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Li C, Chen B, Langda S, Pu P, Zhu X, Zhou S, Kalds P, Zhang K, Bhati M, Leonard A, Huang S, Li R, Cuoji A, Wang X, Zhu H, Wu Y, Cuomu R, Gui B, Li M, Wang Y, Li Y, Fang W, Jia T, Pu T, Pan X, Cai Y, He C, Wang L, Jiang Y, Han JL, Chen Y, Zhou P, Pausch H, Wang X. Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae030. [PMID: 39142817 DOI: 10.1093/gpbjnl/qzae030] [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: 09/17/2023] [Revised: 01/09/2024] [Accepted: 02/29/2024] [Indexed: 08/16/2024]
Abstract
Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.
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Affiliation(s)
- Chao Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Animal Genomics, ETH Zürich, Zürich 8092, Switzerland
| | - Bingchun Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Suo Langda
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Peng Pu
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xiaojia Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Shiwei Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peter Kalds
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ke Zhang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich 8092, Switzerland
| | | | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ran Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Awang Cuoji
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Xiran Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Haolin Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Renqin Cuomu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Ba Gui
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Ming Li
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Yutao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Yan Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenwen Fang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Tianchun Pu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Xiangyu Pan
- Department of Medical Research, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Yudong Cai
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chong He
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs/Shaanxi Key Laboratory of Agricultural Information Perception and Intelligent Service, College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Liming Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Yu Jiang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi 00100, Kenya
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Hubert Pausch
- Animal Genomics, ETH Zürich, Zürich 8092, Switzerland
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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2
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Lu Z, Yuan C, An X, Chen Z, Guo T, Liu J. Chromosome-level genome assembly of Guide Black-Fur sheep (Ovis aries). Sci Data 2024; 11:711. [PMID: 38951548 PMCID: PMC11217409 DOI: 10.1038/s41597-024-03564-x] [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: 12/25/2023] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
Guide Black-Fur sheep (GD) is a breed of Tibetan sheep (Ovis aries) that lives in the Qinghai-Tibetan plateau region at an altitude of over 4,000 m. However, a lack of genomic information has made it difficult to understand the high-altitude adaptation of these sheep. We sequenced and assembled the GD reference genome using PacBio, Hi-C, and Illumina sequencing technologies. The final assembled genome size was 2.73 Gb, with a contig N50 of 20.30 Mb and a scaffold N50 of 107.63 Mb. The genome is predicted to contain 20,759 protein-coding genes, of which 98.42 have functional annotations. Repeat elements account for approximately 52.2% of the genomic landscape. The completeness of the GD genome assembly is highlighted by a BUSCO score of 93.1%. This high-quality genome assembly provides a critical resource for future molecular breeding and genetic improvement of Tibetan sheep.
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Affiliation(s)
- Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xuejiao An
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | | | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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3
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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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4
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Li J, Fan Y, Li N, Guo Y, Wang W, Feng K, He W, Li F, Huang J, Xu Y, Xiao L, Feng Y. Comparative genomics analysis reveals sequence characteristics potentially related to host preference in Cryptosporidium xiaoi. Int J Parasitol 2024; 54:379-390. [PMID: 38492779 DOI: 10.1016/j.ijpara.2024.03.004] [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: 10/25/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi, which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yingying Fan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Weijian Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Kangli Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Wei He
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Falei Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Jianbo Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yanhua Xu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
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5
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Liang Z, Yue X, Liu Y, Ye M, Zhong L, Luan Y, Wang Q. Genome-Wide Identification of Specific Genetic Loci Common to Sheep and Goat. Biomolecules 2024; 14:638. [PMID: 38927042 PMCID: PMC11201639 DOI: 10.3390/biom14060638] [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: 03/11/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/28/2024] Open
Abstract
Sheep and goat may become carriers of some zoonotic diseases. They are important livestock and experimental model animals for human beings. The fast and accurate identification of genetic materials originating from sheep and goat can prevent and inhibit the spread of some zoonotic diseases, monitor market product quality, and maintain the stability of animal husbandry and food industries. This study proposed a methodology for identifying sheep and goat common specific sites from a genome-wide perspective. A total of 150 specific sites were selected from three data sources, including the coding sequences of single copy genes from nine species (sheep, goat, cow, pig, dog, horse, human, mouse, and chicken), the dbSNPs for these species, and human 100-way alignment data. These 150 sites exhibited low intraspecific heterogeneity in the resequencing data of 1450 samples from five species (sheep, goat, cow, pig, and chicken) and high interspecific divergence in the human 100-way alignment data after quality control. The results were proven to be reliable at the data level. Using the process proposed in this study, specific sites of other species can be screened, and genome-level species identification can be performed using the screened sites.
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Affiliation(s)
- Zuoxiang Liang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiaoyu Yue
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Yangxiu Liu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Mengyan Ye
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Ling Zhong
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Yue Luan
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Qin Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
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6
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Zhong T, Hou D, Zhao Q, Zhan S, Wang L, Li L, Zhang H, Zhao W, Yang S, Niu L. Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds. BMC Genomics 2024; 25:480. [PMID: 38750582 PMCID: PMC11094944 DOI: 10.1186/s12864-024-10396-x] [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: 12/28/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its "year-round estrus and multiple births" and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep's high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.
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Affiliation(s)
- Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Dunying Hou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhao
- College of Animal Science, Xichang University, Xichang, 615013, China
| | - Shizhong Yang
- Academy of Agricultural Sciences Liangshan, Xichang, 615000, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
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7
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Wang Y, Huang Y, Zhen Y, Wang J, Wang L, Chen N, Wu F, Zhang L, Shen Y, Bi C, Li S, Pool K, Blache D, Maloney SK, Liu D, Yang Z, Li C, Yu X, Zhang Z, Chen Y, Xue C, Gu Y, Huang W, Yan L, Wei W, Wang Y, Zhang J, Zhang Y, Sun Y, Wang S, Zhao X, Luo C, Wang H, Ding L, Yang QY, Zhou P, Wang M. De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 2024; 11:488. [PMID: 38734729 PMCID: PMC11088706 DOI: 10.1038/s41597-024-03338-5] [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: 12/13/2023] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The high-quality filtered RNA-seq raw reads were deposited in a public database which provides approximately 54 billion high-quality paired-end sequencing reads in total, with an average mapping rate of ~93.92%. Transcriptome databases represent valuable resources that can be used to study patterns of gene expression, and pathways that are related to key biological processes, including important economic traits in herbivores.
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Affiliation(s)
- Yifan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
- College of Life Science, Guizhou University, Guiyang, 550025, P. R. China
| | - Yiming Huang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yongkang Zhen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Jiasheng Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Limin Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Ning Chen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Feifan Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Linna Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071033, P. R. China
| | - Congliang Bi
- College of Life Science, Linyi University, Linyi, 276005, P. R. China
| | - Song Li
- College of Life Science, Guizhou University, Guiyang, 550025, P. R. China
| | - Kelsey Pool
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dominique Blache
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Shane K Maloney
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhiquan Yang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Chuang Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Xiang Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Zhenbin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifei Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Chun Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yalan Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Weidong Huang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Lu Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Wenjun Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yusu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Jinying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifan Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yiquan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Shengbo Wang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xinle Zhao
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Chengfang Luo
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Haodong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China.
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Qing-Yong Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China.
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China.
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China.
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8
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Smith T, Olagunju T, Rosen B, Neibergs H, Becker G, Davenport K, Elsik C, Hadfield T, Koren S, Kuhn K, Rhie A, Shira K, Skibiel A, Stegemiller M, Thorne J, Villamediana P, Cockett N, Murdoch B. The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content. RESEARCH SQUARE 2024:rs.3.rs-4033388. [PMID: 38712074 PMCID: PMC11071540 DOI: 10.21203/rs.3.rs-4033388/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. We assembled complete and gapless telomere to telomere (T2T) Y chromosomes for these species. The pseudo-autosomal regions were similar in length, but the total chromosome size was substantially different, with the cattle Y more than twice the length of the sheep Y. The length disparity was accounted for by expanded ampliconic region in cattle. The genic amplification in cattle contrasts with pseudogenization in sheep suggesting opposite evolutionary mechanisms since their divergence 18MYA. The centromeres also differed dramatically despite the close relationship between these species at the overall genome sequence level. These Y chromosome have been added to the current reference assemblies in GenBank opening new opportunities for the study of evolution and variation while supporting efforts to improve sustainability in these important livestock species that generally use sire-driven genetic improvement strategies.
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Affiliation(s)
- Timothy Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC)
| | | | | | | | | | | | | | | | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
| | | | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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9
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Liu T, Bu Z, Xiang K, Jia Y, Du S. Effects of non-pelleted or pelleted low-native grass and pelleted high-native grass diets on meat quality by regulating the rumen microbiota in lambs. Microbiol Spectr 2024; 12:e0375823. [PMID: 38363135 PMCID: PMC10986533 DOI: 10.1128/spectrum.03758-23] [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: 10/23/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Diet modulates the rumen microbiota, which in turn can impact the animal performance. The rumen microbiota is increasingly recognized for its crucial role in regulating the growth and meat quality of the host. Nevertheless, the mechanism by which the rumen microbiome influences the fatty acid and amino acid profiles of lambs in the grass feeding system remains unclear. This study aimed to evaluate the effects of different native grass-based diets on animal performance, meat quality, fatty acid compositions, amino acid profiles, and rumen microbiota of lamb. Seventy-two Ujumqin lambs were randomly assigned into three treatments according to the initial body weight (27.39 ± 0.51 kg) and age (6 months ± 6 days). The lambs received three diets: (i) non-pelleted native grass hay with 40% concentrate diet; the native grass and concentrate were fed individually; (ii) pelleted native grass hay with 40% concentrate diet (PHLC); (iii) pelleted native grass hay with 60% concentrate diet (PHHC). The results showed that among the three groups, the PHHC and PHLC diets had markedly (P < 0.05) higher average daily gain and pH45 min, respectively. All amino acid levels were significantly (P < 0.05) decreased in the PHHC diet than in the PHLC diet. The principal coordinate analysis of the ruminal microbiota indicated the markedly distinct separation (P = 0.001) among the three groups. In addition, the correlation analysis showed that the Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Succinivibrio, and Succiniclasticum were significantly (P < 0.05) associated with most of the fatty acid and amino acid profiles. The correlation analysis of the association of microbiome with the meat quality provides us with a comprehensive understanding of the composition and function of the rumen microbial community, and these findings will contribute to the direction of future research in lamb. IMPORTANCE Diet modulates the gut microbiome, which in turn impact the meat quality, yet few studies investigate the correlation between the rumen microbiome and the fatty acid profile of meat. Here, the current study develops an experiment to investigate the correlation of the rumen microbiome and fatty acid profile of meat: rumen microbiome responses to feed type and meat quality. The results indicated a unique microbiota in the rumen of lamb in response to diets and meat quality. Associations between utilization and production were widely identified among the affected microbiome and meat quality, and these findings will contribute to the direction of future research in lamb.
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Affiliation(s)
- Tingyu Liu
- College of Agriculture, Inner Mongolia University of Nationalities, Tongliao, China
| | - Zhenkun Bu
- Guangdong Laboratory of Lingnan Modern Agriculture, Agriculture Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agriculture Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kaifeng Xiang
- Forest and Grassland Protection and Development Center, Chifeng, China
| | - Yushan Jia
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Shuai Du
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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10
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Jin M, Wang H, Liu G, Lu J, Yuan Z, Li T, Liu E, Lu Z, Du L, Wei C. Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation. Genet Sel Evol 2024; 56:26. [PMID: 38565986 PMCID: PMC10988870 DOI: 10.1186/s12711-024-00880-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/31/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations. RESULTS Based on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability. CONCLUSIONS Analysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gang Liu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, China
| | - Jian Lu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, China
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Engming Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lan-Zhou, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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11
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Ben Braiek M, Moreno-Romieux C, André C, Astruc JM, Bardou P, Bordes A, Debat F, Fidelle F, Granado-Tajada I, Hozé C, Plisson-Petit F, Rivemale F, Sarry J, Tadi N, Woloszyn F, Fabre S. Searching for homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in the MMUT gene affecting newborn lamb viability. Genet Sel Evol 2024; 56:16. [PMID: 38424485 PMCID: PMC10905913 DOI: 10.1186/s12711-024-00886-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Recessive deleterious variants are known to segregate in livestock populations, as in humans, and some may be lethal in the homozygous state. RESULTS We used phased 50 k single nucleotide polymorphism (SNP) genotypes and pedigree data to scan the genome of 6845 Manech Tête Rousse dairy sheep to search for deficiency in homozygous haplotypes (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1 to 5) were identified, with a homozygous deficiency ranging from 84 to 100%. These haplotypes are located on Ovis aries chromosome (OAR)1 (MTRDHH2 and 3), OAR10 (MTRDHH4), OAR13 (MTRDHH5), and OAR20 (MTRDHH1), and have carrier frequencies ranging from 7.8 to 16.6%. When comparing at-risk matings between DHH carriers to safe matings between non-carriers, two DHH (MTRDHH1 and 2) were linked with decreased insemination success and/or increased stillbirth incidence. We investigated the MTRDHH1 haplotype, which substantially increased stillbirth rate, and identified a single nucleotide variant (SNV) inducing a premature stop codon (p.Gln409*) in the methylmalonyl-CoA mutase (MMUT) gene by using a whole-genome sequencing approach. We generated homozygous lambs for the MMUT mutation by at-risk mating between heterozygous carriers, and most of them died within the first 24 h after birth without any obvious clinical symptoms. Reverse transcriptase-qPCR and western blotting on post-mortem liver and kidney biological samples showed a decreased expression of MMUT mRNA in the liver and absence of a full-length MMUT protein in the mutant homozygous lambs. CONCLUSIONS We identified five homozygous deficient haplotypes that are likely to harbor five independent deleterious recessive variants in sheep. One of these was detected in the MMUT gene, which is associated with lamb lethality in the homozygous state. A specific management of these haplotypes/variants in the MTR dairy sheep selection program would help enhance the overall fertility and lamb survival.
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Affiliation(s)
- Maxime Ben Braiek
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | | | - Jean-Michel Astruc
- Institut de l'Elevage, 24 Chemin de Borde-Rouge, 31321, Castanet-Tolosan, France
| | | | - Arnaud Bordes
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Frédéric Debat
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Itsasne Granado-Tajada
- Department of Animal Production, NEIKER-BRTA Basque Institute of Agricultural Research and Development, Agrifood Campus of Arkaute s/n, 01080, Arkaute, Spain
| | - Chris Hozé
- Eliance, 149 Rue de Bercy, 75595, Paris, France
- GABI, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | | | - François Rivemale
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Némuel Tadi
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.
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12
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Deakin S, Coltman DW. Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep ( Ovis canadensis canadensis). PeerJ 2024; 12:e16946. [PMID: 38426129 PMCID: PMC10903336 DOI: 10.7717/peerj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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13
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Steinbinder J, Sachslehner AP, Holthaus KB, Eckhart L. Comparative genomics of monotremes provides insights into the early evolution of mammalian epidermal differentiation genes. Sci Rep 2024; 14:1437. [PMID: 38228724 PMCID: PMC10791643 DOI: 10.1038/s41598-024-51926-7] [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: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
The function of the skin as a barrier against the environment depends on the differentiation of epidermal keratinocytes into highly resilient corneocytes that form the outermost skin layer. Many genes encoding structural components of corneocytes are clustered in the epidermal differentiation complex (EDC), which has been described in placental and marsupial mammals as well as non-mammalian tetrapods. Here, we analyzed the genomes of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus) to determine the gene composition of the EDC in the basal clade of mammals, the monotremes. We report that mammal-specific subfamilies of EDC genes encoding small proline-rich proteins (SPRRs) and late cornified envelope proteins as well as single-copy EDC genes such as involucrin are conserved in monotremes, suggesting that they have originated in stem mammals. Monotremes have at least one gene homologous to the group of filaggrin (FLG), FLG2 and hornerin (HRNR) in placental mammals, but no clear one-to-one pairwise ortholog of either FLG, FLG2 or HRNR. Caspase-14, a keratinocyte differentiation-associated protease implicated in the processing of filaggrin, is encoded by at least 3 gene copies in the echidna. Our results reveal evolutionarily conserved and clade-specific features of the genetic regulation of epidermal differentiation in monotremes.
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Affiliation(s)
- Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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14
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Cinar MU, Oliveira RD, Hadfield TS, Lichtenwalner A, Brzozowski RJ, Settlemire CT, Schoenian SG, Parker C, Neibergs HL, Cockett NE, White SN. Genome-wide association with footrot in hair and wool sheep. Front Genet 2024; 14:1297444. [PMID: 38288162 PMCID: PMC10822918 DOI: 10.3389/fgene.2023.1297444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/31/2023] [Indexed: 01/31/2024] Open
Abstract
Ovine footrot is an infectious disease with important contributions from Dichelobacter nodosus and Fusobacterium necrophorum. Footrot is characterized by separation of the hoof from underlying tissue, and this causes severe lameness that negatively impacts animal wellbeing, growth, and profitability. Large economic losses result from lost production as well as treatment costs, and improved genetic tools to address footrot are a valuable long-term goal. Prior genetic studies had examined European wool sheep, but hair sheep breeds such as Katahdin and Blackbelly have been reported to have increased resistance to footrot, as well as to intestinal parasites. Thus, footrot condition scores were collected from 251 U.S. sheep including Katahdin, Blackbelly, and European-influenced crossbred sheep with direct and imputed genotypes at OvineHD array (>500,000 single nucleotide polymorphism) density. Genome-wide association was performed with a mixed model accounting for farm and principal components derived from animal genotypes, as well as a random term for the genomic relationship matrix. We identified three genome-wide significant associations, including SNPs in or near GBP6 and TCHH. We also identified 33 additional associated SNPs with genome-wide suggestive evidence, including a cluster of 6 SNPs in a peak near the genome-wide significance threshold located near the glutamine transporter gene SLC38A1. These findings suggest genetic susceptibility to footrot may be influenced by genes involved in divergent biological processes such as immune responses, nutrient availability, and hoof growth and integrity. This is the first genome-wide study to investigate susceptibility to footrot by including hair sheep and also the first study of any kind to identify multiple genome-wide significant associations with ovine footrot. These results provide a foundation for developing genetic tests for marker-assisted selection to improve resistance to ovine footrot once additional steps like fine mapping and validation are complete.
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Affiliation(s)
- Mehmet Ulas Cinar
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri, Turkiye
| | - Ryan D. Oliveira
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Tracy S. Hadfield
- Department of Animal, Agricultural Experiment Station, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Anne Lichtenwalner
- School of Food and Agriculture, University of Maine, Orono, ME, United States
- Cooperative Extension, University of Maine, Orono, ME, United States
| | | | | | - Susan G. Schoenian
- Western Maryland Research and Education Center, University of Maryland, College Park, MD, United States
| | - Charles Parker
- Department of Animal Sciences, Professor Emeritus, The Ohio State University, Columbus, OH, United States
| | - Holly L. Neibergs
- Department of Animal Science, Washington State University, Pullman, WA, United States
| | - Noelle E. Cockett
- Department of Animal, Agricultural Experiment Station, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Stephen N. White
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
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15
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Li M, Lu Y, Gao Z, Yue D, Hong J, Wu J, Xi D, Deng W, Chong Y. Pan-Omics in Sheep: Unveiling Genetic Landscapes. Animals (Basel) 2024; 14:273. [PMID: 38254442 PMCID: PMC10812798 DOI: 10.3390/ani14020273] [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: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.
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Affiliation(s)
- Mengfei Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dan Yue
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
- Faculty of Animal Science and Technology, Yuxi Agricultural Vocational and Technical College, Yuxi 653106, China
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
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16
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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [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: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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17
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Du S, Bu Z, You S, Jiang Z, Su W, Wang T, Jia Y. Integrated rumen microbiome and serum metabolome analysis responses to feed type that contribution to meat quality in lambs. Anim Microbiome 2023; 5:65. [PMID: 38115081 PMCID: PMC10729572 DOI: 10.1186/s42523-023-00288-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 12/10/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Lifestyle factors, such as diet, are known to be a driver on the meat quality, rumen microbiome and serum metabolites. Rumen microbiome metabolites may be important for host health, the correlation between rumen microbiome and production of rumen metabolites are reported, while the impact of rumen microbiome on the serum metabolome and fatty acid of meat are still unclear. This study was designed to explore the rumen microbiome, serum metabolome and fatty acid of meat in response to the grass diet and concentrate diet to lambs, and the relationship of which also investigated. METHODS In the present study, 12 lambs were randomly divided into two groups: a grass diet (G) and a concentrate diet (C). Here, multiple physicochemical analyses combined with 16S rRNA gene sequences and metabolome analysis was performed to reveal the changes that in response to feed types. RESULTS The concentrate diet could improve the growth performance of lambs compared to that fed with the grass diet. The microbiome composition was highly individual, compared to the concentrate group, the abundance of Rikenellaceae_RC9_gut_group, F082_unclassified, Muribaculaceae_unclassified, Ruminococcaceae_NK4A214_group, Bacteroidetes_unclassified, and Bacteroidales_UCG-001_unclassified were significantly (P < 0.05) lower in the grass group, while, the abundance of Succinivibrio, Succinivibrionaceae_UCG-002, Fibrobacter and Christensenellaceae_R-7_group were significantly (P < 0.05) higher in the grass group. Serum metabolomics analysis combined with enrichment analysis revealed that serum metabolites were influenced by feed type as well as the metabolic pathway, and significantly affected serum metabolites involved in amino acids, peptides, and analogues, bile acids, alcohols and derivatives, linoleic acids derivatives, fatty acids and conjugates. Most of the amino acids, peptides, and analogues metabolites were positively associated with the fatty acid contents. Among the bile acids, alcohols and derivatives metabolites, glycocholic was positively associated with all fatty acid contents, except C18:0, while 25-Hydroxycholesterol and lithocholic acid metabolites were negatively associated with most of the fatty acid contents. CONCLUSION Correlation analysis of the association of microbiome with metabolite features, metabolite features with fatty acid provides us with comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified among affected microbiome, metabolites and fatty acid, and these findings will contribute to the direction of future research in lamb.
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Affiliation(s)
- Shuai Du
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Key Laboratory of Grassland Resources, Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China
| | - Zhenkun Bu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agriculture Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Sihan You
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Key Laboratory of Grassland Resources, Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China
| | - Zipeng Jiang
- National Engineering Laboratory of Biological Feed Safety and Pollution Prevention and Control, Key Laboratory of Molecular Nutrition, Ministry of Education, Key Laboratory of Animal Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Nutrition and Feed Science of Zhejiang Province, Institute of Feed Science, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Weifa Su
- National Engineering Laboratory of Biological Feed Safety and Pollution Prevention and Control, Key Laboratory of Molecular Nutrition, Ministry of Education, Key Laboratory of Animal Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Nutrition and Feed Science of Zhejiang Province, Institute of Feed Science, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tenghao Wang
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Key Laboratory of Grassland Resources, Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China.
- Zhejiang Qinglian Food Co., Ltd., Jiaxing, 314399, China.
| | - Yushan Jia
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Key Laboratory of Grassland Resources, Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China.
- National Engineering Laboratory of Biological Feed Safety and Pollution Prevention and Control, Key Laboratory of Molecular Nutrition, Ministry of Education, Key Laboratory of Animal Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Nutrition and Feed Science of Zhejiang Province, Institute of Feed Science, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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18
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Lv X, Chen W, Wang S, Cao X, Yuan Z, Getachew T, Mwacharo JM, Haile A, Sun W. Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits. Anim Biotechnol 2023; 34:3016-3026. [PMID: 36200839 DOI: 10.1080/10495398.2022.2127409] [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] [Indexed: 11/01/2022]
Abstract
Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (Fst) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in both the Fst results and XP-EHH results in HY vs DB and in DB vs HY, respectively. In HY vs DB, 106 genes were enriched in 12 GO terms and 83 KEGG pathways, such as ATP binding (GO:0005524) and PI3K-Akt signaling pathway (oas04151). In DB vs HY, 515 genes were enriched in 109 GO terms and 215 KEGG pathways, such as skeletal muscle cell differentiation (GO:0035914) and MAPK signaling pathway (oas04010). According to the annotation results, we identified a series of candidate genes associated with reproduction (UNC5C, BMPR1B, and GLIS1), meat quality (MECOM, MEF2C, and MYF6), and immunity (GMDS, GALK1, and ITGB4). Our investigation has uncovered genomic information for important traits in sheep and provided a basis for subsequent studies of related traits.
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Affiliation(s)
- Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Weihao Chen
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Tesfaye Getachew
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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19
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He X, Wang W, Du X, Chu M. Association between single-nucleotide polymorphism in PIK3CD gene and litter size in Small Tail Han sheep. Anim Biotechnol 2023; 34:3337-3342. [PMID: 36332162 DOI: 10.1080/10495398.2022.2140059] [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] [Indexed: 11/06/2022]
Abstract
The p110δ isoform of the PI3K catalytic subunit (encoded by the PIK3CD gene) is a key component of the PI3K pathway for follicle growth in mammalian ovarian granulosa cells. Nevertheless, little is known about the association of its polymorphisms with ovine litter size. In this study, the distribution of different genotypes of two SNPs in the PIK3CD gene was calculated in more than forty sheep breeds, and the associations between SNPs and litter size in Small Tail Han (STH) sheep were also analyzed. Besides, the mRNA expression of the PIK3CD gene was also detected in some reproduction-related tissues. The results showed that the "A" allele frequency was higher in rs412889931 (g.41926327G > A) in a typical polytocous sheep breed (p < 0.01). The association's analysis showed rs412889931 was correlated with ovine fecundity as assessed by three parity litter sizes (p < 0.05). Finally, we found the expression of PIK3CD in the ovary had significant differences in different fecundity sheep breeds, indicating that SNP may regulate the litter size by influencing the PIK3CD gene expression. The present results demonstrated that rs412889931 could be used in the marker-assisted selection of the litter size in sheep breeding.
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Affiliation(s)
- Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolong Du
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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20
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Woolley SA, Salavati M, Clark EL. Recent advances in the genomic resources for sheep. Mamm Genome 2023; 34:545-558. [PMID: 37752302 PMCID: PMC10627984 DOI: 10.1007/s00335-023-10018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
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Affiliation(s)
- Shernae A Woolley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Scotland's Rural College, Parkgate, Barony Campus, Dumfries, DG1 3NE, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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21
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Arias-Sardá C, Quigley S, Farré M. Patterns of chromosome evolution in ruminants. Mol Ecol 2023. [PMID: 37937367 DOI: 10.1111/mec.17197] [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: 06/08/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Studying when and where gross genomic rearrangements occurred during evolution is key to understanding changes in genome structure with functional consequences that might eventually lead to speciation. Here we identified chromosome rearrangements in ruminants, a clade characterized by large chromosome differences. Using 26 genome assemblies, we reconstructed five ancestral karyotypes and classified the rearrangement events occurring in each lineage. With these reconstructions, we then identified evolutionary breakpoints regions (EBRs) and synteny fragments. Ruminant karyotype evolution is characterized by inversions, while interchromosomal rearrangements occurred preferentially in the oldest ancestor of ruminants. We found that EBRs are depleted of protein coding genes, including housekeeping genes. Similarly, EBRs are not enriched in high GC regions, suggesting that meiotic double strand breaks might not be their origin. Overall, our results characterize at fine detail the location of chromosome rearrangements in ruminant evolution and provide new insights into the formation of EBRs.
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Affiliation(s)
| | - Sarah Quigley
- School of Biosciences, University of Kent, Canterbury, UK
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, UK
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22
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Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [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: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
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23
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Amato S, Ramsey J, Ahern TP, Rovnak J, Barlow J, Weaver D, Eyasu L, Singh R, Cintolo-Gonzalez J. Exploring the presence of bovine leukemia virus among breast cancer tumors in a rural state. Breast Cancer Res Treat 2023; 202:325-334. [PMID: 37517027 DOI: 10.1007/s10549-023-07061-4] [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: 09/29/2022] [Accepted: 05/31/2023] [Indexed: 08/01/2023]
Abstract
PURPOSE The bovine leukemia virus (BLV) is a deltaretrovirus that causes malignant lymphoma and lymphosarcomas in cattle globally and has high prevalence among large scale U.S. dairy herds. Associations between presence of BLV DNA in human mammary tissue and human breast cancer incidence have been reported. We sought to estimate the prevalence of BLV DNA in breast cancer tissue samples in a rural state with an active dairy industry. METHODS We purified genomic DNA from 56 fresh-frozen breast cancer tissue samples (51 tumor samples, 5 samples representing adjacent normal breast tissue) banked between 2016 and 2019. Using nested PCR assays, multiple BLV tax sequence primers and primers for the long terminal repeat (LTR) were used to detect BLV DNA in tissue samples and known positive control samples, including the permanently infected fetal lamb kidney cell line (FLK-BLV) and blood from BLV positive cattle. RESULTS The median age of patients from which samples were obtained at the time of treatment was 60 (40-93) and all were female. Ninety percent of patients had invasive ductal carcinoma. The majority were poorly differentiated (60%). On PCR assay, none of the tumor samples tested positive for BLV DNA, despite having consistent signals in positive controls. CONCLUSION We did not find BLV DNA in fresh-frozen breast cancer tumors from patients presenting to a hospital in Vermont. Our findings suggest a low prevalence of BLV in our patient population and a need to reevaluate the association between BLV and human breast cancer.
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Affiliation(s)
- Stas Amato
- Department of General Surgery, University of Vermont Medical Center, Burlington, VT, USA
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Jon Ramsey
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Thomas P Ahern
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - John Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Donald Weaver
- Department of Pathology, University of Vermont Medical Center, Burlington, VT, USA
| | - Lud Eyasu
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Rohit Singh
- Division of Hematology/Oncology, Department of Medicine, University of Vermont Medical Center, Burlington, VT, USA
| | - Jessica Cintolo-Gonzalez
- Department of General Surgery, University of Vermont Medical Center, Burlington, VT, USA.
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA.
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24
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Berry DP, Spangler ML. Animal board invited review: Practical applications of genomic information in livestock. Animal 2023; 17:100996. [PMID: 37820404 DOI: 10.1016/j.animal.2023.100996] [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: 08/29/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic evaluations exploit genome-wide genotype information to improve the accuracy of predicting an animal's (and by extension its progeny's) genetic merit. Genomic data also provide a huge resource for research, albeit the outcome from this research, if successful, should eventually be realised through one of the ten applications already mentioned. The process for generating a genotype all the way from sample procurement to identifying erroneous genotypes is described, as are the steps that should be considered when developing a bespoke genotyping panel for practical application.
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Affiliation(s)
- D P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland.
| | - M L Spangler
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
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Zhang W, Jin M, Lu Z, Li T, Wang H, Yuan Z, Wei C. Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep. Animals (Basel) 2023; 13:3265. [PMID: 37893989 PMCID: PMC10603731 DOI: 10.3390/ani13203265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.
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Affiliation(s)
- Wentao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Meilin Jin
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Taotao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Huihua Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China;
| | - Caihong Wei
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
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26
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O’Callaghan E, Navarrete-Lopez P, Štiavnická M, Sánchez JM, Maroto M, Pericuesta E, Fernández-González R, O’Meara C, Eivers B, Kelleher MM, Evans RD, Mapel XM, Lloret-Villas A, Pausch H, Balastegui-Alarcón M, Avilés M, Sanchez-Rodriguez A, Roldan ERS, McDonald M, Kenny DA, Fair S, Gutiérrez-Adán A, Lonergan P. Adenylate kinase 9 is essential for sperm function and male fertility in mammals. Proc Natl Acad Sci U S A 2023; 120:e2305712120. [PMID: 37812723 PMCID: PMC10589668 DOI: 10.1073/pnas.2305712120] [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: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 10/11/2023] Open
Abstract
Despite passing routine laboratory tests for semen quality, bulls used in artificial insemination exhibit significant variation in fertility. Routine analysis of fertility data identified a dairy bull with extreme subfertility (10% pregnancy rate). To characterize the subfertility phenotype, a range of in vitro, in vivo, and molecular assays were carried out. Sperm from the subfertile bull exhibited reduced motility and severely reduced caffeine-induced hyperactivation compared to controls. Ability to penetrate the zona pellucida, cleavage rate, cleavage kinetics, and blastocyst yield after IVF or AI were significantly lower than in control bulls. Whole-genome sequencing from semen and RNA sequencing of testis tissue revealed a critical mutation in adenylate kinase 9 (AK9) that impaired splicing, leading to a premature termination codon and a severely truncated protein. Mice deficient in AK9 were generated to further investigate the function of the gene; knockout males were phenotypically indistinguishable from their wild-type littermates but produced immotile sperm that were incapable of normal fertilization. These sperm exhibited numerous abnormalities, including a low ATP concentration and reduced motility. RNA-seq analysis of their testis revealed differential gene expression of components of the axoneme and sperm flagellum as well as steroid metabolic processes. Sperm ultrastructural analysis showed a high percentage of sperm with abnormal flagella. Combined bovine and murine data indicate the essential metabolic role of AK9 in sperm motility and/or hyperactivation, which in turn affects sperm binding and penetration of the zona pellucida. Thus, AK9 has been found to be directly implicated in impaired male fertility in mammals.
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Affiliation(s)
- Elena O’Callaghan
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
| | - Paula Navarrete-Lopez
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Miriama Štiavnická
- Department of Biological Sciences, Bernal Institute, Faculty of Science and Engineering, University of Limerick, LimerickV94 T9PX, Ireland
| | - José M. Sánchez
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Maria Maroto
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Raul Fernández-González
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Ciara O’Meara
- National Cattle Breeding Centre, County KildareW91 WF59, Ireland
| | - Bernard Eivers
- National Cattle Breeding Centre, County KildareW91 WF59, Ireland
| | - Margaret M. Kelleher
- Irish Cattle Breeding Federation, Link Road, Ballincollig, County CorkP31 D452, Ireland
| | - Ross D. Evans
- Irish Cattle Breeding Federation, Link Road, Ballincollig, County CorkP31 D452, Ireland
| | - Xena M. Mapel
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Zürich8092, Switzerland
| | - Audald Lloret-Villas
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Zürich8092, Switzerland
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Zürich8092, Switzerland
| | - Miriam Balastegui-Alarcón
- Departamento de Biología Celular e Histología, Universidad de Murcia-Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, Murcia30120, Spain
| | - Manuel Avilés
- Departamento de Biología Celular e Histología, Universidad de Murcia-Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, Murcia30120, Spain
| | - Ana Sanchez-Rodriguez
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid28006, Spain
| | - Eduardo R. S. Roldan
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid28006, Spain
| | - Michael McDonald
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
| | - David A. Kenny
- Animal and Bioscience Department, Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, County MeathC15 PW93, Ireland
| | - Sean Fair
- Department of Biological Sciences, Bernal Institute, Faculty of Science and Engineering, University of Limerick, LimerickV94 T9PX, Ireland
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Patrick Lonergan
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. MICROBIOME 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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Kaseja K, Mucha S, Yates J, Smith E, Banos G, Conington J. Genome-wide association study of health and production traits in meat sheep. Animal 2023; 17:100968. [PMID: 37738702 DOI: 10.1016/j.animal.2023.100968] [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: 04/03/2023] [Revised: 08/11/2023] [Accepted: 08/25/2023] [Indexed: 09/24/2023] Open
Abstract
Genotypes are currently widely used in animal breeding programmes to enhance the speed of genetic progress. With sufficient data, a Genome-Wide Association Study (GWAS) can be performed to identify informative markers. The aim of this study was to investigate the genetic background of health (footrot and mastitis) and production (birth weight, weaning weight, scan weight, and fat and muscle depth) traits using the available phenotypic and Single Nucleotide Polymorphism (SNP) data collected on the UK Texel sheep population. Initially, 10 193 genotypes were subject to quality control, leaving 9 505 genotypes for further analysis. Selected genotypes, recorded on four different Illumina chip types from low density (15 k SNPs) to high density (606 006 SNPs), were imputed to a subset of 45 686 markers from 50 k array, distributed on 27 chromosomes. Phenotypes collected on 32 farms across the UK for footrot and mastitis and extracted from the UK National database (iTexel) for the production traits were used along with pre-estimated variance components to obtain de-regressed breeding values and used to perform GWAS. Results showed three SNPs being significant on the genome-wise level ('OAR8_62240378.1' on chromosome 8 for birth weight, 's14444.1' on chromosome 19 for weaning weight and 's65197.1' on chromosome 23 for scan weight). Fourteen subsequent SNPs were found to be significant at the chromosome-wise level. These SNPs are located within or close to previously reported QTLs impacting on animal health (such as faecal egg count or somatic cell count) and production (such as body or carcass weight and fat amount). These results indicate that the studied traits are highly polygenic with complex genetic architecture.
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Affiliation(s)
- K Kaseja
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK.
| | - S Mucha
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK
| | - J Yates
- The British Texel Sheep Society, Stoneleigh Park, Warwickshire CV8 2LG, UK
| | - E Smith
- The British Texel Sheep Society, Stoneleigh Park, Warwickshire CV8 2LG, UK
| | - G Banos
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK
| | - J Conington
- SRUC Easter Bush, Roslin Institute Building, Edinburgh EH25 9RG, UK
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29
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Tabata E, Kobayashi I, Morikawa T, Kashimura A, Bauer PO, Oyama F. Evolutionary activation of acidic chitinase in herbivores through the H128R mutation in ruminant livestock. iScience 2023; 26:107254. [PMID: 37502259 PMCID: PMC10368815 DOI: 10.1016/j.isci.2023.107254] [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: 11/14/2022] [Revised: 05/04/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Placental mammals' ancestors were insectivores, suggesting that modern mammals may have inherited the ability to digest insects. Acidic chitinase (Chia) is a crucial enzyme hydrolyzing significant component of insects' exoskeleton in many species. On the other hand, herbivorous animal groups, such as cattle, have extremely low chitinase activity compared to omnivorous species, e.g., mice. The low activity of cattle Chia has been attributed to R128H mutation. The presence of either of these amino acids correlates with the feeding behavior of different bovid species with R and H determining the high and low enzymatic activity, respectively. Evolutionary analysis indicated that selective constraints were relaxed in 67 herbivorous Chia in Cetartiodactyla. Despite searching for another Chia paralog that could compensate for the reduced chitinase activity, no active paralogs were found in this order. Herbivorous animals' Chia underwent genetic alterations and evolved into a molecule with low activity due to the chitin-free diet.
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Affiliation(s)
- Eri Tabata
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo 192-0015, Japan
- Research Fellow of Japan Society for the Promotion of Science (PD), Koujimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Ikuto Kobayashi
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo 192-0015, Japan
| | - Takuya Morikawa
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo 192-0015, Japan
| | - Akinori Kashimura
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo 192-0015, Japan
| | - Peter O. Bauer
- Bioinova a.s., Videnska 1083, 142 00 Prague, Czech Republic
| | - Fumitaka Oyama
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo 192-0015, Japan
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30
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Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Res 2023; 33:1299-1316. [PMID: 37463752 PMCID: PMC10552650 DOI: 10.1101/gr.277663.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Eli Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Inna Biryukova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Vaishnovi Sekar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
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31
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Thorne JW, Redden R, Bowdridge SA, Becker GM, Stegemiller MR, Murdoch BM. Genome-Wide Analysis of Sheep Artificially or Naturally Infected with Gastrointestinal Nematodes. Genes (Basel) 2023; 14:1342. [PMID: 37510248 PMCID: PMC10379027 DOI: 10.3390/genes14071342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The anthelmintic resistance of gastrointestinal nematodes (GINs) poses a significant threat to sheep worldwide, but genomic selection can serve as an alternative to the use of chemical treatment as a solution for parasitic infection. The objective of this study is to conduct genome-wide association studies (GWASs) to identify single nucleotide polymorphisms (SNPs) in Rambouillet (RA) and Dorper × White Dorper (DWD) lambs associated with the biological response to a GIN infection. All lambs were genotyped with a medium-density genomic panel with 40,598 markers used for analysis. Separate GWASs were conducted using fecal egg counts (FECs) from lambs (<1 year of age) that acquired their artificial infections via an oral inoculation of 10,000 Haemonchus contortus larvae (n = 145) or naturally while grazing on pasture (n = 184). A GWAS was also performed for packed cell volume (PCV) in artificially GIN-challenged lambs. A total of 26 SNPs exceeded significance and 21 SNPs were in or within 20 kb of genes such as SCUBE1, GALNT6, IGF1R, CAPZB and PTK2B. The ontology analysis of candidate genes signifies the importance of immune cell development, mucin production and cellular signaling for coagulation and wound healing following epithelial damage in the abomasal gastric pits via H. contortus during GIN infection in lambs. These results add to a growing body of the literature that promotes the use of genomic selection for increased sheep resistance to GINs.
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Affiliation(s)
- Jacob W Thorne
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
- Texas A&M AgriLife Research and Extension, San Angelo, TX 76901, USA
| | - Reid Redden
- Texas A&M AgriLife Research and Extension, San Angelo, TX 76901, USA
| | - Scott A Bowdridge
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Gabrielle M Becker
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Morgan R Stegemiller
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
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Pan X, Ma Z, Sun X, Li H, Zhang T, Zhao C, Wang N, Heller R, Hung Wong W, Wang W, Jiang Y, Wang Y. CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:632-648. [PMID: 36494035 PMCID: PMC10787174 DOI: 10.1016/j.gpb.2022.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 11/12/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined toolkit transcription factors (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.
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Affiliation(s)
- Xiangyu Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Department of Medical Research, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Zhaoxia Ma
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinqi Sun
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Tingting Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chen Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Yong Wang
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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Pinto B, Valente R, Caramelo F, Ruivo R, Castro LFC. Decay of Skin-Specific Gene Modules in Pangolins. J Mol Evol 2023:10.1007/s00239-023-10118-z. [PMID: 37249590 DOI: 10.1007/s00239-023-10118-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
The mammalian skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation, Awat1/2, show patterns of inactivation in the stem pangolin branch, while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function is intact and expressed in the pangolin skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.
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Affiliation(s)
- Bernardo Pinto
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raul Valente
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Filipe Caramelo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raquel Ruivo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - L Filipe C Castro
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
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Ali A, Mir GJ, Ayaz A, Maqbool I, Ahmad SB, Mushtaq S, Khan A, Mir TM, Rehman MU. In silico analysis and molecular docking studies of natural compounds of Withania somnifera against bovine NLRP9. J Mol Model 2023; 29:171. [PMID: 37155030 PMCID: PMC10165590 DOI: 10.1007/s00894-023-05570-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
CONTEXT NLRP9 is a member of nucleotide-binding domain leucine-rich repeat-containing receptors and is found to be associated with many inflammatory diseases. In the current scenario, the identification of promising anti-inflammatory compounds from natural sources by repurposing approach is still relevant for the early prevention and effective management of the disease. METHODS In the present study, we docked bioactives of Ashwagandha (Withanoside IV, Withanoside V, Withanolide A, Withanolide B, and Sitoindoside IX) and two control drugs against bovine NLRP9 protein. ADME/T analysis was used to determine the physiochemical properties of compounds and standard drugs. Molecular modeling was used to evaluate the correctness and quality of protein structures. In silico docking analysis revealed Withanolide B had the highest binding affinity score of -10.5 kcal/mol, whereas, among control drugs, doxycycline hydrochloride was most effective (-10.3 kcal/mol). The results of this study revealed that bioactives of Withania somnifera could be promising inhibitors against bovine NLRP9. In the present study, molecular simulation was used to measure protein conformational changes over time. The Rg value was found to be 34.77A°. RMSD and B-factor were also estimated to provide insights into the flexibility and mobile regions of protein structure. A functional protein network interaction was constructed from information collected from non-curative sources as protein-protein interactions (PPI) that play an important role in determining the function of the target protein and the ability of the drug molecule. Thus, in the present situation, it is important to identify bioactives with the potential to combat inflammatory diseases and provide strength and immunity to the host. However, there is still a need to study in vitro and in vivo to further support these findings.
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Affiliation(s)
- Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, 190006, J&K, India
| | - Gh Jeelani Mir
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, 190006, J&K, India
| | - Aadil Ayaz
- Department of Microbiology, SKIMS Medical College Bemina, Srinagar, 190018, J&K, India
| | - Illiyas Maqbool
- Department of Microbiology, Government Medical College, Baramulla, 193101, J&K, India
| | - Sheikh Bilal Ahmad
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir (SKUAST-K), Shuhama, Srinagar, 190006, J&K, India
| | - Saima Mushtaq
- Veterinary Microbiology Department, Indian Veterinary Research Institute (IVRI), Bareilly, Uttar Pradesh, 243122, India
| | - Altaf Khan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Tahir Maqbool Mir
- National Centre for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA
| | - Muneeb U Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.
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Miao X, Luo Q, Zhao H, Qin X. Comparison of alternative splicing (AS) events in adipose tissue of polled dorset versus small tail han sheep. Heliyon 2023; 9:e14938. [PMID: 37095997 PMCID: PMC10121611 DOI: 10.1016/j.heliyon.2023.e14938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Background During the alternative splicing (AS), the exons of primary transcripts are spliced in various arrangements, resulting in structurally and functionally distinct mRNAs and proteins. This study aimed to examine genes with AS events from Small Tail Han sheep and Dorset sheep to explore the mechanism of adipose developments. Methods This study identified the genes with AS events in adipose tissues of two different sheep with next-generation sequencing. In this paper, genes with significantly different AS events were performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Results 364 genes with 411 A S events showed significant differences in adipose tissues between the two breeds; 108 genes with 120 A S events were extremely significant differences between the two breeds. We identified several novel genes that are related with adipose growth and development. The results of KEGG and GO analysis indicated that oocyte meiosis, mitogen-activated protein kinase (Wnt), mitogen-activated protein kinase (MAPK) signaling pathway, etc. Were closely related to the adipose tissue developments. Conclusions This paper revealed that the genes with AS events are important for adipose tissues in sheep, exploring the mechanisms of AS events associated with adipose tissue developments in sheep of different breeds.
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Ma X, Liu A, Tian S. A meta-analysis of mRNA expression profiling studies in sheep with different FecB genotypes. Anim Genet 2023; 54:225-238. [PMID: 36811249 DOI: 10.1111/age.13304] [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: 01/26/2023] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023]
Abstract
The FecB mutation in the sheep BMPRIB is strongly correlated with high ovulation traits but its mechanism remains unclear. This study explored differentially expressed genes (DEGs) and their associated molecular mechanisms that may be involved in FecB mutation-induced high ovulation from the perspective of the hypothalamic-pituitary-gonadal (HPG) axis by conducting a systematic review and meta-analysis. The PubMed, EMBASE, CNKI, WanFang, and CBM databases were searched for eligible articles published before August 2022, focusing on mRNA sequencing of different tissues in the HPG axis in sheep with different FecB genotypes. A total of 6555 DEGs were identified from the analysis of six published articles and experimental results from our laboratory. The DEGs were screened by vote-counting rank and robust rank aggregation. Among these, in the follicular phase, FKBP5, CDCA7 and CRABP1 were upregulated in the hypothalamus. INSM2 was upregulated, while LDB3 was downregulated in the pituitary. CLU, SERPINA14, PENK, INHA and STAR were upregulated, while FERMT2 and NPY1R were downregulated in the ovary. On the HPG axis, TAC1 was upregulated and NPNT was downregulated. Many DEGs were found in sheep with different FecB genotypes. The genes FKBP5, CDCA7, CRABP1, INSM2, LDB3, CLU, SERPINA14, PENK, INHA, STAR, FERMT2, NPY1R, TAC1 and NPNT, may be associated with FecB mutation-induced high ovulation in different tissues. These candidate genes will further improve the mechanism of multiple fertility traits induced by the FecB mutation from the perspective of the HPG axis.
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Affiliation(s)
- Xiaofei Ma
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Aiju Liu
- Department of Agricultural and Animal Husbandry Engineering, Cangzhou Technical College, Cangzhou, Hebei, China
| | - Shujun Tian
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
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Alini M, Diwan AD, Erwin WM, Little CB, Melrose J. An update on animal models of intervertebral disc degeneration and low back pain: Exploring the potential of artificial intelligence to improve research analysis and development of prospective therapeutics. JOR Spine 2023; 6:e1230. [PMID: 36994457 PMCID: PMC10041392 DOI: 10.1002/jsp2.1230] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 02/03/2023] Open
Abstract
Animal models have been invaluable in the identification of molecular events occurring in and contributing to intervertebral disc (IVD) degeneration and important therapeutic targets have been identified. Some outstanding animal models (murine, ovine, chondrodystrophoid canine) have been identified with their own strengths and weaknesses. The llama/alpaca, horse and kangaroo have emerged as new large species for IVD studies, and only time will tell if they will surpass the utility of existing models. The complexity of IVD degeneration poses difficulties in the selection of the most appropriate molecular target of many potential candidates, to focus on in the formulation of strategies to effect disc repair and regeneration. It may well be that many therapeutic objectives should be targeted simultaneously to effect a favorable outcome in human IVD degeneration. Use of animal models in isolation will not allow resolution of this complex issue and a paradigm shift and adoption of new methodologies is required to provide the next step forward in the determination of an effective repairative strategy for the IVD. AI has improved the accuracy and assessment of spinal imaging supporting clinical diagnostics and research efforts to better understand IVD degeneration and its treatment. Implementation of AI in the evaluation of histology data has improved the usefulness of a popular murine IVD model and could also be used in an ovine histopathological grading scheme that has been used to quantify degenerative IVD changes and stem cell mediated regeneration. These models are also attractive candidates for the evaluation of novel anti-oxidant compounds that counter inflammatory conditions in degenerate IVDs and promote IVD regeneration. Some of these compounds also have pain-relieving properties. AI has facilitated development of facial recognition pain assessment in animal IVD models offering the possibility of correlating the potential pain alleviating properties of some of these compounds with IVD regeneration.
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Affiliation(s)
- Mauro Alini
- AO Research Institute Davos Platz Switzerland
| | - Ashish D. Diwan
- Spine Service, Department of Orthopedic Surgery, St. George & Sutherland Campus, Clinical School University of New South Wales Sydney New South Wales Australia
| | - W. Mark Erwin
- Department of Surgery University of Toronto Ontario Canada
| | - Chirstopher B. Little
- Raymond Purves Bone and Joint Research Laboratory Kolling Institute, Sydney University Faculty of Medicine and Health, Northern Sydney Area Health District, Royal North Shore Hospital St. Leonards New South Wales Australia
| | - James Melrose
- Raymond Purves Bone and Joint Research Laboratory Kolling Institute, Sydney University Faculty of Medicine and Health, Northern Sydney Area Health District, Royal North Shore Hospital St. Leonards New South Wales Australia
- Graduate School of Biomedical Engineering The University of New South Wales Sydney New South Wales Australia
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Sánchez-Ramos R, Trujano-Chavez MZ, Gallegos-Sánchez J, Becerril-Pérez CM, Cadena-Villegas S, Cortez-Romero C. Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes. Animals (Basel) 2023; 13:ani13020272. [PMID: 36670812 PMCID: PMC9854690 DOI: 10.3390/ani13020272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (FST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.
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Affiliation(s)
- Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | | | - Jaime Gallegos-Sánchez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | - Carlos Miguel Becerril-Pérez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Agroecosistemas Tropicales, Colegio de Postgraduados, Campus Veracruz, Carretera Xalapa-Veracruz Km. 88.5, Manlio Favio Altamirano, Veracruz 91690, Mexico
| | - Said Cadena-Villegas
- Producción Agroalimentaria en Trópico, Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Ranchería Rio Seco y Montaña, Heroica Cárdenas 86500, Mexico
| | - César Cortez-Romero
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Innovación en Manejo de Recursos Naturales, Colegio de Postgraduados, Campus San Luis Potosí, Agustín de Iturbide No. 73, Salinas de Hidalgo, San Luis Potosí 78622, Mexico
- Correspondence: ; Tel.: +52-5959-520-200 (ext. 4000)
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James C, Pemberton JM, Navarro P, Knott S. The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep. Ecol Evol 2022; 12:e9639. [PMID: 36532132 PMCID: PMC9750819 DOI: 10.1002/ece3.9639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/01/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Understanding the genetic architecture underpinning quantitative traits in wild populations is pivotal to understanding the processes behind trait evolution. The 'animal model' is a popular method for estimating quantitative genetic parameters such as heritability and genetic correlation and involves fitting an estimate of relatedness between individuals in the study population. Genotypes at genome-wide markers can be used to estimate relatedness; however, relatedness estimates vary with marker density, potentially affecting results. Increasing density of markers is also expected to increase the power to detect quantitative trait loci (QTL). In order to understand how the density of genetic markers affects the results of quantitative genetic analyses, we estimated heritability and performed genome-wide association studies (GWAS) on five body size traits in an unmanaged population of Soay sheep using two different SNP densities: a dataset of 37,037 genotyped SNPs and an imputed dataset of 417,373 SNPs. Heritability estimates did not differ between the two SNP densities, but the high-density imputed SNP dataset revealed four new SNP-trait associations that were not found with the lower density dataset, as well as confirming all previously-found QTL. We also demonstrated that fitting fixed and random effects in the same step as performing GWAS is a more powerful approach than pre-correcting for covariates in a separate model.
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Affiliation(s)
- Caelinn James
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
| | - Josephine M. Pemberton
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
| | - Pau Navarro
- MRC Human Genetics UnitInstitute of Genetics and CancerThe University of EdinburghEdinburghScotland
| | - Sara Knott
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
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Diet evolution of carnivorous and herbivorous mammals in Laurasiatheria. BMC Ecol Evol 2022; 22:82. [PMID: 35729512 PMCID: PMC9210794 DOI: 10.1186/s12862-022-02033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/09/2021] [Indexed: 11/15/2022] Open
Abstract
Background Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear. Results In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, APOB, across carnivorous taxa. Conclusions Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02033-6.
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Jones HE, Wilson PB. Progress and opportunities through use of genomics in animal production. Trends Genet 2022; 38:1228-1252. [PMID: 35945076 DOI: 10.1016/j.tig.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
Abstract
The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.
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Affiliation(s)
- Huw E Jones
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK.
| | - Philippe B Wilson
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK
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42
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Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov A, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji S, Bignell A, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Charkhchi M, Cockburn A, Da Rin Fiorretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Ghattaoraya GS, Martinez JG, Guijarro C, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Marques-Coelho D, Marugán JC, Merino G, Mirabueno L, Mushtaq A, Hossain S, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Prosovetskaia I, Pérez-Silva JG, Salam A, Saraiva-Agostinho N, Schuilenburg H, Sheppard D, Sinha S, Sipos B, Stark W, Steed E, Sukumaran R, Sumathipala D, Suner MM, Surapaneni L, Sutinen K, Szpak M, Tricomi F, Urbina-Gómez D, Veidenberg A, Walsh T, Walts B, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley G, Loveland J, Moore B, Mudge J, Tate J, Thybert D, Trevanion S, Winterbottom A, Frankish A, Hunt SE, Ruffier M, Cunningham F, Dyer S, Finn R, Howe K, Harrison PW, Yates AD, Flicek P. Ensembl 2023. Nucleic Acids Res 2022; 51:D933-D941. [PMID: 36318249 PMCID: PMC9825606 DOI: 10.1093/nar/gkac958] [Citation(s) in RCA: 259] [Impact Index Per Article: 129.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.
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Affiliation(s)
- Fergal J Martin
- To whom correspondence should be addressed. Tel: +44 1223 49 44 44;
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Alisha Aneja
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Olanrewaju Austine-Orimoloye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Arne Becker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Simarpreet Kaur Bhurji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Paulo R Branco Lins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Lucy Brooks
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Shashank Budhanuru Ramaraju
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Mehrnaz Charkhchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Alexander Cockburn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Luca Da Rin Fiorretto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Bilal El Houdaigui
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Tamara El Naboulsi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Thiago Genez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Gurpreet S Ghattaoraya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Cristi Guijarro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Vinay Kaykala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Diego Marques-Coelho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - José Carlos Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Gabriela Alejandra Merino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Louisse Paola Mirabueno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Syed Nakib Hossain
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Denye N Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Manoj Pandian Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Malcolm Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ivana Piližota
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Irina Prosovetskaia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - José G Pérez-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Nuno Saraiva-Agostinho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Swati Sinha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Botond Sipos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - William Stark
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ranjit Sukumaran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Dulika Sumathipala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Kyösti Sutinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - David Urbina-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andres Veidenberg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Thomas A Walsh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Natalie Willhoft
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
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Zheng K, Guo L, Ullah S, Cao Y, Huang X, shan H, Jiang J, Wu J, Jiang Y. Proteome changes of sheep rumen epithelium during postnatal development. Front Genet 2022; 13:1031707. [PMID: 36386827 PMCID: PMC9641056 DOI: 10.3389/fgene.2022.1031707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/13/2022] [Indexed: 12/03/2022] Open
Abstract
Background: The development of the rumen epithelium is a critical physiological challenge for sheep. However, the molecular mechanism underlying postnatal rumen development in sheep remains rarely understood. Results: Here, we used a shotgun approach and bioinformatics analyses to investigate and compare proteomic profiles of sheep rumen epithelium tissue on day 0, 15, 30, 45, and 60 of age. A total of 4,523 proteins were identified, in which we found 852, 342, 164, and 95 differentially expressed proteins (DEPs) between day 0 and day 15, between day 15 and day 30, between day 30 and day 45, between day 45 and day 60, respectively. Furthermore, subcellular localization analysis showed that the DEPs were majorly localized in mitochondrion between day 0 and day 15, after which nucleus proteins were the most DEPs. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DEPs significantly enriched in mitochondrion, ubiquitination, histone modifications, glutathione synthase activity, and wnt and nortch signaling pathways. Conclusion: Our data indicate that the biogenesis of mitochondrion in rumen epithelial cell is essential for the initiation of rumen epithelial development. Glutathione, wnt signaling pathway and nortch signaling pathway participated in rumen epithelial growth. Ubiquitination, post-translational modifications of histone might be key molecular functions in regulating rumen epithelial development.
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Affiliation(s)
- Kaizhi Zheng
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liangyong Guo
- Huzhou Academy of Agricultural Sciences, Huzhou, China
| | - Saif Ullah
- Faculty of Veterinary and Animal Sciences, Lasbela University of Agriculture Water and Marine Sciences, Lasbela, Pakistan
| | - Yang Cao
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Huang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huili shan
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junfang Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianliang Wu
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Jianliang Wu, ; Yongqing Jiang,
| | - Yongqing Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Jianliang Wu, ; Yongqing Jiang,
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44
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Davies ES, Morphew RM, Cutress D, Morton AJ, McBride S. Characterization of microtubule-associated protein tau isoforms and Alzheimer's disease-like pathology in normal sheep (Ovis aries): relevance to their potential as a model of Alzheimer's disease. Cell Mol Life Sci 2022; 79:560. [PMID: 36269420 PMCID: PMC9587068 DOI: 10.1007/s00018-022-04572-z] [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: 03/04/2022] [Revised: 08/26/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Alzheimer's disease is a chronic neurodegenerative disease that accounts for up to 80% of all dementias. Characterised by deteriorations of memory and cognitive function, the key neuropathological features are accumulations of β-amyloid and hyperphosphorylated tau, as 'plaques' and 'tangles', respectively. Despite extensive study, however, the exact mechanism underlying aggregate formation in Alzheimer's disease remains elusive, as does the contribution of these aggregates to disease progression. Importantly, a recent evaluation of current Alzheimer's disease animal models suggested that rodent models are not able to fully recapitulate the pathological intricacies of the disease as it occurs in humans. Therefore, increasing attention is being paid to species that might make good alternatives to rodents for studying the molecular pathology of Alzheimer's disease. The sheep (Ovis aries) is one such species, although to date, there have been few molecular studies relating to Alzheimer's disease in sheep. Here, we investigated the Alzheimer's disease relevant histopathological characteristics of 22 sheep, using anti-β-amyloid (Abcam 12267 and mOC64) and phosphorylation specific anti-tau (AT8 and S396) antibodies. We identified numerous intraneuronal aggregates of both β-amyloid and tau that are consistent with early Alzheimer's disease-like pathology. We confirmed the expression of two 3-repeat (1N3R, 2N3R) and two 4-repeat (1N4R, 2N4R) tau isoforms in the ovine brain, which result from the alternative splicing of two tau exons. Finally, we investigated the phosphorylation status of the serine396 residue in 30 sheep, and report that the phosphorylation of this residue begins in sheep aged as young as 2 years. Together, these data show that sheep exhibit naturally occurring β-amyloid and tau pathologies, that reflect those that occur in the early stages of Alzheimer's disease. This is an important step towards the validation of the sheep as a feasible large animal species in which to model Alzheimer's disease.
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Affiliation(s)
- Emma S. Davies
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - David Cutress
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - A. Jennifer Morton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sebastian McBride
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
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Quantification of cytosol and membrane proteins in rumen epithelium of sheep with low or high CH4 emission phenotype. PLoS One 2022; 17:e0273184. [PMID: 36256644 PMCID: PMC9578583 DOI: 10.1371/journal.pone.0273184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Ruminant livestock are a major contributor to Australian agricultural sector carbon emissions. Variation in methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen of sheep differs with different digestive functions. METHOD We isolated rumen epithelium enzymatically to extract membrane and cytosol proteins from sheep with high (H) and low (L) CH4 emission. Protein abundance was quantified using SWATH-mass spectrometry. RESULTS The research found differences related to the metabolism of glucose, lactate and processes of cell defence against microbes in sheep from each phenotype. Enzymes in the methylglyoxal pathway, a side path of glycolysis, resulting in D-lactate production, differed in abundance. In the H CH4 rumen epithelium the enzyme hydroxyacylglutathione hydrolase (HAGH) was 2.56 fold higher in abundance, whereas in the L CH4 epithelium lactate dehydrogenase D (LDHD) was 1.93 fold higher. Malic enzyme 1 which converts D-lactate to pyruvate via the tricarboxylic cycle was 1.57 fold higher in the L CH4 phenotype. Other proteins that are known to regulate cell defence against microbes had differential abundance in the epithelium of each phenotype. CONCLUSION Differences in the abundance of enzymes involved in the metabolism of glucose were associated with H and L CH4 phenotype sheep. Potentially this represents an opportunity to use protein markers in the rumen epithelium to select low CH4 emitting sheep.
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46
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Response of Ruminal Microbiota-Host Gene Interaction to High-Altitude Environments in Tibetan Sheep. Int J Mol Sci 2022; 23:ijms232012430. [PMID: 36293284 PMCID: PMC9604387 DOI: 10.3390/ijms232012430] [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: 09/24/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022] Open
Abstract
Altitude is the main external environmental pressure affecting the production performance of Tibetan sheep, and the adaptive evolution of many years has formed a certain response mechanism. However, there are few reports on the response of ruminal microbiota and host genomes of Tibetan sheep to high-altitude environments. Here, we conducted an integrated analysis of volatile fatty acids (VFAs), microbial diversity (16S rRNA), epithelial morphology, and epithelial transcriptome in the rumen of Tibetan sheep at different altitudes to understand the changes in ruminal microbiota−host interaction in response to high altitude. The differences in the nutritional quality of forage at different altitudes, especially the differences in fiber content (ADF/NDF), led to changes in rumen VFAs of Tibetan sheep, in which the A/P value (acetic acid/propionic acid) was significantly decreased (p < 0.05). In addition, the concentrations of IgA and IgG in Middle-altitude (MA) and High-altitude Tibetan sheep (HA) were significantly increased (p < 0.05), while the concentrations of IgM were significantly increased in MA (p < 0.05). Morphological results showed that the width of the rumen papilla and the thickness of the basal layer increased significantly in HA Tibetan sheep (p < 0.05). The 16S rRNA analysis found that the rumen microbial diversity of Tibetan sheep gradually decreased with increasing altitude, and there were some differences in phylum- and genus-level microbes at the three altitudes. RDA analysis found that the abundance of the Rikenellaceae RC9 gut group and the Ruminococcaceae NK4A214 group increased with altitudes. Furthermore, a functional analysis of the KEGG microbial database found the “lipid metabolism” function of HA Tibetan sheep to be significantly enriched. WGCNA revealed that five gene modules were enriched in “energy production and conversion”, “lipid transport and metabolism”, and “defense mechanisms”, and cooperated with microbiota to regulate rumen fermentation and epithelial immune barrier function, so as to improve the metabolism and immune level of Tibetan sheep at high altitude.
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47
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Hawley E, Mia K, Yusuf M, Swanson KC, Doetkott C, Dorsam GP. Messenger RNA Gene Expression Screening of VIP and PACAP Neuropeptides and Their Endogenous Receptors in Ruminants. BIOLOGY 2022; 11:biology11101512. [PMID: 36290416 PMCID: PMC9598725 DOI: 10.3390/biology11101512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/29/2022]
Abstract
Vasoactive Intestinal Peptide (VIP) and Pituitary Adenylate-Cyclase-Activating Peptide (PACAP) are anti-inflammatory neuropeptides that play important roles in human and rodent gut microbiota homeostasis and host immunity. Pharmacologically regulating these neuropeptides is expected to have significant health and feed efficiency benefits for agriculturally relevant animals. However, their expression profile in ruminant tissues is not well characterized. To this end, we screened for VIP and PACAP neuropeptides and their endogenous GPCRs using 15 different tissues from wethers and steers by RT-qPCR. Our results revealed relatively similar expression profiles for both VIP and PACAP neuropeptide ligands in the brain and intestinal tissue of both species. In contrast, the tissue expression profiles for VPAC1, VPAC2, and PAC1 were more widespread and disparate, with VPAC1 being the most diversely expressed receptor with mRNA detection in the brain and throughout the gastrointestinal tract. These data are an important first step to allow for future investigations regarding the VIP and PACAP signaling pathways in livestock ruminant species.
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Affiliation(s)
- Emma Hawley
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Kafi Mia
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Mustapha Yusuf
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Kendall C. Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Curt Doetkott
- Information Technology Services, North Dakota State University, Fargo, ND 58102, USA
| | - Glenn P. Dorsam
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
- Correspondence:
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Sparks AM, Johnston SE, Handel I, Pilkington JG, Berry J, Pemberton JM, Nussey DH, Mellanby RJ. Vitamin D status is heritable and under environment-dependent selection in the wild. Mol Ecol 2022; 31:4607-4621. [PMID: 34888965 PMCID: PMC9545857 DOI: 10.1111/mec.16318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 11/12/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022]
Abstract
Vitamin D has a well-established role in skeletal health and is increasingly linked to chronic disease and mortality in humans and companion animals. Despite the clear significance of vitamin D for health and obvious implications for fitness under natural conditions, no longitudinal study has tested whether the circulating concentration of vitamin D is under natural selection in the wild. Here, we show that concentrations of dietary-derived vitamin D2 and endogenously produced vitamin D3 metabolites are heritable and largely polygenic in a wild population of Soay sheep (Ovis aries). Vitamin D2 status was positively associated with female adult survival, and vitamin D3 status predicted female fecundity in particular, good environment years when sheep density and competition for resources was low. Our study provides evidence that vitamin D status has the potential to respond to selection, and also provides new insights into how vitamin D metabolism is associated with fitness in the wild.
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Affiliation(s)
- Alexandra M. Sparks
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
- Faculty of Biological SciencesSchool of BiologyUniversity of LeedsLeedsUK
| | - Susan E. Johnston
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Ian Handel
- Royal (Dick) School of Veterinary Studies and The Roslin InstituteThe University of EdinburghHospital for Small AnimalsRoslinUK
| | - Jill G. Pilkington
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Jacqueline Berry
- Specialist Assay Laboratory (Vitamin D)Clinical BiochemistryManchester Royal InfirmaryManchesterUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Daniel H. Nussey
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Richard J. Mellanby
- Royal (Dick) School of Veterinary Studies and The Roslin InstituteThe University of EdinburghHospital for Small AnimalsRoslinUK
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Wang H, Zhong L, Dong Y, Meng L, Ji C, Luo H, Fu M, Qi Z, Mi L. Whole-genome resequencing reveals domestication and signatures of selection in Ujimqin, Sunit, and Wu Ranke Mongolian sheep breeds. Anim Biosci 2022; 35:1303-1313. [PMID: 35507861 PMCID: PMC9449395 DOI: 10.5713/ab.21.0569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/09/2022] [Indexed: 11/27/2022] Open
Abstract
Objective: The current study aimed to perform whole-genome resequencing of Chinese indigenous Mongolian sheep breeds including Ujimqin, Sunit, and Wu Ranke sheep breeds (UJMQ, SNT, WRK) and deeply analyze genetic variation, population structure, domestication, and selection for domestication traits among these Mongolian sheep breeds.Methods: Blood samples were collected from a total of 60 individuals comprising 20 WRK, 20 UJMQ, and 20 SNT. For genome sequencing, about 1.5 μg of genomic DNA was used for library construction with an insert size of about 350 bp. Pair-end sequencing were performed on Illumina NovaSeq platform, with the read length of 150 bp at each end. We then investigated the domestication and signatures of selection in these sheep breeds.Results: According to the population and demographic analyses, WRK and SNT populations were very similar, which were different from UJMQ populations. Genome wide association study identified 468 and 779 significant loci from SNT vs UJMQ, and UJMQ vs WRK, respectively. However, only 3 loci were identified from SNT vs WRK. Genomic comparison and selective sweep analysis among these sheep breeds suggested that genes associated with regulation of secretion, metabolic pathways including estrogen metabolism and amino acid metabolism, and neuron development have undergone strong selection during domestication.Conclusion: Our findings will facilitate the understanding of Chinese indigenous Mongolian sheep breeds domestication and selection for complex traits and provide a valuable genomic resource for future studies of sheep and other domestic animal breeding.
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