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Wang W, Bai Y, Wang X, Zhang J, Li B, Zhang H, Zhou X, Wang H, Liu B. Identification of key genes and variants associated with boar sperm freezability using whole genome resequencing. Int J Biol Macromol 2025; 294:139268. [PMID: 39733895 DOI: 10.1016/j.ijbiomac.2024.139268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 12/24/2024] [Accepted: 12/26/2024] [Indexed: 12/31/2024]
Abstract
Cryopreservation induces various cryodamages to the structural or functional aspects of boar sperm, resulting in the deterioration of sperm quality. The extent of cryodamages varies significantly among different individual boars. In our study, 50 boars with either good sperm freezability (GSF) or poor sperm freezability (PSF) were selected from a population of 402 boars. These two groups exhibited significant differences in sperm quality, acrosome integrity, mitochondrial membrane potential, and plasma membrane integrity. Subsequent whole-genome resequencing and FST analysis of GSF and PSF boars uncovered genetic differentiation among 5632 genes. Spermatogenesis, sperm structure, and lipid composition were identified as the potential factors, and 35 genes, such as RNF8, PACRG, CADM1, SPAG16, PPP3CA and MFF, were identified as key candidate genes associated with sperm freezability. Furthermore, by using MassARRAY genotyping and a general linear model, nine variants, including seven single nucleotide polymorphisms (SNPs) and two insertion variants, were found to be significantly correlated with sperm freezability. These variants, located within the candidate genes, represent potential molecular markers for sperm freezability. Our research contributes novel insights into the genetic mechanisms underlying freezability differences in boar sperm and identifies candidate genes and key molecular markers that could be applied in boar breeding practices.
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Affiliation(s)
- Wenjun Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Yifan Bai
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaokang Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiajun Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Bushe Li
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Hejun Zhang
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongyang Wang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry &Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Whole-Genome Profile of Greek Patients with Teratozοοspermia: Identification of Candidate Variants and Genes. Genes (Basel) 2022; 13:genes13091606. [PMID: 36140773 PMCID: PMC9498395 DOI: 10.3390/genes13091606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 01/09/2023] Open
Abstract
Male infertility is a global health problem that affects a large number of couples worldwide. It can be categorized into specific subtypes, including teratozoospermia. The present study aimed to identify new variants associated with teratozoospermia in the Greek population and to explore the role of genes on which these were identified. For this reason, whole-genome sequencing (WGS) was performed on normozoospermic and teratozoospermic individuals, and after selecting only variants found in teratozoospermic men, these were further prioritized using a wide range of tools, functional and predictive algorithms, etc. An average of 600,000 variants were identified, and of them, 61 were characterized as high impact and 153 as moderate impact. Many of these are mapped in genes previously associated with male infertility, yet others are related for the first time to teratozoospermia. Furthermore, pathway enrichment analysis and Gene ontology (GO) analyses revealed the important role of the extracellular matrix in teratozoospermia. Therefore, the present study confirms the contribution of genes studied in the past to male infertility and sheds light on new molecular mechanisms by providing a list of variants and candidate genes associated with teratozoospermia in the Greek population.
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Jansen S, Baulain U, Habig C, Ramzan F, Schauer J, Schmitt AO, Scholz AM, Sharifi AR, Weigend A, Weigend S. Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests. Genes (Basel) 2021; 12:702. [PMID: 34066823 PMCID: PMC8151682 DOI: 10.3390/genes12050702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
Skeletal disorders, including fractures and osteoporosis, in laying hens cause major welfare and economic problems. Although genetics have been shown to play a key role in bone integrity, little is yet known about the underlying genetic architecture of the traits. This study aimed to identify genes associated with bone breaking strength and bone mineral density of the tibiotarsus and the humerus in laying hens. Potentially informative single nucleotide polymorphisms (SNP) were identified using Random Forests classification. We then searched for genes known to be related to bone stability in close proximity to the SNPs and identified 16 potential candidates. Some of them had human orthologues. Based on our findings, we can support the assumption that multiple genes determine bone strength, with each of them having a rather small effect, as illustrated by our SNP effect estimates. Furthermore, the enrichment analysis showed that some of these candidates are involved in metabolic pathways critical for bone integrity. In conclusion, the identified candidates represent genes that may play a role in the bone integrity of chickens. Although further studies are needed to determine causality, the genes reported here are promising in terms of alleviating bone disorders in laying hens.
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Affiliation(s)
- Simon Jansen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt, Germany; (U.B.); (C.H.); (J.S.); (A.W.); (S.W.)
| | - Ulrich Baulain
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt, Germany; (U.B.); (C.H.); (J.S.); (A.W.); (S.W.)
| | - Christin Habig
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt, Germany; (U.B.); (C.H.); (J.S.); (A.W.); (S.W.)
| | - Faisal Ramzan
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany; (F.R.); (A.O.S.)
| | - Jens Schauer
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt, Germany; (U.B.); (C.H.); (J.S.); (A.W.); (S.W.)
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany; (F.R.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany;
| | - Armin Manfred Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleissheim, Germany;
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany;
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt, Germany; (U.B.); (C.H.); (J.S.); (A.W.); (S.W.)
| | - Steffen Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt, Germany; (U.B.); (C.H.); (J.S.); (A.W.); (S.W.)
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany;
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