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Igoshin AV, Romashov GA, Yurchenko AA, Yudin NS, Larkin DM. Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits. Animals (Basel) 2024; 14:2059. [PMID: 39061521 PMCID: PMC11274160 DOI: 10.3390/ani14142059] [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: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and FST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds.
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Affiliation(s)
- Alexander V. Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Grigorii A. Romashov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Andrey A. Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, 94800 Villejuif, France
| | - Nikolay S. Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Denis M. Larkin
- Royal Veterinary College, University of London, London NW1 0TU, UK
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Ritter SW, Ensslin S, Gastl MI, Becker TM. Identification of key aroma compounds of faba beans (Vicia faba) and their development during germination - a SENSOMICS approach. Food Chem 2024; 435:137610. [PMID: 37806201 DOI: 10.1016/j.foodchem.2023.137610] [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: 06/25/2023] [Revised: 09/17/2023] [Accepted: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Faba beans are a promising source of valuable plant protein. However, their aroma impression is often a hindrance for the use in a broad range of food products. To develop mitigation strategies, a deeper insight into the faba bean aroma is required. Therefore, for the first time, the SENSOMICS concept was applied. First, 52 aroma active compounds in raw and malted faba beans were identified and semi-quantitatively preselected by aroma extract dilution analysis. Afterwards, the aroma compounds were quantified, odor activity values were calculated, and the 17 prominent odors were selected and used in the reconstitution of the faba bean aroma. Seven statistically significant key aroma compounds 3-methylbutanoic acid, (E)-non-2-enal, hexanal, methional, 3-methylbutanal, sotolon, and 2-methylbutan-1-ol were identified in omission experiments. Finally, their development upon malting was studied. To conclude, by knowing the key aroma compounds, specific mitigation strategies can be developed, which facilitates the broader use of faba beans.
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Affiliation(s)
- Stefan W Ritter
- Technical University Munich, Institute of Brewing and Beverage Technology, 85354 Freising, Germany.
| | - Sarah Ensslin
- Technical University Munich, Institute of Brewing and Beverage Technology, 85354 Freising, Germany
| | - Martina I Gastl
- Technical University Munich, Research Center Weihenstephan for Brewing and Food Quality, 85354 Freising, Germany.
| | - Thomas M Becker
- Technical University Munich, Institute of Brewing and Beverage Technology, 85354 Freising, Germany.
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Kar D, Ganguly I, Singh S, Bhatia AK, Dixit SP. Genome-wide runs of homozygosity signatures in diverse Indian goat breeds. 3 Biotech 2024; 14:81. [PMID: 38375512 PMCID: PMC10874352 DOI: 10.1007/s13205-024-03921-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/05/2024] [Indexed: 02/21/2024] Open
Abstract
The present study analyzed ROH and consensus ROH regions in 102 animals of eleven diverse Indian goat (Capra hircus) breeds using whole genome sequencing. A total of 51,705 ROH and 21,271 consensus regions were identified. The mean number of ROH per animal was highest in the meat breed, Jharkhand Black (2693) and lowest in the pashmina breed, Changthangi (60). The average length of ROH (ALROH) was maximum in Kanniadu (974.11 Kb) and minimum in Tellicherry (146.98 Kb). Long ROH is typically associated with more recent inbreeding, whereas short ROH is connected to more ancient inbreeding. The overall ROH-based genomic inbreeding (FROH) was highest for Jharkhand Black (0.602) followed by Kanniadu (0.120) and Sangamneri (0.108) among all breeds. FROH of Jharkhand Black was higher than Kanniadu up to 5 Mb ROH length category. However, in > 20 Mb ROH length category, Kanniadu (0.98) exhibited significantly higher FROH than Jharkhand Black (0.46). This implies that Kanniadu had higher levels of recent inbreeding than Jharkhand Black. Despite this, due to the presence of both recent and ancient inbreeding, Jharkhand Black demonstrated higher overall FROH compared to Kanniadu. ROH patterns revealed dual purpose (meat and dairy) and pashmina breeds as less consanguineous while recent inbreeding was apparent in meat breeds. Analysis of ROH consensus regions identified selection sweeps in key genes governing intramuscular fat deposition, meat tenderisation, lean meat production and carcass weight (CDK4, ALOX15, CASP9, PRDM16, DVL1) in meat breeds; milk fat percentage and mammary gland development (POLD1, NOTCH2, ARHGAP35) in dual purpose (meat and dairy) breeds; while cold adaptation and hair follicle development (APOBEC1, DNAJC3, F2RL1, FGF9) in pashmina breed. MAPK, RAS, BMP and Wnt signaling pathways associated with hair follicle morphogenesis in Changthangi were also identified. PCA analysis based on ROH consensus regions revealed that meat breeds are more diverse than other goat breeds/populations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03921-y.
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Affiliation(s)
- Dibyasha Kar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Indrajit Ganguly
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Sanjeev Singh
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Avnish Kumar Bhatia
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - S. P. Dixit
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
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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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Zhang W, Hu W, Zhu Q, Niu M, An N, Feng Y, Kawamura K, Fu P. Hydroxy fatty acids in the surface Earth system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167358. [PMID: 37793460 DOI: 10.1016/j.scitotenv.2023.167358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/06/2023]
Abstract
Lipids are ubiquitous and highly abundant in a wide range of organisms and have been found in various types of environmental media. These molecules play a crucial role as organic tracers by providing a chemical perspective on viewing the material world, as well as offering a wealth of information on metabolic activities. Among the diverse lipid compounds, hydroxy fatty acids (HFAs) with one to multiple hydroxyl groups attached to the carbon chain stand out as important biomarkers for different sources of organic matter. HFAs are widespread in nature and are involved in biotransformation and oxidation processes in living organisms. The unique chemical and physical properties attributed to the hydroxyl group make HFAs ideal biomarkers in biomedicine and environmental toxicology, as well as organic geochemistry. The molecular distribution patterns of HFAs can be unique and diagnostic for a given class of organisms, including animals, plants, and microorganisms. Thus, HFAs can act as a valuable proxy for understanding the ecological relationships between different organisms and their environment. Furthermore, HFAs have numerous industrial applications due to their higher reactivity, viscosity, and solvent miscibility. This review paper integrates the latest research on the sources and chemical analyses of HFAs, as well as their applications in industrial/medicinal production and as biomarkers in environmental studies. This review article also provides insights into the biogeochemical cycles of HFAs in the surface Earth system, highlighting the importance of these compounds in understanding the complex interactions between living organisms and the environment.
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Affiliation(s)
- Wenxin Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China.
| | - Quanfei Zhu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Mutong Niu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Na An
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yuqi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Kimitaka Kawamura
- Chubu Institute for Advanced Studies, Chubu University, Kasugai 487-8501, Japan
| | - Pingqing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China.
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Polo-Like Kinase 2 Plays an Essential Role in Cytoprotection against MG132-Induced Proteasome Inhibition via Phosphorylation of Serine 19 in HSPB5. Int J Mol Sci 2022; 23:ijms231911257. [PMID: 36232565 PMCID: PMC9569985 DOI: 10.3390/ijms231911257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/27/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Abstract
Protein homeostasis, including protein folding, refolding, and degradation, is thought to decline with aging. HSPB5 (also known as αB-crystallin) prevents target protein aggregation as a molecular chaperone and exhibits a cytoprotective function against various cell stresses. To elucidate the effect of HSPB5 on endoplasmic reticulum (ER) stress, we searched for novel binding proteins of HSPB5 using the proximity-dependent biotin labeling method. Proteins presumed to interact with HSPB5 in cells treated with the proteasome inhibitor MG132 were identified by a reversible biotin-binding capacity method combining tamavidin2-REV magnetic beads and mass spectrometry. We discovered a new binding protein for HSPB5, polo-like kinase 2 (PLK2), which is an apoptosis-related enzyme. The expression of PLK2 was upregulated by MG132 treatment, and it was co-localized with HSPB5 near the ER in L6 muscle cells. Inhibition of PLK2 decreased ER stress-induced phosphorylation of serine 19 in HSPB5 and increased apoptosis by activation of caspase 3 under ER stress. Overexpression of HSPB5 (WT) suppressed the ER stress-induced caspase 3 activity, but this was not observed with phospho-deficient HSPB5 (3A) mutants. These results clarify the role of HSPB5 phosphorylation during ER stress and suggest that the PLK2/HSPB5 pathway plays an essential role in cytoprotection against proteasome inhibition-induced ER stress.
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Ueda S, Takashima Y, Gotou Y, Sasaki R, Nakabayashi R, Suzuki T, Sasazaki S, Fukuda I, Kebede B, Kadowaki Y, Tamura M, Nakanishi H, Shirai Y. Application of Mass Spectrometry for Determining the Geographic Production Area of Wagyu Beef. Metabolites 2022; 12:777. [PMID: 36144182 PMCID: PMC9506216 DOI: 10.3390/metabo12090777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Japanese Black cattle (Japanese Wagyu) beef is attracting attention for its aroma and marbling, and its handling is increasing worldwide. Here, we focused on the origin discrimination of Wagyu beef and analyzed the nutritional components of Japanese Wagyu (produced in multiple prefectures of Japan), Hybrid Wagyu (a cross between Angus and Wagyu cattle born in Australia and transported to Japan), and Australian Wagyu beef using mass spectrometry (MS). Triple-quadrupole liquid chromatography-MS was used to clarify the molecular species of lipids in Wagyu beef. Fourteen classes of lipids were separated, and 128 different triacylglycerides (TGs) were detected. A simple comparative analysis of these TGs using high-performance liquid chromatography revealed significantly higher levels of triolein (C18:1/C18:1/C18:1; abbreviated OOO) and C18:1/C18:1/C16:1 (OOPo) in Japanese Wagyu. Wagyu elements beef were comprehensively analyzed using inductively coupled plasma (ICP)-MS and ICP-optical emission spectrometry. We found significant differences in the rubidium, cesium, and lithium levels of Japanese and Australian Wagyu beef. On comparing metabolites using gas chromatography-MS, we identified significant differences in the levels of amino acids and other components of the Japanese and Australian Wagyu beef. These results suggest the possibility of determining the origin of Wagyu cattle breeds using MS and genetic discrimination.
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Affiliation(s)
- Shuji Ueda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Yasuharu Takashima
- Incorporated Administrative Agency Food and Agricultural Materials Inspection Center, Saitama 330-0081, Japan
| | - Yunosuke Gotou
- Incorporated Administrative Agency Food and Agricultural Materials Inspection Center, Saitama 330-0081, Japan
| | - Ryo Sasaki
- Food Oil and Fat Research Laboratory, Miyoshi Oil & Fat Co., Ltd., Tokyo 124-8510, Japan
| | - Rio Nakabayashi
- Food Oil and Fat Research Laboratory, Miyoshi Oil & Fat Co., Ltd., Tokyo 124-8510, Japan
| | - Takeshi Suzuki
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Shinji Sasazaki
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Ituko Fukuda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
| | - Biniam Kebede
- Department of Food Science, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | | | | | | | - Yasuhito Shirai
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo 657-8501, Japan
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