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Cortes O, Cañon J, Andrino S, Fernanadez M, Carleos C. Inbreeding depression and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection. J Anim Breed Genet 2024; 141:440-452. [PMID: 38303546 DOI: 10.1111/jbg.12853] [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: 06/19/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree-based inbreeding coefficients. However, with the development of single-nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding depression in 6 growth and 2 reproductive traits in the Asturiana de los Valles cattle breed using both genealogical and molecular information. The pedigree group comprised 225,848 records and an average equivalent number of complete generations of 2.3. The molecular data comprised genotypes of 2693 animals using the Affymetrix medium-density chip. Using the pedigree information, three different inbreeding coefficients were estimated for the genotyped animals: the full pedigree coefficient (FPED), and the recent and ancient inbreeding coefficients based on the information of the last three generations (FPED<3G) and until the last three generations (FPED>3G), respectively. Using the molecular data, seven inbreeding coefficients were calculated. Four of them were estimated based on runs of homozygosity (ROH), considering (1) the total length (FROH), (2) segments shorter than 4 megabases (FROH<4), (3) between 4 and 17 megabases (FROH4-17), and (4) longer than 17 Mb (FROH>17). Additionally, the three inbreeding coefficients implemented in the Plink software (FHAT1-3) were estimated. Inbreeding depression was estimated using linear mixed-effects model with inbreeding coefficients used as covariates. All analysed traits (birth weight, preweaning average daily gain, weaning weight adjusted at 180 days, carcass weight, calving ease, age at first calving, calving interval) showed a statistically significant non-zero effect of inbreeding depression estimated from the pedigree group, except for the Postweaning Average Daily Gain trait. When inbreeding coefficients were based on the genomic group, statistically significant inbreeding depression was observed for two traits, Preweaning Average Daily Gain and Weaning Weight based on FROH, FROH>17, and FHAT3 inbreeding coefficients. Nevertheless, similar to inbreeding depression estimated based on pedigree information, estimates of inbreeding depression based on genomic information had no relevant economic impact. Despite this, from a long-term perspective, genotyped data could be included to maximize genetic progress in genetic programs following an optimal genetic contribution strategy and to consider individual inbreeding load instead global inbreeding. ROH islands were identified on chromosomes 2, 3, 8, 10, and 16. Such regions contain several candidate genes for growth development, intramuscular fat, body weight and lipid metabolism that are related to production traits selected in Asturiana de los Valles breed.
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Affiliation(s)
- Oscar Cortes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Javier Cañon
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Sara Andrino
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - María Fernanadez
- Asociación Española de Criadores de Ganado Vacuno Selecto de la Raza Asturiana de los Valles, Llanera, Spain
| | - Carlos Carleos
- Departamento Estadística e Investigación Operativa, Universidad de Oviedo, Oviedo, Spain
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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3
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Abebe BK, Wang H, Li A, Zan L. A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle. J Anim Breed Genet 2024; 141:235-256. [PMID: 38146089 DOI: 10.1111/jbg.12841] [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: 09/30/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Department of Animal Science, Werabe University, Werabe, Ethiopia
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Zhang G, Wang J, Li Y, Zhang Z, Wang X, Chen F, Shi Q, Huang Y, Wang E, Lyu S. POLB Regulates Proliferation and Apoptosis of Bovine Primary Myocytes. Animals (Basel) 2024; 14:1323. [PMID: 38731327 PMCID: PMC11083859 DOI: 10.3390/ani14091323] [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: 02/06/2024] [Revised: 03/30/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
DNA polymerase β (DNA polymerase beta (POLB)) belongs to a member of the DNA polymerase X family, mainly involved in various biological metabolic processes, such as eukaryotic DNA replication, DNA damage repair, gene recombination, and cell cycle regulation. In this study, the muscle development-related gene POLB was screened by selection signature and RNA-seq analysis and then validated for the proliferation and apoptosis of bovine primary myocytes. It was also found that overexpression of the POLB gene had a pro-apoptosis effect, but interfering with the expression of the gene had no significant effect on cells. Then, the analysis of related apoptotic genes revealed that POLB overexpression affected CASP9 gene expression.
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Affiliation(s)
- Geyang Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (J.W.); (Y.H.)
| | - Yulong Li
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Xiangnan Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Fuying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (J.W.); (Y.H.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Ueda S, Yoshida Y, Kebede B, Kitamura C, Sasaki R, Shinohara M, Fukuda I, Shirai Y. New Implications of Metabolites and Free Fatty Acids in Quality Control of Crossbred Wagyu Beef during Wet Aging Cold Storage. Metabolites 2024; 14:95. [PMID: 38392987 PMCID: PMC10890485 DOI: 10.3390/metabo14020095] [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: 12/30/2023] [Accepted: 01/11/2024] [Indexed: 02/25/2024] Open
Abstract
Efficient cold-chain delivery is essential for maintaining a sustainable global food supply. This study used metabolomic analysis to examine meat quality changes during the "wet aging" of crossbred Wagyu beef during cold storage. The longissimus thoracic (Loin) and adductor muscles (Round) of hybrid Wagyu beef, a cross between the Japanese Black and Holstein-Friesian breeds, were packaged in vacuum film and refrigerated for up to 40 days. Sensory evaluation indicated an increase in the umami and kokumi taste owing to wet aging. Comprehensive analysis using gas chromatography-mass spectrometry identified metabolite changes during wet aging. In the Loin, 94 metabolites increased, and 24 decreased; in the Round, 91 increased and 18 decreased. Metabolites contributing to the umami taste of the meat showed different profiles during wet aging. Glutamic acid increased in a cold storage-dependent manner, whereas creatinine and inosinic acid degraded rapidly even during cold storage. In terms of lipids, wet aging led to an increase in free fatty acids. In particular, linoleic acid, a polyunsaturated fatty acid, increased significantly among the free fatty acids. These results provide new insight into the effects of wet aging on Wagyu-type beef, emphasizing the role of free amino acids, organic acids, and free fatty acids generated during cold storage.
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Affiliation(s)
- Shuji Ueda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Yuka Yoshida
- Japan Meat Science and Technology Institute, Tokyo 150-0013, Japan
| | - Biniam Kebede
- Department of Food Science, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Chiaki Kitamura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Ryo Sasaki
- Food Oil and Fat Research Laboratory, Miyoshi Oil & Fat Co., Ltd., Tokyo 124-8510, Japan
| | - Masakazu Shinohara
- The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, Hyogo 650-0017, Japan
| | - Itsuko Fukuda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Yasuhito Shirai
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
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Qian X, Klatt S, Bennewitz K, Wohlfart DP, Lou B, Meng Y, Buettner M, Poschet G, Morgenstern J, Fleming T, Sticht C, Hausser I, Fleming I, Szendroedi J, Nawroth PP, Kroll J. Impaired Detoxification of Trans, Trans-2,4-Decadienal, an Oxidation Product from Omega-6 Fatty Acids, Alters Insulin Signaling, Gluconeogenesis and Promotes Microvascular Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302325. [PMID: 38059818 PMCID: PMC10811472 DOI: 10.1002/advs.202302325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/22/2023] [Indexed: 12/08/2023]
Abstract
Omega-6 fatty acids are the primary polyunsaturated fatty acids in most Western diets, while their role in diabetes remains controversial. Exposure of omega-6 fatty acids to an oxidative environment results in the generation of a highly reactive carbonyl species known as trans, trans-2,4-decadienal (tt-DDE). The timely and efficient detoxification of this metabolite, which has actions comparable to other reactive carbonyl species, such as 4-hydroxynonenal, acrolein, acetaldehyde, and methylglyoxal, is essential for disease prevention. However, the detoxification mechanism for tt-DDE remains elusive. In this study, the enzyme Aldh9a1b is identified as having a key role in the detoxification of tt-DDE. Loss of Aldh9a1b increased tt-DDE levels and resulted in an abnormal retinal vasculature and glucose intolerance in aldh9a1b-/- zebrafish. Transcriptomic and metabolomic analyses revealed that tt-DDE and aldh9a1b deficiency in larval and adult zebrafish induced insulin resistance and impaired glucose homeostasis. Moreover, alterations in hyaloid vasculature is induced by aldh9a1b knockout or by tt-DDE treatment can be rescued by the insulin receptor sensitizers metformin and rosiglitazone. Collectively, these results demonstrated that tt-DDE is the substrate of Aldh9a1b which causes microvascular damage and impaired glucose metabolism through insulin resistance.
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Affiliation(s)
- Xin Qian
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| | - Stephan Klatt
- Institute for Vascular SignalingCentre for Molecular MedicineGoethe‐Universityam Main60590FrankfurtGermany
- The German Centre for Cardiovascular Research (DZHK)Partner site RheinMain60590FrankfurtGermany
| | - Katrin Bennewitz
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| | - David Philipp Wohlfart
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| | - Bowen Lou
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
- Present address:
Cardiovascular Department, the First Affiliated Hospital of Xi'an Jiaotong University277 West Yanta RoadXi'an710061China
| | - Ye Meng
- Bone Marrow Transplantation CenterThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Michael Buettner
- Metabolomics Core Technology PlatformCentre for Organismal StudiesHeidelberg University69120HeidelbergGermany
| | - Gernot Poschet
- Metabolomics Core Technology PlatformCentre for Organismal StudiesHeidelberg University69120HeidelbergGermany
| | - Jakob Morgenstern
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Thomas Fleming
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Carsten Sticht
- NGS Core FacilityMedical Faculty MannheimHeidelberg University68167MannheimGermany
| | - Ingrid Hausser
- Institute of Pathology IPHEM LabHeidelberg University Hospital69120HeidelbergGermany
| | - Ingrid Fleming
- Institute for Vascular SignalingCentre for Molecular MedicineGoethe‐Universityam Main60590FrankfurtGermany
- The German Centre for Cardiovascular Research (DZHK)Partner site RheinMain60590FrankfurtGermany
| | - Julia Szendroedi
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Peter Paul Nawroth
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Jens Kroll
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
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Cao C, Cai Y, Li Y, Li T, Zhang J, Hu Z, Zhang J. Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq. Poult Sci 2023; 102:103122. [PMID: 37832186 PMCID: PMC10568565 DOI: 10.1016/j.psj.2023.103122] [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: 06/27/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Duck is an economically important poultry, and there is currently a major focus on improving its meat quality through breeding. There are wide variations in the growth regulation mechanisms of different duck breeds, that fundamental research on skeletal muscle growth is essential for understanding the regulation of unknown genes. The study aimed to broaden the understanding the duck skeletal muscle development and thereby to improve the performance of domestic ducks. In this study, RNA-seq data from skeletal muscles (breast muscle and leg muscle) of Pekin duck and Hanzhong Ma duck sampled at d 17, 21, and 27 of embryo (E17d, E21d, and E27d), as well as at 6-mo-old following birth (M6), to investigate and compare the mRNA temporal expression profiles and associated pathways that regulate skeletal myogenesis of different duck breeds. There were 331 to 1,440 annotated differentially expressed genes (DEGs) in breast muscle and 380 to 1,790 annotated DEGs in leg muscle from different databases between 2 duck breeds. Gene ontology (GO) enrichment in skeletal muscles indicated that these DEGs were mainly involved in biosynthetic process, developmental process, regulation of protein metabolic process and regulation of gene expression. KEGG analysis in skeletal muscles showed that a total of 41 DEGs were mapped to 7 KEGG pathways, including ECM-receptor interaction, focal adhesion, carbon metabolism, regulation of actin cytoskeleton, calcium signaling pathway, biosynthesis of amino acids and PPAR signaling pathway. The differential expression of 8 selected DEGs was verified by qRT-PCR, and the results were consistent with RNA-seq data. The identified DEGs, such as SDC, SPP1, PAK1, MYL9, PGK1, NOS1, PHGDH, TNNT2, FN1, and AQP4, were specially highlighted, indicating their associations with muscle development in the Pekin duck and Hanzhong Ma duck. This study provides a basis for revealing the differences in skeletal muscle development between Pekin duck and Hanzhong Ma duck.
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Affiliation(s)
- Chang Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Yingjie Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Yuxiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Tao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Jiqiao Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Zhigang Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Jianqin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China.
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Wu J, Wu T, Xie X, Niu Q, Zhao Z, Zhu B, Chen Y, Zhang L, Gao X, Niu X, Gao H, Li J, Xu L. Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle. Foods 2023; 12:3986. [PMID: 37959106 PMCID: PMC10647706 DOI: 10.3390/foods12213986] [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: 09/17/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.
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Affiliation(s)
- Jiayuan Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Tianyi Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xueyuan Xie
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Qunhao Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Zhida Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Bo Zhu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Yan Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lupei Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xue Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xiaoyan Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Huijiang Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Junya Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lingyang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
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Yuan S, Tian S, Meng C, Ji F, Zhou B, Rushdi HE, Ye M. The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis. Animals (Basel) 2023; 13:3256. [PMID: 37893980 PMCID: PMC10603692 DOI: 10.3390/ani13203256] [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: 08/05/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme-substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.
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Affiliation(s)
- Siyu Yuan
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
| | - Shaoqi Tian
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
| | - Chuang Meng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Feng Ji
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100089, China;
| | - Bin Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Hossam E. Rushdi
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Manhong Ye
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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Chen B, Yue Y, Li J, Yuan C, Guo T, Zhang D, Liu J, Yang B, Lu Z. Global DNA Methylation, miRNA, and mRNA Profiles in Sheep Skeletal Muscle Promoted by Hybridization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15398-15406. [PMID: 37815113 DOI: 10.1021/acs.jafc.3c02173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
With the development of high-throughput sequencing technology, several nongenetic variations, including noncoding RNAs such as miRNAs, and DNA methylation, have been found to play an important role in animal muscle development and fat metabolism. In this study, Southdown and Suffolk were selected as male parents for hybridization with Hu sheep (Southdown × Hu (NH), Suffolk × Hu (SH), and Hu × Hu (HH)). RNA sequencing, bisulfite sequencing, and small-RNA sequencing were used to study the methylation patterns and differences in miRNA and mRNA expression in the F1 sheep longissimus dorsi muscle tissue. We identified 765 differentially expressed genes (DEGs), 10,161 differentially methylated regions (DMRs), and 164 differentially expressed miRNAs, which were significantly enriched in AMPK signaling, fatty acid degradation, metabolism, and other related pathways (P < 0.05). In addition, we constructed a DNA methylation-mRNA and miRNA-mRNA coexpression network. A total of 42 common genes were identified from DMRs and DEGs. Importantly, we predicted that 33 differentially expressed miRNAs directly or indirectly targeted the SLC27A6. The data obtained in this study provide useful information and evidence to support further understanding of the miRNA and DNA methylation of key genes regulating muscle growth and fat metabolism in hybrid sheep populations.
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Affiliation(s)
- Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Dan Zhang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Bohui Yang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
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