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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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Lee H, Seeger MR, Lippok N, Nadkarni SK, van Soest G, Bouma BE. Nanosecond SRS fiber amplifier for label-free near-infrared photoacoustic microscopy of lipids. PHOTOACOUSTICS 2022; 25:100331. [PMID: 35096525 PMCID: PMC8783138 DOI: 10.1016/j.pacs.2022.100331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 05/18/2023]
Abstract
Near-infrared photoacoustics receives increasing interest as an intravital modality to sense key biomolecules. One of the most central types of biomolecules of interest are lipids as they constitute essential bio-hallmarks of cardiovascular and metabolic diseases and their in-vivo detection holds insightful information about disease progression and treatment monitoring. However, the full potential of near-infrared photoacoustic for high-resolution and high-sensitivity biomedical studies of lipids has so far not been exploited due a lack of appropriate excitation sources delivering short-pulses at high-repetition-rate, high-pulse-energy, and wavelength around 1200 nm. Here, we demonstrate a custom-built SRS fiber amplifier that provides optical excitations at 1192.8 nm, repetition rates of 200 kHz, pulse durations below 2 ns, and pulse energies beyond 5 μJ. We capitalize on the performance of our excitation source and show near-infrared photoacoustics resolving intrinsic lipid contrast in biomedically relevant specimens ranging from single cells to lipid-rich tissue with subcellular resolution.
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Affiliation(s)
- Hwidon Lee
- Harvard Medical School, Boston, Massachusetts, MA 02115, USA
- Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
| | - Markus R. Seeger
- Harvard Medical School, Boston, Massachusetts, MA 02115, USA
- Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
| | - Norman Lippok
- Harvard Medical School, Boston, Massachusetts, MA 02115, USA
- Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
| | - Seemantini K. Nadkarni
- Harvard Medical School, Boston, Massachusetts, MA 02115, USA
- Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
| | - Gijs van Soest
- Department of Biomedical Engineering, Erasmus Medical Center, PO Box 2040, 3000 Rotterdam, CA The Netherlands
| | - Brett E. Bouma
- Harvard Medical School, Boston, Massachusetts, MA 02115, USA
- Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
- Department of Biomedical Engineering, Erasmus Medical Center, PO Box 2040, 3000 Rotterdam, CA The Netherlands
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Corresponding author at: Harvard Medical School, Boston, Massachusetts, MA 02115, USA.
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Zhang Y, Zhang X, Li F, Li C, Zhang D, Li X, Zhao Y, Wang W. Exploring the Ruminal Microbial Community Associated with Fat Deposition in Lambs. Animals (Basel) 2021; 11:ani11123584. [PMID: 34944359 PMCID: PMC8698113 DOI: 10.3390/ani11123584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary In modern sheep production systems, less energy is required to gain lean tissue than to deposit fat; therefore, producers are attempting to decrease fat deposition costs by altering nutrient use to benefit the production of leaner carcasses. Microbes in the rumen have vital functions in feed digestion; however, limited research has been performed on the rumen microbiome’s effect on fat deposition. This study revealed variations in microbial populations in rumen carrying different fat deposition phenotypes in a characteristic way, and these findings could aid in developing strategies for manipulating rumen microbiota to alter the production performance of sheep. Abstract Microbial communities of the sheep rumen have been studied extensively; however, their involvement in the regulation of fat deposition is unknown. Herein, we aimed to identify the correlations among fat deposition-related phenotypes and the effect of microbiota on changes in body fat accumulation. The rumen microbiota of 141 lambs was profiled by 16S ribosomal RNA sequencing, and the volatile fatty acids’ (VFAs’) concentrations were quantified by gas chromatography. Subsequently, the animals were grouped according to body mass index (BMI) to compare the microbiota of the rumen among the sheep with different fat deposition levels. Results further revealed differences in terms of the species abundance, diversity, and microbial composition between sheep with different fat deposition levels. Linear discriminant analysis (LDA) Effect Size (LEfSe) analysis and Random Forest (RF) regression analysis identified changes in 29 ruminal bacteria, which may be the main driver for different fat deposition.
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Affiliation(s)
- Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (X.Z.); (C.L.); (X.L.); (Y.Z.)
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (X.Z.); (C.L.); (X.L.); (Y.Z.)
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co., Ltd., Wuwei 733300, China;
| | - Fadi Li
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co., Ltd., Wuwei 733300, China;
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China;
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (X.Z.); (C.L.); (X.L.); (Y.Z.)
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China;
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (X.Z.); (C.L.); (X.L.); (Y.Z.)
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (X.Z.); (C.L.); (X.L.); (Y.Z.)
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (X.Z.); (C.L.); (X.L.); (Y.Z.)
- Correspondence:
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Yang C, Han L, Li P, Ding Y, Zhu Y, Huang Z, Dan X, Shi Y, Kang X. Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq. Front Genet 2021; 12:741878. [PMID: 34675965 PMCID: PMC8524388 DOI: 10.3389/fgene.2021.741878] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = -0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.
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Affiliation(s)
- Chaoyun Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Liyun Han
- Ningxia Agriculture Reclamation Helanshan Diary Co.Ltd., Yinchuan, China
| | - Peng Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yanling Ding
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Zhu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Zengwen Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Xingang Dan
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yuangang Shi
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Xiaolong Kang
- School of Agriculture, Ningxia University, Yinchuan, China
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Han J, Guo T, Yue Y, Lu Z, Liu J, Yuan C, Niu C, Yang M, Yang B. Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs. PLoS One 2021; 16:e0246279. [PMID: 33529214 PMCID: PMC7853479 DOI: 10.1371/journal.pone.0246279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022] Open
Abstract
Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.
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Affiliation(s)
- Jilong Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Min Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
- * E-mail: (MY); (BY)
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
- * E-mail: (MY); (BY)
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