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Davoudi P, Do DN, Rathgeber B, Colombo S, Sargolzaei M, Plastow G, Wang Z, Miar Y. Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data. J Anim Breed Genet 2024; 141:507-520. [PMID: 38389405 DOI: 10.1111/jbg.12859] [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: 11/30/2023] [Revised: 01/27/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- Select Sires Inc., Plain City, Ohio, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
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Lang LI, Wang ZZ, Liu B, Chang-Qing SHEN, Jing-Yi TU, Shi-Cheng WANG, Rui-Ling LEI, Si-Qi PENG, Xiong XIAO, Yong-Ju ZHAO, Qiu XY. The effects and mechanisms of heat stress on mammalian oocyte and embryo development. J Therm Biol 2024; 124:103927. [PMID: 39153259 DOI: 10.1016/j.jtherbio.2024.103927] [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: 10/26/2023] [Revised: 07/15/2024] [Accepted: 07/20/2024] [Indexed: 08/19/2024]
Abstract
The sum of nonspecific physiological responses exhibited by mammals in response to the disruption of thermal balance caused by high-temperature environments is referred to as heat stress (HS). HS affects the normal development of mammalian oocyte and embryos and leads to significant economic losses. Therefore, it is of great importance to gain a deep understanding of the mechanisms underlying the effects of HS on oocyte and embryonic development and to explore strategies for mitigating or preventing its detrimental impacts in the livestock industry. This article provides an overview of the negative effects of HS on mammalian oocyte growth, granulosa cell maturation and function, and embryonic development. It summarizes the mechanisms by which HS affects embryonic development, including generation of reactive oxygen species (ROS), endocrine disruption, the heat shock system, mitochondrial autophagy, and molecular-level alterations. Furthermore, it discusses various measures to ameliorate the effects of HS, such as antioxidant use, enhancement of mitochondrial function, gene editing, cultivating varieties possessing heat-resistant genes, and optimizing the animals'rearing environment. This article serves as a valuable reference for better understanding the relationship between HS and mammalian embryonic development as well as for improving the development of mammalian embryos and economic benefits under HS conditions in livestock production.
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Affiliation(s)
- L I Lang
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - Zhen-Zhen Wang
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - Bin Liu
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - S H E N Chang-Qing
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - T U Jing-Yi
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - W A N G Shi-Cheng
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - L E I Rui-Ling
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - P E N G Si-Qi
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - X I A O Xiong
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, China
| | - Z H A O Yong-Ju
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - Xiao-Yan Qiu
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China.
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Yan W, Liu X, Wang X. The heat shock protein 20 gene family in large yellow croaker (Larimichthys crocea): Identification, phylogenetic relationships, expression analyses. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 264:106700. [PMID: 37837866 DOI: 10.1016/j.aquatox.2023.106700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/16/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is an economically important fish in China, but its aquaculture industry has been threatened by both biotic and abiotic stressors such as hypoxia and pathogens. In the current study, hsp20 genes were identified and analyzed systematically for the first time from the genome of large yellow croaker, and their roles in hypoxia response and Aeromonas hydrophila, Pseudomonas plecoglossicida infection were investigated. Herein, 11 hsp20 genes were identified and annotated, phylogenetic analysis and selection pressure analysis showed that the hsp20 genes were evolutionarily-constrained and their function was conserved among fishes. Besides, we observed the expression patterns of the hsp20 genes under hypoxia and two pathogens' stress. In brief, seven, four, seven genes responded to hypoxia stress, A. hydrophila infection and P. plecoglossicida challenge, respectively, which indicated that they were involved in hypoxia and disease responses. Furthermore, pathogen- and time-specific pattern was observed after A. hydrophila and P. plecoglossicida infection whereas tissue-specific pattern was observed after hypoxia exposure, revealing that hsp20 genes showed differential functions in response to hypoxia and immune stress. Taken together, these results provided preliminary information for future analysis of the roles of hsp20 genes in both biotic and abiotic stress response in fish.
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Affiliation(s)
- Weijie Yan
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of marine biotechnology and Engineering, Ningbo University, China.
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