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Xu Z, Mei S, Zhou J, Zhang Y, Qiao M, Sun H, Li Z, Li L, Dong B, Oyelami FO, Wu J, Peng X. Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed. Front Genet 2021; 12:720081. [PMID: 34539748 PMCID: PMC8440853 DOI: 10.3389/fgene.2021.720081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/06/2021] [Indexed: 01/31/2023] Open
Abstract
The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.
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Affiliation(s)
- Zhong Xu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Shuqi Mei
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Jiawei Zhou
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Yu Zhang
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Mu Qiao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Hua Sun
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Zipeng Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Lianghua Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Binke Dong
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Junjing Wu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Xianwen Peng
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
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Jaillard S, Bell K, Akloul L, Walton K, McElreavy K, Stocker WA, Beaumont M, Harrisson C, Jääskeläinen T, Palvimo JJ, Robevska G, Launay E, Satié AP, Listyasari N, Bendavid C, Sreenivasan R, Duros S, van den Bergen J, Henry C, Domin-Bernhard M, Cornevin L, Dejucq-Rainsford N, Belaud-Rotureau MA, Odent S, Ayers KL, Ravel C, Tucker EJ, Sinclair AH. New insights into the genetic basis of premature ovarian insufficiency: Novel causative variants and candidate genes revealed by genomic sequencing. Maturitas 2020; 141:9-19. [PMID: 33036707 DOI: 10.1016/j.maturitas.2020.06.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/12/2020] [Accepted: 06/07/2020] [Indexed: 11/20/2022]
Abstract
Ovarian deficiency, including premature ovarian insufficiency (POI) and diminished ovarian reserve (DOR), represents one of the main causes of female infertility. POI is a genetically heterogeneous condition but current understanding of its genetic basis is far from complete, with the cause remaining unknown in the majority of patients. The genes that regulate DOR have been reported but the genetic basis of DOR has not been explored in depth. Both conditions are likely to lie along a continuum of degrees of decrease in ovarian reserve. We performed genomic analysis via whole exome sequencing (WES) followed by in silico analyses and functional experiments to investigate the genetic cause of ovarian deficiency in ten affected women. We achieved diagnoses for three of them, including the identification of novel variants in STAG3, GDF9, and FANCM. We identified potentially causative FSHR variants in another patient. This is the second report of biallelic GDF9 and FANCM variants, and, combined with functional support, validates these genes as bone fide autosomal recessive "POI genes". We also identified new candidate genes, NRIP1, XPO1, and MACF1. These genes have been linked to ovarian function in mouse, pig, and zebrafish respectively, but never in humans. In the case of NRIP1, we provide functional support for the deleterious nature of the variant via SUMOylation and luciferase/β-galactosidase reporter assays. Our study provides multiple insights into the genetic basis of POI/DOR. We have further elucidated the involvement of GDF9, FANCM, STAG3 and FSHR in POI pathogenesis, and propose new candidate genes, NRIP1, XPO1, and MACF1, which should be the focus of future studies.
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Affiliation(s)
- Sylvie Jaillard
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France; CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
| | - Katrina Bell
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Linda Akloul
- CHU Rennes, Service de Génétique Clinique, CLAD Ouest, F-35033, Rennes, France
| | - Kelly Walton
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, VIC, 3800, Australia
| | | | - William A Stocker
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, VIC, 3800, Australia; Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Marion Beaumont
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - Craig Harrisson
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, VIC, 3800, Australia
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, FI-70211 Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, FI-70211 Kuopio, Finland
| | - Gorjana Robevska
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Erika Launay
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - Anne-Pascale Satié
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Nurin Listyasari
- Doctoral Program of Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Claude Bendavid
- INRAE, INSERM, Univ Rennes, Institut NuMeCan, Rennes, Saint-Gilles, France; CHU Rennes, Laboratoire de Biochimie et Toxicologie, F-35033, Rennes, France
| | - Rajini Sreenivasan
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Solène Duros
- CHU Rennes, Département de Gynécologie Obstétrique et Reproduction Humaine, F-35033, Rennes, France
| | - Jocelyn van den Bergen
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Catherine Henry
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - Mathilde Domin-Bernhard
- CHU Rennes, Département de Gynécologie Obstétrique et Reproduction Humaine, F-35033, Rennes, France
| | - Laurence Cornevin
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
| | - Nathalie Dejucq-Rainsford
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France; CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France; CHU Rennes, Service de Biologie de la Reproduction-CECOS, F-35033, Rennes, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, CLAD Ouest, F-35033, Rennes, France; Univ Rennes, CNRS UMR 6290, Institut de Génétique et Développement, F-35000, Rennes, France
| | - Katie L Ayers
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Célia Ravel
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France; CHU Rennes, Service de Biologie de la Reproduction-CECOS, F-35033, Rennes, France
| | - Elena J Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia.
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia
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Onuma A, Fujioka YA, Fujii W, Sugiura K, Naito K. Expression and function of exportin 6 in full-grown and growing porcine oocytes. J Reprod Dev 2019; 65:407-412. [PMID: 31204365 PMCID: PMC6815735 DOI: 10.1262/jrd.2019-040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Exportin 6, which functions specifically in the nuclear export of actin family proteins, has been reported to be absent in immature Xenopus oocytes, which have a huge
nucleus containing a large amount of actin. In mammalian oocytes, however, the presence and the function of exportin 6 remain uninvestigated. In this study, we assessed the expression and
effects of exportin 6 on meiotic resumption in porcine oocytes after cloning porcine exportin 6 cDNA and carrying out overexpression and expression inhibition by mRNA and antisense RNA
injection, respectively. We found for the first time that exportin 6 was expressed in mammalian full-grown germinal-vesicle-stage oocytes and was involved in the nuclear export of actin. In
contrast, exportin 6 was absent from the growing oocytes, which are meiotically incompetent and maintain the germinal-vesicle structure in the long term; the regulatory mechanism appeared to
be active degradation. We examined the effects of exportin 6 on meiotic resumption of porcine oocytes and noted that its expression did not affect the onset time but increased the rate of
germinal vesicle breakdown at 24 h via regulation of the nuclear actin level, which directly influences the physical strength of the germinal-vesicle membrane. Our results suggest that
exportin 6 affects the nuclear transport of actin and meiotic resumption in mammalian oocytes.
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Affiliation(s)
- Asuka Onuma
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshie A Fujioka
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Wataru Fujii
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Koji Sugiura
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kunihiko Naito
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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