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Niu Y, Li Y, Zhao Y, He X, Zhao Q, Pu Y, Ma Y, Jiang L. Whole-Genome Sequencing Identifies Functional Genes for Environmental Adaptation in Chinese Sheep. J Genet Genomics 2024:S1673-8527(24)00234-0. [PMID: 39260683 DOI: 10.1016/j.jgg.2024.08.011] [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: 02/22/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024]
Abstract
Sheep (Ovis aries), among the first domesticated species, are now globally widespread and exhibit remarkable adaptability to diverse environments. In this study, we perform whole-genome sequencing of 266 animals from 18 distinct Chinese sheep populations, each displaying unique phenotypes indicative of adaptation to varying environmental conditions. Integrating 131 environmental factors with single nucleotide polymorphism variations, we conduct a comprehensive genetic-environmental association analysis. This analysis identifies 35 key genes likely integral to the environmental adaptation of sheep. The functions of these genes include fat tail formation (HOXA10, HOXA11, JAZF1), wool characteristics (FER, FGF5, MITF, PDE4B), horn phenotypes (RXFP2), reproduction (HIBADH, TRIM71, C6H4orf22) and growth traits (ADGRL3, TRHDE). Notably, we observe a significant correlation between the frequency of missense mutations in the PAPSS2 and RXFP2 genes and variations in altitude. Our study reveals candidate genes for adaptive variation in sheep and demonstrates the diversity in the ways sheep adapt to their environment.
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Affiliation(s)
- Yinan Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yefang Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuhetian Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaohong He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yabin Pu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Lin Jiang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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Gao Z, Lu Y, Li M, Chong Y, Hong J, Wu J, Wu D, Xi D, Deng W. Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants. Int J Mol Sci 2024; 25:9271. [PMID: 39273219 PMCID: PMC11394796 DOI: 10.3390/ijms25179271] [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: 07/30/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
The economic significance of ruminants in agriculture underscores the need for advanced research methodologies to enhance their traits. This review aims to elucidate the transformative role of pan-omics technologies in ruminant research, focusing on their application in uncovering the genetic mechanisms underlying complex traits such as growth, reproduction, production performance, and rumen function. Pan-omics analysis not only helps in identifying key genes and their regulatory networks associated with important economic traits but also reveals the impact of environmental factors on trait expression. By integrating genomics, epigenomics, transcriptomics, metabolomics, and microbiomics, pan-omics enables a comprehensive analysis of the interplay between genetics and environmental factors, offering a holistic understanding of trait expression. We explore specific examples of economic traits where these technologies have been pivotal, highlighting key genes and regulatory networks identified through pan-omics approaches. Additionally, we trace the historical evolution of each omics field, detailing their progression from foundational discoveries to high-throughput platforms. This review provides a critical synthesis of recent advancements, offering new insights and practical recommendations for the application of pan-omics in the ruminant industry. The broader implications for modern animal husbandry are discussed, emphasizing the potential for these technologies to drive sustainable improvements in ruminant production systems.
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Affiliation(s)
- Zhendong Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Kunming 650201, China
| | - Ying Lu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengfei Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yuqing Chong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jieyun Hong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiao Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongmei Xi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Kunming 650201, China
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Fonseca PAS, Suárez-Vega A, Arranz JJ, Gutiérrez-Gil B. Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits. Genet Sel Evol 2024; 56:40. [PMID: 38773423 PMCID: PMC11106937 DOI: 10.1186/s12711-024-00910-w] [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: 12/08/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). RESULTS In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. CONCLUSIONS The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain.
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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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Bradford BJ, Contreras GA. Adipose Tissue Inflammation: Linking Physiological Stressors to Disease Susceptibility. Annu Rev Anim Biosci 2024; 12:261-281. [PMID: 38064480 DOI: 10.1146/annurev-animal-021122-113212] [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: 02/16/2024]
Abstract
The study of adipose tissue (AT) is enjoying a renaissance. White, brown, and beige adipocytes are being investigated in adult animals, and the critical roles of small depots like perivascular AT are becoming clear. But the most profound revision of the AT dogma has been its cellular composition and regulation. Single-cell transcriptomic studies revealed that adipocytes comprise well under 50% of the cells in white AT, and a substantial portion of the rest are immune cells. Altering the function of AT resident leukocytes can induce or correct metabolic syndrome and, more surprisingly, alter adaptive immune responses to infection. Although the field is dominated by obesity research, conditions such as rapid lipolysis, infection, and heat stress impact AT immune dynamics as well. Recent findings in rodents lead to critical questions that should be explored in domestic livestock as potential avenues for improved animal resilience to stressors, particularly as animals age.
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Affiliation(s)
- Barry J Bradford
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA;
| | - G Andres Contreras
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA;
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Han Y, He X, Yun Y, Chen L, Huang Y, Wu Q, Qin X, Wu H, Wu J, Sha R, Borjigin G. The Characterization of Subcutaneous Adipose Tissue in Sunit Sheep at Different Growth Stages: A Comprehensive Analysis of the Morphology, Fatty Acid Profile, and Metabolite Profile. Foods 2024; 13:544. [PMID: 38397521 PMCID: PMC10887640 DOI: 10.3390/foods13040544] [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: 12/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Adipose tissue is a crucial economically significant trait that significantly influences the meat quality and growth performance of domestic animals. To reveal the changes in adipose tissue metabolism during the growth of naturally grazing sheep, we evaluated the thickness, adipocyte morphology, fatty acid profile, and metabolite profile of subcutaneous adipose tissue (SAT) from naturally grazing Sunit sheep at 6, 18, and 30 months of age (referred to as Mth-6, Mth-18, and Mth-30, respectively). The fat thickness and adipocyte number were significantly increased with the growth of the sheep (p < 0.05), and the increase of which from Mth-18 to Mth-30 was less than that from Mth-6 to Mth-18. Additionally, the alpha-linolenic acid metabolism was enhanced and fatty acid (FA) elongation increased with growth. The metabolomic analysis revealed 76 differentially expressed metabolites (DEMs) in the SAT in different growth stages. Interestingly, we observed elongation of FAs in lipids correlated with sheep growth. Furthermore, the expression of acylcarnitines was downregulated, and fatty acid amides, aspartic acid, acetic acid and phosphocholine were upregulated in Mth-18 and Mth-30 compared to Mth-6. Altogether, the study found that the difference in SAT in Mth-6 was great compared to Mth-18 and Mth-30. An increase in fat deposition via adipocyte proliferation with the growth of the sheep in naturally grazing. The DEMs of acylcarnitines, fatty acid amides, aspartic acid, acetic acid, and phosphocholine emerged as potential key regulators of adipose tissue metabolism. These findings illustrate the variation in and metabolic mechanism of sheep adipose tissue development under natural grazing, thus providing valuable insights into improving the edible quality of sheep meat and developing the mutton sheep industry.
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Affiliation(s)
- Yunfei Han
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Xige He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Yueying Yun
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China;
| | - Lu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Yajuan Huang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Qiong Wu
- Ke Er Qin You Yi Front Banner Administration for Market Regulation, Xing’an League 137400, China;
| | - Xia Qin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Haiyan Wu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Jindi Wu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Rina Sha
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China; (Y.H.); (X.H.); (L.C.); (Y.H.); (X.Q.); (H.W.); (J.W.); (R.S.)
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7
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Bakhtiarizadeh MR. Deciphering the role of alternative splicing as a potential regulator in fat-tail development of sheep: a comprehensive RNA-seq based study. Sci Rep 2024; 14:2361. [PMID: 38287039 PMCID: PMC10825154 DOI: 10.1038/s41598-024-52855-1] [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: 10/30/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024] Open
Abstract
Although research on alternative splicing (AS) has been widely conducted in mammals, no study has investigated the splicing profiles of genes involved in fat-tail formation in sheep. Here, for the first time, a comprehensive study was designed to investigate the profile of AS events and their involvement in fat-tail development of sheep. In total, 45 RNA-Seq samples related to seven different studies, which have compared the fat-tailed vs thin-tailed sheep breeds, were analyzed. Two independent tools, rMATS and Whippet, along with a set of stringent filters were applied to identify differential AS (DAS) events between the breeds per each study. Only DAS events that were detected by both tools as well as in at least three datasets with the same ΔPSI trend (percent spliced in), were considered as the final high-confidence set of DAS genes. Final results revealed 130 DAS skipped exon events (69 negative and 61 positive ΔPSI) belonged to 124 genes. Functional enrichment analysis highlighted the importance of the genes in the underlying molecular mechanisms of fat metabolism. Moreover, protein-protein interaction network analysis revealed that DAS genes are significantly connected. Of DAS genes, five transcription factors were found that were enriched in the biological process associated with lipid metabolism like "Fat Cell Differentiation". Further investigations of the findings along with a comprehensive literature review provided a reliable list of candidate genes that may potentially contribute to fat-tail formation including HSD11B1, SIRT2, STRN3 and TCF7L2. Based on the results, it can be stated that the AS patterns may have evolved, during the evolution of sheep breeds, as another layer of regulation to contribute to biological complexity by reprogramming the gene regulatory networks. This study provided the theoretical basis of the molecular mechanisms behind the sheep fat-tail development in terms of AS.
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Yang L, Zhang X, Hu Y, Zhu P, Li H, Peng Z, Xiang H, Zhou X, Zhao X. Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia. J Genet Genomics 2024; 51:87-95. [PMID: 37330109 DOI: 10.1016/j.jgg.2023.06.002] [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: 04/22/2023] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/19/2023]
Abstract
Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.
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Affiliation(s)
- Liu Yang
- National Engineering Laboratory for Animal Breeding, Key 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; Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Xing Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Yaning Hu
- National Engineering Laboratory for Animal Breeding, Key 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
| | - Piao Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Zhenyu Peng
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China.
| | - Xinying Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding, Key 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.
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9
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Farhadi S, Hasanpur K, Ghias JS, Palangi V, Maggiolino A, Landi V. Comprehensive Gene Expression Profiling Analysis of Adipose Tissue in Male Individuals from Fat- and Thin-Tailed Sheep Breeds. Animals (Basel) 2023; 13:3475. [PMID: 38003093 PMCID: PMC10668686 DOI: 10.3390/ani13223475] [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: 09/06/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
It has been shown that tail fat content varies significantly among sheep breeds and plays a significant role in meat quality. Recently, significant efforts have been made to understand the physiological, biochemical, and genomic regulation of fat deposition in sheep tails in order to unravel the mechanisms underlying energy storage and adipose tissue lipid metabolism. RNA-seq has enabled us to provide a high-resolution snapshot of differential gene expression between fat- and thin-tailed sheep breeds. Therefore, three RNA-seq datasets were meta-analyzed for the current work to elucidate the transcriptome profile differences between them. Specifically, we identified hub genes, performed gene ontology (GO) analysis, carried out enrichment analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and validated hub genes using machine learning algorithms. This approach revealed a total of 136 meta-genes, 39 of which were not significant in any of the individual studies, indicating the higher statistical power of the meta-analysis. Furthermore, the results derived from the use of machine learning revealed POSTN, K35, SETD4, USP29, ANKRD37, RTN2, PRG4, and LRRC4C as substantial genes that were assigned a higher weight (0.7) than other meta-genes. Among the decision tree models, the Random Forest ones surpassed the others in adipose tissue predictive power fat deposition in fat- and thin-tailed breeds (accuracy > 0.85%). In this regard, combining meta-analyses and machine learning approaches allowed for the identification of three important genes (POSTN, K35, SETD4) related to lipid metabolism, and our findings could help animal breeding strategies optimize fat-tailed breeds' tail sizes.
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Affiliation(s)
- Sana Farhadi
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz 51666-16471, Iran; (S.F.); (J.S.G.)
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz 51666-16471, Iran; (S.F.); (J.S.G.)
| | - Jalil Shodja Ghias
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz 51666-16471, Iran; (S.F.); (J.S.G.)
| | - Valiollah Palangi
- Department of Animal Science, Faculty of Agriculture, Ege University, 35100 Izmir, Türkiye;
| | - Aristide Maggiolino
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy;
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy;
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10
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Wang J, Suo J, Yang R, Zhang CL, Li X, Han Z, Zhou W, Liu S, Gao Q. Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin. Front Genet 2023; 14:1281601. [PMID: 38028584 PMCID: PMC10666172 DOI: 10.3389/fgene.2023.1281601] [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: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Local sheep in the northeastern Tarim Basin can adapt to dry and low-rainfall regional environments. In this study, three local sheep breeds in the northeastern Tarim Basin, LOP (LOP) sheep, Bayinbuluke (BYK) sheep, and Kunlun (KUN, also known as the Qiemo sheep) sheep, and three introduced sheep breeds, Suffolk (SUF) sheep, Dorset (APD) sheep, and Texel (TEX) sheep, were analyzed for genetic diversity, population structure, and selective signature using the Illumina OvineSNP50K BeadChip. We found that LOP, BYK, and KUN had lower observed heterozygosity and expected heterozygosity than TEX, SUF, and ADP, which were differentiated based on geographic distribution. We performed fixation index (FST) analysis on three local sheep breeds in the northeastern Tarim Basin (LOP, BYK, and KUN) and introduced sheep breeds (TEX, SUF, and ADP) to measure genetic differentiation. Nucleotide diversity (PI) analysis was performed on single-nucleotide polymorphism (SNP) data of LOP, BYK, and KUN. A total of 493 candidate genes were obtained by taking the intersection at a threshold of 5%. Among them, SMAD2, ESR2, and HAS2 were related to reproductive traits. PCDH15, TLE4, and TFAP2B were related to growth traits. SOD1, TSHR, and DNAJB5 were related to desert environmental adaptation. Analyzing the genetic patterns of local sheep in the northeastern Tarim Basin can protect the germplasm resources of local sheep and promote the development and utilization of sheep genetic resources.
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Affiliation(s)
- Jieru Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Jiajia Suo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Ruizhi Yang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Cheng-Long Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Xiaopeng Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Zhipeng Han
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Wen Zhou
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Shudong Liu
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Qinghua Gao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
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Wang B, Du M. Increasing adipocyte number and reducing adipocyte size: the role of retinoids in adipose tissue development and metabolism. Crit Rev Food Sci Nutr 2023:1-18. [PMID: 37427553 PMCID: PMC10776826 DOI: 10.1080/10408398.2023.2227258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The rising prevalence of obesity is a grave public health threat. In response to excessive energy intake, adipocyte hypertrophy impairs cellular function and leads to metabolic dysfunctions while de novo adipogenesis leads to healthy adipose tissue expansion. Through burning fatty acids and glucose, the thermogenic activity of brown/beige adipocytes can effectively reduce the size of adipocytes. Recent studies show that retinoids, especially retinoic acid (RA), promote adipose vascular development which in turn increases the number of adipose progenitors surrounding the vascular vessels. RA also promotes preadipocyte commitment. In addition, RA promotes white adipocyte browning and stimulates the thermogenic activity of brown/beige adipocytes. Thus, vitamin A is a promising anti-obesity micronutrient.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Min Du
- Laboratory of Nutrigenomics and Growth Biology, Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
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Salehian-Dehkordi H, Huang JH, Pirany N, Mehrban H, Lv XY, Sun W, Esmailizadeh A, Lv FH. Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep. Genes (Basel) 2023; 14:1256. [PMID: 37372436 PMCID: PMC10298528 DOI: 10.3390/genes14061256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.
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Affiliation(s)
- Hosein Salehian-Dehkordi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Jia-Hui Huang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
| | - Nasrollah Pirany
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Hossein Mehrban
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Xiao-Yang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
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