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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Rehman SU, Zhen Y, Ding L, Saleh AA, Zhang Y, Zhang J, He F, Husien HM, Zhou P, Wang M. Integrative Meta-Analysis: Unveiling Genetic Factors in Meat Sheep Growth and Muscular Development through QTL and Transcriptome Studies. Animals (Basel) 2024; 14:1679. [PMID: 38891726 PMCID: PMC11171046 DOI: 10.3390/ani14111679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
OBJECTIVE The study aimed to investigate the effects of castration on performance, carcass characteristics, and meat quality in sheep, as well as explore the expression of key genes related to metabolic pathways and muscle growth following castration. METHODS A meta-analysis approach was utilized to analyze data from multiple studies to compare the performance, carcass characteristics, and meat quality of castrated sheep (wethers) with intact rams. Additionally, protein-protein interaction (PPI) networks, differential gene expression (DEG) interactions, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify molecular mechanisms associated with fat metabolism and muscle development in sheep tails. RESULTS The analysis revealed that castrated sheep (wethers) exhibited improved average daily gain, increased tenderness, lower backfat thickness, and a tendency for greater loin muscle area compared to intact rams. This suggests that castration promotes faster growth and results in leaner carcasses with potentially higher muscle content. Furthermore, the identification of downregulated DEGs like ACLY, SLC27A2, and COL1A1 and upregulated DEGs such as HOXA9, PGM2L1, and ABAT provides insights into the molecular mechanisms underlying fat deposition and muscle development in sheep. CONCLUSIONS The findings support the practice of castration in sheep production as it enhances growth performance, leads to leaner carcasses with higher muscle content, and improves meat tenderness. The identified changes in gene expression offer valuable insights for further research into understanding the impact of castration on muscle development and fat metabolism in sheep. This meta-analysis contributes to the knowledge of molecular mechanisms involved in fat deposition in sheep, opening avenues for future investigations in livestock fat metabolism research.
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Affiliation(s)
- Shahab Ur Rehman
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Yongkang Zhen
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Luoyang Ding
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
- Animal and Fish Production Department, Faculty of Agriculture (Al-Shatby), Alexandria University, Alexandria City 11865, Egypt
| | - Yifan Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Jinying Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Feiyang He
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Hosameldeen Mohamed Husien
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
| | - Mengzhi Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
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Yuan H, Wei W, Zhang Y, Li C, Zhao S, Chao Z, Xia C, Quan J, Gao C. Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China's Native Pig Breeds via Whole-Genome Resequencing. Int J Mol Sci 2024; 25:5843. [PMID: 38892031 PMCID: PMC11172908 DOI: 10.3390/ijms25115843] [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: 04/10/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Copy number variations (CNVs) critically influence individual genetic diversity and phenotypic traits. In this study, we employed whole-genome resequencing technology to conduct an in-depth analysis of 50 pigs from five local swine populations [Rongchang pig (RC), Wuzhishan pig (WZS), Tibetan pig (T), Yorkshire (YL) and Landrace (LR)], aiming to assess their genetic potential and explore their prospects in the field of animal model applications. We identified a total of 96,466 CNVs, which were subsequently integrated into 7112 non-redundant CNVRs, encompassing 1.3% of the swine genome. Functional enrichment analysis of the genes within these CNVRs revealed significant associations with sensory perception, energy metabolism, and neural-related pathways. Further selective scan analyses of the local pig breeds RC, T, WZS, along with YL and LR, uncovered that for the RC variety, the genes PLA2G10 and ABCA8 were found to be closely related to fat metabolism and cardiovascular health. In the T breed, the genes NCF2 and CSGALNACT1 were associated with immune response and connective tissue characteristics. As for the WZS breed, the genes PLIN4 and CPB2 were primarily linked to fat storage and anti-inflammatory responses. In summary, this research underscores the pivotal role of CNVs in fostering the diversity and adaptive evolution of pig breeds while also offering valuable insights for further exploration of the advantageous genetic traits inherent to China's local pig breeds. This facilitates the creation of experimental animal models tailored to the specific characteristics of these breeds, contributing to the advancement of livestock and biomedical research.
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Affiliation(s)
- Haonan Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Wenjing Wei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Yue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Changwen Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin 150069, China; (C.L.); (C.X.)
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou 571100, China;
| | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin 150069, China; (C.L.); (C.X.)
| | - Jinqiang Quan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Caixia Gao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin 150069, China; (C.L.); (C.X.)
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Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2024; 10:1334434. [PMID: 38274664 PMCID: PMC10808162 DOI: 10.3389/fvets.2023.1334434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
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5
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Davoudi P, Do DN, Colombo S, Rathgeber B, Sargolzaei M, Plastow G, Wang Z, Hu G, Valipour S, Miar Y. Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 2024; 14:24. [PMID: 38167844 PMCID: PMC10762091 DOI: 10.1038/s41598-023-50497-3] [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: 10/04/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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6
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Salehian-Dehkordi H, Huang JH, Pirany N, Mehrban H, Lv XY, Sun W, Esmailizadeh A, Lv FH. Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep. Genes (Basel) 2023; 14:1256. [PMID: 37372436 PMCID: PMC10298528 DOI: 10.3390/genes14061256] [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: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.
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Affiliation(s)
- Hosein Salehian-Dehkordi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Jia-Hui Huang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
| | - Nasrollah Pirany
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Hossein Mehrban
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Xiao-Yang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
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Liu W, Lin L, Yang Q, Jin S, Jiang H. Prkra Mutation Alters mRNA Expression During Embryonic External Ear Development. J Craniofac Surg 2023; 34:e387-e391. [PMID: 37185168 DOI: 10.1097/scs.0000000000009318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/16/2023] [Indexed: 05/17/2023] Open
Abstract
To understand the changes in mRNA expression during the embryonic development of the external mouse ear after the point mutation of the Prkra gene, Prkra short ear mouse model was used to study the development of the embryonic external ear. The tissues of the embryonic external ear were obtained when mouse embryos developed to E15.5 and E17.5. The changes in the mRNA expression profile were detected and analyzed. Find_circ and CIRI2 softwares were used to identify the upregulated and down-regulated expression of mRNA in the experimental and control groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional annotations were conducted on the differentially expressed mRNA, and the related signal pathways were analyzed after the upregulation and down-regulation of mRNA expression. This study aimed to understand the regulation of mRNA expression in Prkra short-ear mice during the external ear development in embryos. The results showed a correlation between abnormally expressed mRNA and signal pathways and the regulation of the development of the external ear of Prkra short-ear mice, and there were differences in some key regulatory mRNA changes after the Prkra gene point mutation. This study will provide a new clue for the mechanism of mRNA regulating the development of the external mouse ear. The change in mRNA expression profile can also provide clues for studying the biological regulation mechanism of external ear embryonic development.
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Affiliation(s)
- Wei Liu
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Listyarini K, Sumantri C, Rahayu S, Islam MA, Akter SH, Uddin MJ, Gunawan A. Hepatic Transcriptome Analysis Reveals Genes, Polymorphisms, and Molecules Related to Lamb Tenderness. Animals (Basel) 2023; 13:ani13040674. [PMID: 36830461 PMCID: PMC9951696 DOI: 10.3390/ani13040674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Tenderness is a key meat quality trait that determines the public acceptance of lamb consumption, so genetic improvement toward lamb with higher tenderness is pivotal for a sustainable sheep industry. However, unravelling the genomics controlling the tenderness is the first step. Therefore, this study aimed to identify the transcriptome signatures and polymorphisms related to divergent lamb tenderness using RNA deep sequencing. Since the molecules and enzymes that control muscle growth and tenderness are metabolized and synthesized in the liver, hepatic tissues of ten sheep with divergent phenotypes: five high- and five low-lamb tenderness samples were applied for deep sequencing. Sequence analysis identified the number of reads ranged from 21.37 to 25.37 million bases with a mean value of 22.90 million bases. In total, 328 genes are detected as differentially expressed (DEGs) including 110 and 218 genes that were up- and down-regulated, respectively. Pathway analysis showed steroid hormone biosynthesis as the dominant pathway behind the lamb tenderness. Gene expression analysis identified the top high (such as TP53INP1, CYP2E1, HSD17B13, ADH1C, and LPIN1) and low (such as ANGPTL2, IGFBP7, FABP5, OLFML3, and THOC5) expressed candidate genes. Polymorphism and association analysis revealed that mutation in OLFML3, ANGPTL2, and THOC5 genes could be potential candidate markers for tenderness in sheep. The genes and pathways identified in this study cause variation in tenderness, thus could be potential genetic markers to improve meat quality in sheep. However, further validation is needed to confirm the effect of these markers in different sheep populations so that these could be used in a selection program for lamb with high tenderness.
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Affiliation(s)
- Kasita Listyarini
- Graduate School of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor 16680, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor 16680, Indonesia
| | - Sri Rahayu
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor 16680, Indonesia
| | - Md. Aminul Islam
- Immunogenomics and Alternative Medicine (IAM) Laboratory, Department of Medicine, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Syeda Hasina Akter
- Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Muhammad Jasim Uddin
- School of Veterinary Medicine, Murdoch University, Murdoch, WA 6150, Australia
- Center for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (M.J.U.); (A.G.)
| | - Asep Gunawan
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor 16680, Indonesia
- Correspondence: (M.J.U.); (A.G.)
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9
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Braga LG, Chud TCS, Watanabe RN, Savegnago RP, Sena TM, do Carmo AS, Machado MA, Panetto JCDC, da Silva MVGB, Munari DP. Identification of copy number variations in the genome of Dairy Gir cattle. PLoS One 2023; 18:e0284085. [PMID: 37036840 PMCID: PMC10085049 DOI: 10.1371/journal.pone.0284085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/23/2023] [Indexed: 04/11/2023] Open
Abstract
Studying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction.
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Affiliation(s)
- Larissa G Braga
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Tatiane C S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Rafael N Watanabe
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Rodrigo P Savegnago
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Thomaz M Sena
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Adriana S do Carmo
- Departamento de Zootecnia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | | | | | - Danísio P Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
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10
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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11
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Hu L, Zhang L, Li Q, Liu H, Xu T, Zhao N, Han X, Xu S, Zhao X, Zhang C. Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing. Front Genet 2022; 13:971464. [PMID: 36160022 PMCID: PMC9490000 DOI: 10.3389/fgene.2022.971464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.
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Affiliation(s)
- Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hongjin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tianwei Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Na Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Shixiao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Cunfang Zhang,
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12
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Taghizadeh S, Gholizadeh M, Rahimi-Mianji G, Moradi MH, Costilla R, Moore S, Di Gerlando R. Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds. Sci Rep 2022; 12:8834. [PMID: 35614300 PMCID: PMC9132911 DOI: 10.1038/s41598-022-12778-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.
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Affiliation(s)
- Shadan Taghizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - Roy Costilla
- Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Stephen Moore
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Rosalia Di Gerlando
- Dipartimento Di Scienze Agrarie, Alimentari E Forestali, Università Degli Studi Di Palermo, Palermo, Italy
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13
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Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds. Animals (Basel) 2022; 12:ani12020217. [PMID: 35049839 PMCID: PMC8773107 DOI: 10.3390/ani12020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.
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