D.); (F.V.); (J.M.A.); (M.P.)
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
| | - François Vialard
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; (A.B.); (E.D.); (F.V.); (J.M.A.); (M.P.)
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
| | - Eric Palmer
- Académie d’Agriculture de France, 75007 Paris, France;
| | - Jean Marc Ayoubi
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; (A.B.); (E.D.); (F.V.); (J.M.A.); (M.P.)
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
- Department of Gynaecology and Obstetrics, Foch Hospital, 92150 Suresnes, France
| | - Marine Poulain
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; (A.B.); (E.D.); (F.V.); (J.M.A.); (M.P.)
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
- Department of Gynaecology and Obstetrics, Foch Hospital, 92150 Suresnes, France
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France; (A.B.); (E.D.); (F.V.); (J.M.A.); (M.P.)
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
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