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Monedero Cobeta I, Gomez Bris R, Rodríguez-Rodríguez P, Saez A, Quintana-Villamandos B, González Granado JM, Arribas SM. Fetal programming and lactation: modulating gene expression in response to undernutrition during intrauterine life. Pediatr Res 2024; 95:1764-1774. [PMID: 38326476 DOI: 10.1038/s41390-024-03042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND Adverse environmental conditions during intrauterine life, known as fetal programming, significantly contribute to the development of diseases in adulthood. Fetal programming induced by factors like maternal undernutrition leads to low birth weight and increases the risk of cardiometabolic diseases. METHODS We studied a rat model of maternal undernutrition during gestation (MUN) to investigate gene expression changes in cardiac tissue using RNA-sequencing of day 0-1 litters. Moreover, we analyzed the impact of lactation at day 21, in MUN model and cross-fostering experiments, on cardiac structure and function assessed by transthoracic echocardiography, and gene expression changes though qPCR. RESULTS Our analysis identified specific genes with altered expression in MUN rats at birth. Two of them, Agt and Pparg, stand out for being associated with cardiac hypertrophy and fibrosis. At the end of the lactation period, MUN males showed increased expression of Agt and decreased expression of Pparg, correlating with cardiac hypertrophy. Cross-fostering experiments revealed that lactation with control breastmilk mitigated these expression changes reducing cardiac hypertrophy in MUN males. CONCLUSIONS Our findings highlight the interplay between fetal programming, gene expression, and cardiac hypertrophy suggesting that lactation period is a potential intervention window to mitigate the effects of fetal programming. IMPACT Heart remodeling involves the alteration of several groups of genes and lactation period plays a key role in establishing gene expression modification caused by fetal programming. We could identify expression changes of relevant genes in cardiac tissue induced by undernutrition during fetal life. We expose the contribution of the lactation period in modulating the expression of Agt and Pparg, relevant genes associated with cardiac hypertrophy. This evidence reveal lactation as a crucial intervention window for preventing or countering fetal programming.
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Affiliation(s)
- Ignacio Monedero Cobeta
- Department of Physiology, Faculty of Medicine, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Raquel Gomez Bris
- Department of Physiology, Faculty of Medicine, Universidad Autónoma de Madrid, 28029, Madrid, Spain
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041, Madrid, Spain
| | | | - Angela Saez
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041, Madrid, Spain
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria (UFV), 28223, Pozuelo de Alarcón, Spain
| | - Begoña Quintana-Villamandos
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Jose Maria González Granado
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041, Madrid, Spain.
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid, 28040, Madrid, Spain.
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain.
| | - Silvia Magdalena Arribas
- Department of Physiology, Faculty of Medicine, Universidad Autónoma de Madrid, 28029, Madrid, Spain.
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Zhou C, Wang Y, He S, Lin S, Cheng J, Hu Q, Meng F, Gu T, Cai G, Li Z, Wu Z, Hong L. DIA-based quantitative proteomic analysis of porcine endometrium in the peri-implantation phase. J Proteomics 2024; 293:105065. [PMID: 38158016 DOI: 10.1016/j.jprot.2023.105065] [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: 07/18/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
The 12th day of gestation is a critical period for embryo loss and the beginning of imminent implantation in sows. Data independent acquisition (DIA) technology is one of the high-throughput, high-resolution and reproducible proteomics technologies for large-scale digital qualitative and quantitative research. The aim of this study was to identify and characterize the protein abundance landscape of Yorkshire pig endometrium on the 12th day of pregnancy (P12) and estrous cycle (C12) using DIA proteomics. A total of 1251 differentially abundant proteins (DAPs) were identified, of which 882 were up-regulated and 369 were down-regulated at P12. Functional enrichment analysis showed that the identified proteins were related to metabolism, biosynthesis and signaling pathways. Three proteins were selected for Western blot (WB) validation and the results were consistent with the DIA data. Further combined with transcriptome data, fibrinogen like 2 (FGL2) and S100 calcium binding protein A8 (S100A8) were verified to be highly abundant in the P12 endometrial epithelium. In summary, there were significantly different abundance of proteome profiles in C12 and P12 endometrium, suggesting that DAPs are associated with changes in endometrial receptivity, which laid the foundation for further research on related regulatory mechanisms. SIGNIFICANCE: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation. SIGNIFICANCE OF THE STUDY: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation.
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Affiliation(s)
- Chen Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yongzhong Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Simin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shifei Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Jie Cheng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Qun Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Fanming Meng
- Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China; Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China; Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, China.
| | - Linjun Hong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China; Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, China.
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Fernandes AC, Polizel GHG, Cracco RC, Cançado FACQ, Baldin GC, Poleti MD, Ferraz JBS, Santana MHDA. Metabolomics Changes in Meat and Subcutaneous Fat of Male Cattle Submitted to Fetal Programming. Metabolites 2023; 14:9. [PMID: 38248812 PMCID: PMC10819762 DOI: 10.3390/metabo14010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
This study investigated changes in meat and subcutaneous fat metabolomes and possible metabolic pathways related to prenatal nutrition in beef cattle. For this purpose, 18 Nellore bulls were used for meat sampling and 15 for fat sampling. The nutritional treatments during the gestation were: NP-not programmed or control, without protein-energy supplementation; PP-partially programmed, with protein-energy supplementation (0.3% of body weight (BW)) only in the final third of pregnancy; and FP-full programming, with protein-energy supplementation (0.3% of BW) during the entire pregnancy. The meat and fat samples were collected individually 24 h after slaughter, and the metabolites were extracted using a combination of chemical reagents and mechanical processes and subsequently quantified using liquid chromatography or flow injection coupled to mass spectrometry. The data obtained were submitted to principal component analysis (PCA), analysis of variance (ANOVA), and functional enrichment analysis, with a significance level of 5%. The PCA showed an overlap between the treatments for both meat and fat. In meat, 25 metabolites were statistically different between treatments (p ≤ 0.05), belonging to four classes (glycerophospholipids, amino acids, sphingolipids, and biogenic amine). In fat, 10 significant metabolites (p ≤ 0.05) were obtained in two classes (phosphatidylcholine and lysophosphatidylcholine). The functional enrichment analysis showed alterations in the aminoacyl-tRNA pathway in meat (p = 0.030); however, there was no pathway enriched for fat. Fetal programming influenced the meat and fat metabolomes and the aminoacyl-tRNA metabolic pathway, which is an important candidate for the biological process linked to meat quality and related to fetal programming in beef cattle.
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Affiliation(s)
- Arícia Christofaro Fernandes
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (G.H.G.P.); (M.H.d.A.S.)
| | - Guilherme Henrique Gebim Polizel
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (G.H.G.P.); (M.H.d.A.S.)
| | - Roberta Cavalcante Cracco
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (G.H.G.P.); (M.H.d.A.S.)
| | - Fernando Augusto Correia Queiroz Cançado
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (G.H.G.P.); (M.H.d.A.S.)
| | - Geovana Camila Baldin
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (G.H.G.P.); (M.H.d.A.S.)
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.D.P.); (J.B.S.F.)
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.D.P.); (J.B.S.F.)
| | - Miguel Henrique de Almeida Santana
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (USP), Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (G.H.G.P.); (M.H.d.A.S.)
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Huang N, Chen W, Jiang H, Yang J, Zhang Y, Shi H, Wang Y, Yuan P, Qiao J, Wei Y, Zhao Y. Metabolic dynamics and prediction of sFGR and adverse fetal outcomes: a prospective longitudinal cohort study. BMC Med 2023; 21:455. [PMID: 37996847 PMCID: PMC10666385 DOI: 10.1186/s12916-023-03134-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Selective fetal growth restriction (sFGR) is an extreme complication that significantly increases the risk of perinatal mortality and long-term adverse neurological outcomes in offspring, affecting approximately 15% of monochorionic diamniotic (MCDA) twin pregnancies. The lack of longitudinal cohort studies hinders the early prediction and intervention of sFGR. METHODS We constructed a prospective longitudinal cohort study of sFGR, and quantified 25 key metabolites in 337 samples from maternal plasma in the first, second, and third trimester and from cord plasma. In particular, our study examined fetal growth and brain injury data from ultrasonography and used the Ages and Stages Questionnaire-third edition subscale (ASQ-3) to evaluate the long-term neurocognitive behavioral development of infants aged 2-3 years. Furthermore, we correlated metabolite levels with ultrasound data, including physical development and brain injury indicators, and ASQ-3 data using Spearman's-based correlation tests. In addition, special combinations of differential metabolites were used to construct predictive models for the occurrence of sFGR and fetal brain injury. RESULTS Our findings revealed various dynamic patterns for these metabolites during pregnancy and a maximum of differential metabolites between sFGR and MCDA in the second trimester (n = 8). The combination of L-phenylalanine, L-leucine, and L-isoleucine in the second trimester, which were closely related to fetal growth indicators, was highly predictive of sFGR occurrence (area under the curve [AUC]: 0.878). The combination of L-serine, L-histidine, and L-arginine in the first trimester and creatinine in the second trimester was correlated with long-term neurocognitive behavioral development and showed the capacity to identify fetal brain injury with high accuracy (AUC: 0.94). CONCLUSIONS The performance of maternal plasma metabolites from the first and second trimester is superior to those from the third trimester and cord plasma in discerning sFGR and fetal brain injury. These metabolites may serve as useful biomarkers for early prediction and promising targets for early intervention in clinical settings.
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Affiliation(s)
- Nana Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Wei Chen
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
| | - Hai Jiang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Jing Yang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Youzhen Zhang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Huifeng Shi
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Ying Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Pengbo Yuan
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China.
- Beijing Advanced Innovation Center for Genomics, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China.
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 Huayuan North Road, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- National Center for Healthcare Quality Management in Obstetrics, Beijing, China.
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Salavati M, Clark R, Becker D, Kühn C, Plastow G, Dupont S, Moreira GCM, Charlier C, Clark EL. Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing. G3 (BETHESDA, MD.) 2023; 13:jkad108. [PMID: 37216666 PMCID: PMC10411599 DOI: 10.1093/g3journal/jkad108] [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: 02/27/2023] [Revised: 02/27/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]
Abstract
Understanding the genomic control of tissue-specific gene expression and regulation can help to inform the application of genomic technologies in farm animal breeding programs. The fine mapping of promoters [transcription start sites (TSS)] and enhancers (divergent amplifying segments of the genome local to TSS) in different populations of cattle across a wide diversity of tissues provides information to locate and understand the genomic drivers of breed- and tissue-specific characteristics. To this aim, we used Cap Analysis Gene Expression (CAGE) sequencing, of 24 different tissues from 3 populations of cattle, to define TSS and their coexpressed short-range enhancers (<1 kb) in the ARS-UCD1.2_Btau5.0.1Y reference genome (1000bulls run9) and analyzed tissue and population specificity of expressed promoters. We identified 51,295 TSS and 2,328 TSS-Enhancer regions shared across the 3 populations (dairy, beef-dairy cross, and Canadian Kinsella composite cattle from 2 individuals, 1 of each sex, per population). Cross-species comparative analysis of CAGE data from 7 other species, including sheep, revealed a set of TSS and TSS-Enhancers that were specific to cattle. The CAGE data set will be combined with other transcriptomic information for the same tissues to create a new high-resolution map of transcript diversity across tissues and populations in cattle for the BovReg project. Here we provide the CAGE data set and annotation tracks for TSS and TSS-Enhancers in the cattle genome. This new annotation information will improve our understanding of the drivers of gene expression and regulation in cattle and help to inform the application of genomic technologies in breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Richard Clark
- Edinburgh Clinical Research Facility, Genetics Core, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock 18059, Germany
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton T6G 2H1, Canada
| | - Sébastien Dupont
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège 4000, Belgium
| | | | - Carole Charlier
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège 4000, Belgium
- Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
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Muroya S, Otomaru K, Oshima K, Oshima I, Ojima K, Gotoh T. DNA Methylation of Genes Participating in Hepatic Metabolisms and Function in Fetal Calf Liver Is Altered by Maternal Undernutrition during Gestation. Int J Mol Sci 2023; 24:10682. [PMID: 37445858 DOI: 10.3390/ijms241310682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
This study aimed to elucidate the effects of maternal undernutrition (MUN) on epigenetic modification of hepatic genes in Japanese Black fetal calves during gestation. Using a previously established experimental design feeding the dams with 60% (LN) or 120% (HN) of their global nutritional requirements during the 8.5-month gestational period, DNA methylation in the fetal liver was analyzed with reduced representation bisulfite sequencing (RRBS). The promoters and gene bodies in the LN fetuses were hypomethylated compared to HN fetuses. Pathway analysis showed that the genes with DMR in the exon/intron in the LN group were associated with pathways involved in Cushing syndrome, gastric acid secretion, and aldosterone synthesis and secretion. Promoter hypomethylation in the LN group was frequently observed in genes participating in various signaling pathways (thyroid hormone, Ras/Rap1, PIK3-Akt, cAMP), fatty acid metabolism, and cholesterol metabolism. The promoter hypomethylated genes ALPL and GNAS were upregulated in the LN group, whereas the promoter hypermethylated genes GRB10 and POR were downregulated. The intron/exon hypomethylated genes IGF2, IGF2R, ACAD8, TAT, RARB, PINK1, and SOAT2 were downregulated, whereas the hypermethylated genes IGF2BP2, NOS3, and NR2F1 were upregulated. Collectively, MUN alters the promoter and gene body methylation of genes associated with hepatic metabolisms (energy, cholesterol, mitochondria) and function, suggesting an impact of altered gene methylation on the dysregulation of gene expression in the fetal liver.
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Affiliation(s)
- Susumu Muroya
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Tsukuba 305-0901, Ibaraki, Japan
| | - Konosuke Otomaru
- Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Kagoshima, Japan
| | - Kazunaga Oshima
- Division of Year-Round Grazing Research, NARO Western Region Agricultural Research Center, 60 Yoshinaga, Ohda 694-0013, Shimane, Japan
| | - Ichiro Oshima
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Kagoshima, Japan
| | - Koichi Ojima
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Tsukuba 305-0901, Ibaraki, Japan
| | - Takafumi Gotoh
- Field Science Center for Northern Biosphere, Hokkaido University, N11W10, Kita, Sapporo 060-0811, Hokkaido, Japan
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Meneses JAM, Nascimento KB, Galvão MC, Ramírez-Zamudio GD, Gionbelli TRS, Ladeira MM, Duarte MDS, Casagrande DR, Gionbelli MP. Protein Supplementation during Mid-Gestation Alters the Amino Acid Patterns, Hepatic Metabolism, and Maternal Skeletal Muscle Turnover of Pregnant Zebu Beef Cows. Animals (Basel) 2022; 12:ani12243567. [PMID: 36552487 PMCID: PMC9774392 DOI: 10.3390/ani12243567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
From 100 to 200 days of gestation, 52 cows carrying male (n = 30) or female (n = 22) fetuses were assigned to CON (basal diet-5.5% of CP, n = 26) or SUP (basal diet + protein supplement [40% CP, 3.5 g/kg BW]-12% of CP, n = 26) treatments. Glucose concentrations decreased at 200 (p ≤ 0.01; CON = 46.9 and SUP = 54.7 mg/dL) and 270 days (p ≤ 0.05; CON = 48.4 and SUP = 53.3 mg/dL) for CON compared to SUP. The same pattern occurred for insulin (p ≤ 0.01). At parturition, the NEFA concentration was greater (p = 0.01, 0.10 vs. 0.08 mmol/L) for CON than for SUP. Total AA increased in SUP (p ≤ 0.03) at mid- and late-gestation compared to CON. At 200 days, CON dams carrying females had less essential AA (p = 0.01) than cows carrying males. The SUP dams had greater expressions of protein synthesis markers, namely eIf4E and GSK3β (p ≤ 0.04), at day 200 and of MuFR1 (protein degradation marker, p ≤ 0.04) at parturition. Supplemented cows had higher hepatic pyruvate carboxylase expressions (p = 0.02). Therefore, PS alleviates the restriction overload on maternal metabolism.
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Affiliation(s)
- Javier Andrés Moreno Meneses
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
- Department of Veterinary Medicine and Animal Science, Universidad de Ciencias Aplicadas y Ambientales, Cartagena 130001, Bolivar, Colombia
| | | | | | | | | | - Marcio Machado Ladeira
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
| | | | - Daniel Rume Casagrande
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
| | - Mateus Pies Gionbelli
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
- Correspondence: ; Tel.: +55-(35)-3829-4618
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8
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The Exploration of Fetal Growth Restriction Based on Metabolomics: A Systematic Review. Metabolites 2022; 12:metabo12090860. [PMID: 36144264 PMCID: PMC9501562 DOI: 10.3390/metabo12090860] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/03/2022] [Accepted: 09/04/2022] [Indexed: 11/30/2022] Open
Abstract
Fetal growth restriction (FGR) is a common complication of pregnancy and a significant cause of neonatal morbidity and mortality. The adverse effects of FGR can last throughout the entire lifespan and increase the risks of various diseases in adulthood. However, the etiology and pathogenesis of FGR remain unclear. This study comprehensively reviewed metabolomics studies related with FGR in pregnancy to identify potential metabolic biomarkers and pathways. Relevant articles were searched through two online databases (PubMed and Web of Science) from January 2000 to July 2022. The reported metabolites were systematically compared. Pathway analysis was conducted through the online MetaboAnalyst 5.0 software. For humans, a total of 10 neonatal and 14 maternal studies were included in this review. Several amino acids, such as alanine, valine, and isoleucine, were high frequency metabolites in both neonatal and maternal studies. Meanwhile, several pathways were suggested to be involved in the development of FGR, such as arginine biosynthesis, arginine, and proline metabolism, glyoxylate and dicarboxylate metabolism, and alanine, aspartate, and glutamate metabolism. In addition, we also included 8 animal model studies, in which three frequently reported metabolites (glutamine, phenylalanine, and proline) were also present in human studies. In general, this study summarized several metabolites and metabolic pathways which may help us to better understand the underlying metabolic mechanisms of FGR.
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9
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Muroya S. An insight into farm animal skeletal muscle metabolism based on a metabolomics approach. Meat Sci 2022; 195:108995. [DOI: 10.1016/j.meatsci.2022.108995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 01/10/2023]
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10
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Ghanem N, Zayed M, Mohamed I, Mohammady M, Shehata MF. Co-expression of candidate genes regulating growth performance and carcass traits of Barki lambs in Egypt. Trop Anim Health Prod 2022; 54:260. [PMID: 35953554 PMCID: PMC9372007 DOI: 10.1007/s11250-022-03263-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/29/2022] [Indexed: 12/02/2022]
Abstract
Sheep are considered one of the main sources of animal protein in Egypt and the producers of sheep mutton eagers to find biological criteria for selecting fast-growing lambs that reach market weight early. Therefore, the present study aimed to find a link between the expression profile of selected candidate genes with growth performance and carcass traits of Barki lambs. Thirty-eight Barki lambs were kept and fed individually after weaning till 12 months of age and were divided into 3 groups according to growth performance (fast, intermediate, and slow-growing). Three samples were taken from different body tissues (eye muscle, liver, and fat tail) of each group, directly during slaughtering and stored at − 80 °C until RNA isolation. Real-time PCR was used to profile selected candidate genes (RPL7, CTP1, FABP4, ADIPOQ, and CAPN3) and GAPDH was used as a housekeeping gene. The results indicated that the final body weight was significantly (P ≤ 0.05) greater in the fast (49.9 kg) and intermediate (40.7 kg) compared to slow-growing animals (30.8 kg). The hot carcass weight was heavier (P ≤ 0.05) in the fast and intermediate-growing (24.57 and 19.07 kg) than slow-growing lambs (15.10 kg). The blood profiles of T3 and T4 hormones in addition to other parameters such as total protein, total lipids, and calcium level showed no clear variations among different experimental groups. At the molecular level, our data demonstrated upregulation of genes involved in protein biosynthesis (RPL7), fatty acid oxidation (CPT1), and lipolysis (FABP4) in the fast and intermediate-growing lambs in all studied tissues which facilitate protein accretion, energy expenditure, and fatty acid partitioning required for muscle building up. Moreover, the expression profile of the gene involved in muscle development (CAPN3) was increased in fast and intermediate-growing compared to slow-growing lambs in order to support muscle proper development. On the other hand, a candidate gene involved in lipogenesis (ADIPOQ) was expressed similarly in fat and liver tissues; however, its expression was increased in muscles of fast and intermediate-growing lambs compared to slow-growing animals. In conclusion, the current study indicated that the expression profile of genes involved in metabolic activities of liver, muscle, and adipose tissue is linked with the growth performance of lambs although no variations were detected in blood parameters. This provides an evidence for the importance of co-expression of these genes in body tissues to determine the final body weight and carcass characteristics of Barki sheep.
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Affiliation(s)
- Nasser Ghanem
- Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamaa Street, Giza, 12613, Egypt. .,Faculty of Agriculture, Cairo University Research Park, Cairo University, Cairo, Egypt.
| | - Mohamed Zayed
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
| | - Ismail Mohamed
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
| | - Mona Mohammady
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
| | - M F Shehata
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
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11
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Schalch Junior FJ, Polizel GHG, Cançado FACQ, Fernandes AC, Mortari I, Pires PRL, Fukumasu H, Santana MHDA, Saran Netto A. Prenatal Supplementation in Beef Cattle and Its Effects on Plasma Metabolome of Dams and Calves. Metabolites 2022; 12:metabo12040347. [PMID: 35448533 PMCID: PMC9028846 DOI: 10.3390/metabo12040347] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 02/04/2023] Open
Abstract
This study investigated the effect of different prenatal nutrition on the plasma metabolome of Nellore dams and their offspring. For that purpose, three nutritional treatments were used in 126 cows during pregnancy: NP—(control) only mineral supplementation; PP—protein-energy supplementation in the final third; and FP—protein-energy supplementation during the entire pregnancy. Targeted metabolomics were analyzed in plasma at the beginning of pregnancy and in pre-delivery of cows (n = 27) as well as in calves (n = 27, 30 ± 9.6 days of age). Data were analyzed by the analysis of variance, partial least squares discriminant analysis, and the principal component analysis (PCA). The PCA showed a clear clustering in the periods investigated only in cows (early gestation and pre-delivery). We found significant metabolites in both supervised analyses (p < 0.05 and VIP score > 1) for cows (Taurine, Glutamic acid, Histidine, and PC aa C42:2) and for calves (Carnosine, Alanine, and PC aa C26:0). The enrichment analysis revealed biological processes (p < 0.1) common among cows and calves (histidine metabolism and beta-alanine metabolism), which may be indicative of transgenerational epigenetic changes. In general, fetal programming affected mainly the metabolism of amino acids.
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Affiliation(s)
- Fernando José Schalch Junior
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (F.J.S.J.); (G.H.G.P.); (A.C.F.); (I.M.); (A.S.N.)
| | - Guilherme Henrique Gebim Polizel
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (F.J.S.J.); (G.H.G.P.); (A.C.F.); (I.M.); (A.S.N.)
| | - Fernando Augusto Correia Queiroz Cançado
- Department of Basic Sciences, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil;
| | - Arícia Christofaro Fernandes
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (F.J.S.J.); (G.H.G.P.); (A.C.F.); (I.M.); (A.S.N.)
| | - Isabela Mortari
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (F.J.S.J.); (G.H.G.P.); (A.C.F.); (I.M.); (A.S.N.)
| | - Pedro Ratto Lisboa Pires
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (P.R.L.P.); (H.F.)
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (P.R.L.P.); (H.F.)
| | - Miguel Henrique de Almeida Santana
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (F.J.S.J.); (G.H.G.P.); (A.C.F.); (I.M.); (A.S.N.)
- Correspondence: ; Tel.: +55-19-3565-4190
| | - Arlindo Saran Netto
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (F.J.S.J.); (G.H.G.P.); (A.C.F.); (I.M.); (A.S.N.)
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12
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Muroya S, Zhang Y, Otomaru K, Oshima K, Oshima I, Sano M, Roh S, Ojima K, Gotoh T. Maternal Nutrient Restriction Disrupts Gene Expression and Metabolites Associated with Urea Cycle, Steroid Synthesis, Glucose Homeostasis, and Glucuronidation in Fetal Calf Liver. Metabolites 2022; 12:metabo12030203. [PMID: 35323646 PMCID: PMC8949217 DOI: 10.3390/metabo12030203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/23/2022] Open
Abstract
This study aimed to understand the mechanisms underlying the effects of maternal undernutrition (MUN) on liver growth and metabolism in Japanese Black fetal calves (8.5 months in utero) using an approach that integrates metabolomics and transcriptomics. Dams were fed 60% (low-nutrition; LN) or 120% (high-nutrition; HN) of their overall nutritional requirements during gestation. We found that MUN markedly decreased the body and liver weights of the fetuses; metabolomic analysis revealed that aspartate, glycerol, alanine, gluconate 6-phosphate, and ophthalmate levels were decreased, whereas UDP-glucose, UDP-glucuronate, octanoate, and 2-hydroxybutyrate levels were decreased in the LN fetal liver (p ≤ 0.05). According to metabolite set enrichment analysis, the highly different metabolites were associated with metabolisms including the arginine and proline metabolism, nucleotide and sugar metabolism, propanoate metabolism, glutamate metabolism, porphyrin metabolism, and urea cycle. Transcriptomic and qPCR analyses revealed that MUN upregulated QRFPR and downregulated genes associated with the glucose homeostasis (G6PC, PCK1, DPP4), ketogenesis (HMGCS2), glucuronidation (UGT1A1, UGT1A6, UGT2A1), lipid metabolism (ANGPTL4, APOA5, FADS2), cholesterol and steroid homeostasis (FDPS, HSD11B1, HSD17B6), and urea cycle (CPS1, ASS1, ASL, ARG2). These metabolic pathways were extracted as relevant terms in subsequent gene ontology/pathway analyses. Collectively, these results indicate that the citrate cycle was maintained at the expense of activities of the energy metabolism, glucuronidation, steroid hormone homeostasis, and urea cycle in the liver of MUN fetuses.
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Affiliation(s)
- Susumu Muroya
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Ibaraki, Tsukuba 305-0901, Japan;
- Correspondence: (S.M.); (T.G.)
| | - Yi Zhang
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Japan; (Y.Z.); (I.O.)
| | - Kounosuke Otomaru
- Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Japan;
| | - Kazunaga Oshima
- Division of Year-Round Grazing Research, NARO Western Region Agricultural Research Center, 60 Yoshinaga, Ohda 694-0013, Shimane, Japan;
| | - Ichiro Oshima
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Japan; (Y.Z.); (I.O.)
| | - Mitsue Sano
- Faculty of Human Culture, University of Shiga Prefecture, 2500 Hassaka-cho, Hikone 522-8533, Shiga, Japan;
| | - Sanggun Roh
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Miyagi, Japan;
| | - Koichi Ojima
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Ibaraki, Tsukuba 305-0901, Japan;
| | - Takafumi Gotoh
- Department of Agricultural Sciences and Natural Resources, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-8580, Japan; (Y.Z.); (I.O.)
- Correspondence: (S.M.); (T.G.)
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