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Nishio M, Inoue K, Arakawa A, Ichinoseki K, Kobayashi E, Okamura T, Fukuzawa Y, Ogawa S, Taniguchi M, Oe M, Takeda M, Kamata T, Konno M, Takagi M, Sekiya M, Matsuzawa T, Inoue Y, Watanabe A, Kobayashi H, Shibata E, Ohtani A, Yazaki R, Nakashima R, Ishii K. Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle. Anim Sci J 2023; 94:e13883. [PMID: 37909231 DOI: 10.1111/asj.13883] [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: 06/13/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 11/02/2023]
Abstract
We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP. Meanwhile, DK had the highest prediction accuracy for NIRS-based C18:1 and MUFA, but the difference in accuracies between DK and KAML was slight. For all traits, accuracies of RF and CNN were lower than those of GBLUP. The KAML extends GBLUP methods, of which marker effects are weighted, and involves only additive genetic effects; whereas machine learning methods capture non-additive genetic effects. Thus, KAML is the most suitable method for breeding of fatty acid composition in Japanese Black cattle.
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Affiliation(s)
- Motohide Nishio
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | - Keiichi Inoue
- National Livestock Breeding Center, Fukushima, Japan
- University of Miyazaki, Miyazaki, Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Eiji Kobayashi
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Yo Fukuzawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | - Shinichiro Ogawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Mika Oe
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Takehiro Kamata
- Aomori Prefectural Industrial Technology Research Center, Tsugaru, Japan
| | - Masaru Konno
- Iwate Agricultural Research Center Animal Industry Research Institute, Takizawa, Japan
| | - Michihiro Takagi
- Miyagi Prefecture Animal Industry Experiment Station, Osaki, Japan
| | - Mario Sekiya
- Akita Prefectural Livestock Experiment Station, Daisen, Japan
| | - Tamotsu Matsuzawa
- Livestock Research Centre, Fukushima Agricultural Technology Centre, Fukushima, Japan
| | - Yoshinobu Inoue
- Tottori Prefectural Livestock Research Center, Tottori, Japan
| | | | - Hiroshi Kobayashi
- Institute of Animal Production Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Misaki, Japan
| | - Eri Shibata
- Hiroshima Prefectural Technology Research Institute, Livestock Technology Research Center, Shobara, Japan
| | - Akihumi Ohtani
- Yamaguchi Prefectural Agriculture and Forestry General Technology Center, Mine, Japan
| | - Ryu Yazaki
- Oita Prefectural Agriculture, Forestry, and Fisheries Research Center, Takeda, Japan
| | - Ryotaro Nakashima
- Cattle Breeding Development Institute of Kagoshima Prefecture, Soo, Japan
| | - Kazuo Ishii
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
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Ho KT, Balboula AZ, Homma K, Takanari J, Bai H, Kawahara M, Thi Kim Nguyen K, Takahashi M. Synergistic effect of standardized extract of Asparagus officinalis stem and heat shock on progesterone synthesis with lipid droplets and mitochondrial function in bovine granulosa cells. J Steroid Biochem Mol Biol 2023; 225:106181. [PMID: 36150639 DOI: 10.1016/j.jsbmb.2022.106181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/18/2022] [Indexed: 02/01/2023]
Abstract
Progesterone (P4) is a well-known steroid hormone that plays a key role in oocyte growth and the maintenance of pregnancy in mammals, including cattle. Heat stress (HS) has an adverse effect on P4 synthesis through an imbalance in the cellular redox status. We have recently revealed that a standardized extract of Asparagus officinalis stem (EAS) increases P4 through non-HS induction of heat shock protein 70 (HSP70) and a synergistic increase of HSP70 by enhancing the intracellular redox balance, which was adversely affected by HS in bovine granulosa cells (GCs). Bovine GCs collected from bovine ovarian follicles were cultured at 38.5 °C and 41 °C for 12 h with or without 5 mg/mL EAS. After treatment, cells and culture suppernatant were collected for the analysis. Enzyme-linked immunosorbent assay (ELISA) was performed to detect in P4 levels. Quantitative reverse-transcription polymerase chain reaction (RT-qPCR) was used to detect expression of steroidogenesis related genes. Fluorescence staining was used to detect mitochondrial activity and lipid droplet. P4 level was increased by EAS treatment in association with increase in steroidogenic acute regulatory protein (STAR), 3β-hydroxysteroid dehydrogenase (3β-HSD), mitochondrial membrane activity and lipid droplet both under non-HS and HS conditions. Notably, synergistic effect of EAS with HS co-treatment was observed to show a greater increase in P4 synthesis when comparison with EAS treatment under non-HS condition. Furthermore, inhibition of HSP70 significantly reduced EAS-induced P4 synthesis, mitochondrial activity and synthesis of lipid droplets. These results suggest that P4 synthesis by EAS is mediated by the steroidogenesis pathway via HSP70-regulated activation of STAR and 3β-HSD, together with improved mitochondrial activity and lipid metabolism in bovine GCs. Moreover, effect of EAS has a synergistic effect of with HSP70-regulated steroidogenesis pathway.
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Affiliation(s)
- Khoi Thieu Ho
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan; College of Agriculture, Can Tho University, Can Tho City, Viet Nam
| | | | - Kohei Homma
- AMINO UP Co. Ltd., Sapporo, Hokkaido 004-0839, Japan
| | - Jun Takanari
- AMINO UP Co. Ltd., Sapporo, Hokkaido 004-0839, Japan
| | - Hanako Bai
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Manabu Kawahara
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | | | - Masashi Takahashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
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Association of variants in FABP4, FASN, SCD, SREBP1 and TCAP genes with intramuscular fat, carcass traits and body size in Chinese Qinchuan cattle. Meat Sci 2022; 192:108882. [PMID: 35714427 DOI: 10.1016/j.meatsci.2022.108882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 12/17/2022]
Abstract
This study aimed to genotype the variants in FABP4, FASN, SCD, SREBP1 and TCAP genes, and to analyze their associations with intramuscular fat (IMF) content, carcass traits and body size in Chinese Qinchuan cattle (QC). The association studies showed that the FABP4 c.220A > G polymorphism was significantly associated with ultrasound longissimus muscle depth (ULMD) and IMF, the FASN g.16024A > G polymorphism was significantly associated with ULMD and some body size traits, the SREBP1 84 bp indel was significantly associated with back fat thickness, ULMD and some body size traits. The frequencies of well-characterized A allele in FABP4 c.220A > G in Korean cattle (KOR) and Japanese Black cattle (JB), T allele in SCD g.8586C > T in KOR, SS genotype in SREBP1 84 bp indel in KOR and JB, DELDEL genotype in TCAP g.592-597CTGCAGinsdel in KOR were significantly higher than in Chinese cattle breeds. Thus, the associated four polymorphisms were expected to be genetic selection markers for meat quality, carcass traits and body size of QC.
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Sasazaki S. Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture. Anim Sci J 2021; 92:e13663. [PMID: 34882912 DOI: 10.1111/asj.13663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/28/2023]
Abstract
The polymorphisms associated with economic traits in livestock animals provide useful information as genetic indicators for breeding improvement. Over the last two decades, several DNA markers have been developed in Japanese Black cattle; however, the effect of these markers differs across populations due to differences in their genetic structures and backgrounds. As such, there is a need to verify the effectiveness of these markers in each population. This review summarizes the effectiveness of previously reported markers on carcass traits and the development of novel DNA markers in a Japanese Black cattle population in Hyogo Prefecture. As result of genome wide association studies and resequencing analyses, two novel significant markers associated with meat quality-related traits (beef marbling and fatty acid composition) were developed. These findings will lead to the identification of responsible genes and polymorphisms and contribute to the development of novel DNA markers for numerous traits in various cattle populations.
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Affiliation(s)
- Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Gamarra D, Aldai N, Arakawa A, de Pancorbo MM, Taniguchi M. Effect of a genetic polymorphism in SREBP1 on fatty acid composition and related gene expression in subcutaneous fat tissue of beef cattle breeds. Anim Sci J 2021; 92:e13521. [PMID: 33554418 DOI: 10.1111/asj.13521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 12/25/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Sterol regulatory element-binding factor 1 (SREBP1) plays an important role in the lipogenesis which affects fatty acid (FA) composition in backfat and consequently influences beef nutritional quality. This study analyzed the association of 84 bp-indel, both short (S) and long (L) alleles in intron 5 of SREBP1, with FA composition and gene expression of SREBP1 in backfat of northern Spanish beef breeds (Pirenaica, Salers and Holstein-Friesian). Phylogenetic analysis suggests that 84 bp-indel of ruminants is a highly conserved region compared with those in the full-length sequence of intron 5 or mRNA of SREBP1 among species. Overall, higher content of polyunsaturated FAs was observed in SL genotype compared to LL genotype of 84 bp-Indel (p < .05). In particular, in Pirenaica, SL genotype was associated with a higher content of stearic (18:0), α-linolenic (18:3n-3) acid, and total n-3 content (p < .05). However, the gene expression of SREBP1 did not differ among genotypes of 84 bp-Indel (p > .05).
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Affiliation(s)
- David Gamarra
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Noelia Aldai
- Lactiker Research Group, Pharmacy & Food Sciences Department, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Aisaku Arakawa
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Marian M de Pancorbo
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Masaaki Taniguchi
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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Effect of Five Polymorphisms on Percentage of Oleic Acid in Beef and Investigation of Linkage Disequilibrium to Confirm the Locations of Quantitative Trait Loci on BTA19 in Japanese Black Cattle. Life (Basel) 2021; 11:life11070597. [PMID: 34206576 PMCID: PMC8303249 DOI: 10.3390/life11070597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/17/2022] Open
Abstract
Five polymorphisms associated with the percentage of oleic acid (C18:1) in beef fat were previously reported on bovine chromosome 19 in different Japanese Black cattle populations. This study aimed to verify the effects of these five polymorphisms on C18:1 using the same Japanese Black cattle population and conduct linkage disequilibrium (LD) analysis in order to determine the locations of the quantitative trait loci (QTLs). We genotyped the five polymorphisms (SREBP1 c.1065 + 83 (84bp indel), STARD3 c.1187 C > T, GH c.379 C > G, FASN g.841 G > C, and FASN g.16024 A > G) in two populations, which were bred in Hyogo and Gifu Prefectures, Japan (n = 441 and 443, respectively) in order to analyze their effects on C18:1 using analysis of variance (ANOVA). In the Hyogo population, SREBP1 c.1065 + 83 and STARD3 c.1187 C > T were significantly associated with C18:1 (p < 0.001). Meanwhile, FASN g.841 G > C, FASN g.16024 A > G, and GH c.379 C > G were significantly associated with C18:1 (p < 0.01) in the Gifu population. LD analysis was subsequently conducted to detect the range of the QTLs, which ranged from 32.2 to 46.4 Mbp and from 47.8 to 52.1 Mbp in the Hyogo and Gifu populations, respectively. In conclusion, this study confirmed the existence of QTLs on BTA19 and divided the candidate region for each QTL based on LD coefficients. These results could contribute to efficient searches for responsible genes and polymorphisms for fatty acid composition.
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Kumar A, Kaur M, Ahlawat S, Sharma U, Singh MK, Singh KV, Chhabra P, Vijh RK, Yadav A, Arora R. Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India. Genomics 2021; 113:1639-1646. [PMID: 33862183 DOI: 10.1016/j.ygeno.2021.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/24/2021] [Accepted: 04/07/2021] [Indexed: 01/13/2023]
Abstract
The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions.
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Affiliation(s)
- Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Manoj Kumar Singh
- Incharge Barbari Goat Unit, Genetics and Breeding Division, Central Institute for Research on Goats, Makhdoom, Farah, 281122 Mathura, Uttar Pradesh, India.
| | - Karan Veer Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Anita Yadav
- Kurukshetra University, Kurukshetra 136119, Haryana, India.
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Improving dairy performance through molecular characterization of SREBP-1 gene in Sarda sheep breed. Heliyon 2021; 7:e06489. [PMID: 33786396 PMCID: PMC7988322 DOI: 10.1016/j.heliyon.2021.e06489] [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: 08/12/2019] [Revised: 10/30/2019] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
This research has two aims: (i) to characterize the coding sequence of the SREBP-1 gene in dairy sheep in order to investigate possible relationships between single nucleotide polymorphisms (SNPs) and milk traits; and (ii) to investigate possible relationship between SREBP-1 gene expression and nucleotide variation. Four hundred adult and multiparous lactating Sarda breed ewes were selected from two farms. Milk samples were collected from Day 30 to Day 150 of lactation to determine the mean yield, somatic cell count, lactose, fat, and protein content of the milk. RNA was extracted from the milk samples, after which the SREBP-1 gene coding regions were amplified and sequenced to scan mutations. Whilst eight SNPs were identified, none had statistically significant association with the analysed milk traits. Moreover, the identified expression patterns were not affected by the SNP or combined genotypes. High SREBP-1 gene expression levels were found to be correlated with high milk fat content (P < 0.01), indicating the crucial role of this gene in the milk fat synthesis. In conclusion, the polymorphisms found within SREBP-1 gene exhibited no significant associations with milk traits or with individual SREBP-1 mRNA expression patterns. The findings thus suggest that this small genetic variability may derive from the selection carried out in Sarda breed to improve milk yield.
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Olivieri BF, Braz CU, Brito Lopes F, Peripolli E, Medeiros de Oliveira Silva R, Ruegger Pereira da Silva Corte R, Albuquerque LGD, Pereira ASC, Stafuzza NB, Baldi F. Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle. J Anim Breed Genet 2020; 138:80-90. [PMID: 32424857 DOI: 10.1111/jbg.12483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/13/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.
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Affiliation(s)
- Bianca Ferreira Olivieri
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Camila Urbano Braz
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Fernando Brito Lopes
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil.,Embrapa Cerrados, Brasilia, Brazil
| | - Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | | | | | - Lucia Galvão de Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Angélica Simone Cravo Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Nutrição e Produção Animal, Universidade de São Paulo (USP), Pirassununga, Brazil
| | | | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
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Matsumoto H, Kohara R, Sugi M, Usui A, Oyama K, Mannen H, Sasazaki S. The non-synonymous mutation in bovine SPP1 gene influences carcass weight. Heliyon 2019; 5:e03006. [PMID: 31879711 PMCID: PMC6920195 DOI: 10.1016/j.heliyon.2019.e03006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/12/2019] [Accepted: 12/05/2019] [Indexed: 01/12/2023] Open
Abstract
Meat quality in beef cattle is controlled by genetic factors. SPP1 (secreted phosphoprotein 1) gene, coding a multifunctional cytokine with diverse biological functions, is the candidate gene influencing carcass traits. In this study, we tried to discover DNA polymorphisms associated with beef quality in bovine SPP1 gene, so that two SNPs (single nucleotide polymorphisms) in the promoter region and one SNP in the CDS (coding sequence) region were identified. Although the formers were predicted to alter SPP1 expression, they did not show any effects on the traits. On the contrary, statistical analysis revealed that g.58675C > T, a non-synonymous mutation from threonine to methionine in the conservative region, had a significant effect on carcass weight. Carcass weight of the animals with C/T allele (473.9 ± 6.0 kg) was significantly heavier than that of the C/C homozygotes (459.2 ± 2.8 kg). Because SPP1 gene functions in skeletal muscle cells as a positive regulator, the non-synonymous mutation might influence muscle development and remodeling, resulting in increased carcass weight of the C/T animals. Our results indicate that the SNP can be applied as a DNA marker for the improvement of beef cattle.
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Affiliation(s)
- Hirokazu Matsumoto
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Ryosuke Kohara
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Makoto Sugi
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Azumi Usui
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Kenji Oyama
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, 675-2103, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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Leal-Gutiérrez JD, Mateescu RG. Genetic basis of improving the palatability of beef cattle: current insights. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2019.1616299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Li XZ, Yan CG, Gao QS, Yan Y, Choi SH, Smith SB. Adipogenic/lipogenic gene expression and fatty acid composition in chuck, loin, and round muscles in response to grain feeding of Yanbian Yellow cattle. J Anim Sci 2018; 96:2698-2709. [PMID: 29931237 DOI: 10.1093/jas/sky161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/09/2018] [Indexed: 12/25/2022] Open
Abstract
We hypothesized that gene expression and fatty acid composition would differ among different muscle depots and over time on a grain-based finishing diet. Additionally, we hypothesized that the concentration of SFA would decrease and the concentration of MUFA would increase proportionately with increases in percent intramuscular lipid (%IML). Ten Yanbian Yellow cattle steers (approximately 8 mo of age) were fed a corn-based diet in which the proportion of corn in the ration was increased at 4-mo intervals. Muscle samples were taken by biopsy from the chuck (trapezius), loin (longissimus dorsi), and round (biceps femoris) muscles at 12, 16, 20, 24, and 28 mo of age. The %IML increased from 12 to 28 mo of age, especially between 24 and 28 mo of age, with loin > round > chuck (age × muscle interaction P < 0.001). The percentage (g/100 g total fatty acids) of oleic acid (18:1n-9), linoleic acid (18:2n-6), and α-linolenic acid (18:3n-3), and the MUFA:SFA ratio increased with age, whereas palmitic (16:0) and stearic acid (18:0) decreased with age in all muscles (age effect P < 0.001). The expression of sterol regulatory element binding protein (SREBP1), adipose tissue fatty acid- binding protein (FABP4), stearoyl-CoA desaturase (SCD), acetyl-CoA carboxylase (ACC1), and lipoprotein lipase (LPL) increased, whereas the expression of peroxisome proliferator-activated receptor gamma (PPARγ) and fatty acid synthase (FASN) decreased with age. Expression of PPARγ, FABP4, SREBP1, SCD, FASN, ACC1, and LPL was greater in the loin than in the chuck or round (age × muscle interaction P < 0.001), although the MUFA:SFA ratio was greater in the chuck than in the loin or round (muscle effect P < 0.001). In conclusion, adipogenic gene expression was greater in the loin than in the chuck or round muscles, consistent with the greater %IML of the loin. However, the greater SCD gene expression in the loin did not result in a greater amount of MUFA in the loin, relative to the chuck and round.
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Affiliation(s)
- Xiang Z Li
- Co-Innovation Center of Beef Cattle Science and Industry Technology, Yanbian University, Yanji, Jilin, P.R. China
| | - C G Yan
- Co-Innovation Center of Beef Cattle Science and Industry Technology, Yanbian University, Yanji, Jilin, P.R. China
| | - Qi S Gao
- Co-Innovation Center of Beef Cattle Science and Industry Technology, Yanbian University, Yanji, Jilin, P.R. China
| | - Y Yan
- Co-Innovation Center of Beef Cattle Science and Industry Technology, Yanbian University, Yanji, Jilin, P.R. China
| | - Seong H Choi
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Stephen B Smith
- Department of Animal Science, Texas A&M University, College Station, TX
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13
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Le TNA, Vu HV, Okuda Y, Duong HT, Nguyen TB, Nguyen VH, Le PD, Kunieda T. Genetic characterization of Vietnamese Yellow cattle using mitochondrial DNA and Y-chromosomal haplotypes and genes associated with economical traits. Anim Sci J 2018; 89:1641-1647. [PMID: 30264425 DOI: 10.1111/asj.13099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/26/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Abstract
Vietnamese Yellow cattle are native cattle well adapted to local tropical environment. The aim of this study was to investigate genetic characteristics of the Yellow cattle using molecular markers. We investigated the nucleotide sequences of mitochondrial DNA and SRY gene on Y chromosome, and genotyped SREBP-1, SCD1, EDG1, NCAPG, DGAT1, MC1R, and HSP70 genes in the Yellow cattle population. The sequence analysis of the mitochondrial DNA showed that most of the cattle possesses zebu (Bos indicus) type I1 haplotype, suggesting relatively low genetic diversity in maternal lineage. The sequence analysis of the SRY gene indicates that while most of the males possess zebu type haplotype, taurine (Bos taurus) type haplotype was also observed, suggesting gene-flow from taurine cattle. The results of the genotyping of the functional genes showed that the NCAPG, SCD, MC1R, and HsSP70 genes are polymorphic in the population, whereas the SREBP-1, EDG1, and DGAT1 genes are monomorphic. Particularly, the presence of the desirable and undesirable alleles of the NCAPG and HSP70 genes, respectively, will be important for the selection of animals by potential performances in meat productivity and fertility. The present findings will be informative for future conservation and breeding of the Vietnamese Yellow cattle.
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Affiliation(s)
- Thu N A Le
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Hai V Vu
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Yu Okuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Huong T Duong
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Trung B Nguyen
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Faculty of Agriculture, An Giang University, Long Xuyen, Vietnam
| | - Van H Nguyen
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Phung D Le
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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Gotoh T, Nishimura T, Kuchida K, Mannen H. The Japanese Wagyu beef industry: current situation and future prospects - A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:933-950. [PMID: 29973029 PMCID: PMC6039323 DOI: 10.5713/ajas.18.0333] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022]
Abstract
In Japan, Wagyu cattle include four Japanese breeds; Black, Brown, Shorthorn, and Polled. Today, the renowned brand name Wagyu includes not only cattle produced in Japan, but also cattle produced in countries such as Australia and the United States. In recent years, the intramuscular fat percentage in beef (longissimus muscle) from Japanese Black cattle has increased to be greater than 30%. The Japanese Black breed is genetically predisposed to producing carcass lipids containing higher concentrations of monounsaturated fatty acids than other breeds. However, there are numerous problems with the management of this breed including high production costs, disposal of untreated excrement, the requirement for imported feed, and food security risks resulting from various viral diseases introduced by imported feed. The feeding system needs to shift to one that is more efficient, and improves management for farmers, food security for consumers, and the health environment for residents of Japan. Currently, we are developing a metabolic programming and an information and communications technology (ICT, or Interne of Things) management system for Wagyu beef production as future systems. If successful, we will produce safe, high-quality Wagyu beef using domestic pasture resources while solving the problems of how to utilize increasing areas of abandoned agricultural land and to make use of the plant-based feed resources in Japan’s mountainous areas.
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Affiliation(s)
- Takafumi Gotoh
- Department of Agricultural Sciences and Natural Resources, Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan.,Kuju Agricultural Research Center, Faculty of Agriculture, Kyushu University, Takeda 878-0201, Japan
| | - Takanori Nishimura
- Muscle Biology and Meat Science laboratory, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Keigo Kuchida
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
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15
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Gamarra D, Aldai N, Arakawa A, Barron LJR, López-Oceja A, de Pancorbo MM, Taniguchi M. Distinct correlations between lipogenic gene expression and fatty acid composition of subcutaneous fat among cattle breeds. BMC Vet Res 2018; 14:167. [PMID: 29792205 PMCID: PMC5966917 DOI: 10.1186/s12917-018-1481-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 04/30/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The fatty acid (FA) composition of adipose tissue influences the nutritional quality of meat products. The unsaturation level of FAs is determined by fatty acid desaturases such as stearoyl-CoA desaturases (SCDs), which are under control of the transcription factor sterol regulatory element-binding protein (SREBP). Differences in SCD genotype may thus confer variations in lipid metabolism and FA content among cattle breeds. This study investigated correlations between FA composition and lipogenic gene expression levels in the subcutaneous adipose tissue of beef cattle breeds of different gender from the Basque region of northern Spain. Pirenaica is the most important beef cattle breed in northern Spain, while Salers cattle and Holstein-Friesian cull cows are also an integral part of the regional beef supply. RESULTS Pirenaica heifers showed higher monounsaturated FA (MUFA) and conjugated linoleic acid (CLA) contents in subcutaneous adipose tissue than other breeds (P < 0.001). Alternatively, Salers bulls produced the highest oleic acid content, followed by Pirenaica heifers (P < 0.001). There was substantial variability in SCD gene expression among breeds, consistent with these differences in MUFA and CLA content. Correlations between SCD1 expression and most FA desaturation indexes (DIs) were positive in Salers (P < 0.05) and Pirenaica bulls, while, in general, SCD5 expression showed few significant correlations with DIs. There was a significant linear correlation between SCD1 and SRBEP1 in all breeds, suggesting strong regulation of SCD1 expression by SRBEP1. Pirenaica heifers showed a stronger correlation between SCD1 and SREBP1 than Pirenaica bulls. We also observed a opposite relationship between SCD1 and SCD5 expression levels and opposite associations of isoform expression levels with the ∆9 desaturation indexes. CONCLUSIONS These results suggest that the relationships between FA composition and lipogenic gene expression are influenced by breed and sex. The opposite relationship between SCD isoforms suggests a compensatory regulation of total SCD activity, while opposite relationships between SCD isoforms and desaturation indexes, specially 9c-14:1 DI, previously reported as an indicator of SCD activity, may reflect distinct activities of SCD1 and SCD5 in regulation of FA content. These findings may be useful for beef/dairy breeding and feeding programs to supply nutritionally favorable products.
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Affiliation(s)
- David Gamarra
- Biomics Research Group, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Noelia Aldai
- Lactiker Research Group; Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Aisaku Arakawa
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-0901 Japan
| | - Luis Javier R. Barron
- Lactiker Research Group; Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Andrés López-Oceja
- Biomics Research Group, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Marian M. de Pancorbo
- Biomics Research Group, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Masaaki Taniguchi
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-0901 Japan
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PUTRA DE, PAUL RC, THU LNA, OKUDA Y, YURNALIS, IBI T, KUNIEDA T. Genetic characterization of Indonesian Pesisir cattle using mitochondrial DNA and Y-chromosomal haplotypes and loci associated with economical traits and coat color. ACTA ACUST UNITED AC 2018. [DOI: 10.5924/abgri.46.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Dino Eka PUTRA
- Department of Genetic and Animal Breeding, Faculty of Animal Science, Universitas Andalas, Padang, 25163, Indonesia
| | - Ripon Chandra PAUL
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
- Department of Genetics and Animal Breeding, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Patuakhali-8602, Bangladesh
| | - Le Nu Anh THU
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Yu OKUDA
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
| | - YURNALIS
- Department of Genetic and Animal Breeding, Faculty of Animal Science, Universitas Andalas, Padang, 25163, Indonesia
| | - Takayuki IBI
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
| | - Tetsuo KUNIEDA
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
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Renaville B, Glenn KL, Mote BE, Fan B, Stalder KJ, Rothschild MF. SREBP pathway genes as candidate markers in country ham production. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.4081/ijas.2010.e7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Kimberly L. Glenn
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Benny E. Mote
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Bin Fan
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Kenneth J. Stalder
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
| | - Max F. Rothschild
- Department of Animal Science and the Center for Integrated Animal Genomics, State University, Iowa, USA
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18
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Deng T, Pang C, Ma X, Duan A, Liang S, Lu X, Liang X. Buffalo SREBP1
: molecular cloning, expression and association analysis with milk production traits. Anim Genet 2017; 48:720-721. [DOI: 10.1111/age.12587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
| | - Chunying Pang
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
| | - Xiaoya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
| | - Anqin Duan
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
| | - Shasha Liang
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
| | - Xingrong Lu
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
| | - Xianwei Liang
- Guangxi Provincial Key Laboratory of Buffalo Genetics; Breeding and Reproduction Technology; Buffalo Research Institute; Chinese Academy of Agricultural Sciences; Nanning 530001 China
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Lloyd SS, Steele EJ, Valenzuela JL, Dawkins RL. Haplotypes for Type, Degree, and Rate of Marbling in Cattle Are Syntenic with Human Muscular Dystrophy. Int J Genomics 2017; 2017:6532837. [PMID: 28913347 PMCID: PMC5585636 DOI: 10.1155/2017/6532837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/28/2017] [Indexed: 01/04/2023] Open
Abstract
Traditional analyses of a QTL on Bota 19 implicate a surfeit of candidates, but each is of marginal significance in explaining the deposition of healthy, low melting temperature fat within marbled muscle of Wagyu cattle. As an alternative approach, we have used genomic, multigenerational segregation to identify 14 conserved, ancestral 20 Mb haplotypes. These determine the degree and rate of marbling in Wagyu and other breeds of cattle. The melting temperature of intramuscular fat is highly heritable and traceable by haplotyping. Fortunately, for the production of healthy beef, some of these haplotypes are sufficiently penetrant to be expressed in heterozygous crossbreds, thereby allowing selection of sires which will improve the healthiness of beef produced under even harsh climatic conditions. The region of Bota 19 is syntenic to a region of Hosa 17 known to be important in muscle metabolism and in determining susceptibility to a form of human muscular dystrophy.
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Affiliation(s)
- Sally S. Lloyd
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
- Centre for Innovation in Agriculture, Murdoch University, Murdoch, WA 6150, Australia
| | - Edward J. Steele
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
| | - Jose L. Valenzuela
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
| | - Roger L. Dawkins
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
- Centre for Innovation in Agriculture, Murdoch University, Murdoch, WA 6150, Australia
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Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array. BMC Genomics 2017; 18:464. [PMID: 28615065 PMCID: PMC5471809 DOI: 10.1186/s12864-017-3847-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used to explore the molecular mechanism underlying important traits in cattle. In this study, we performed GWAS using high density SNP array to analyze the association between SNPs and fatty acids and evaluated the accuracy of genomic prediction for fatty acids in Chinese Simmental cattle. RESULTS Using the BayesB method, we identified 35 and 7 regions in Chinese Simmental cattle that displayed significant associations with individual fatty acids and fatty acid groups, respectively. We further obtained several candidate genes which may be involved in fatty acid biosynthesis including elongation of very long chain fatty acids protein 5 (ELOVL5), fatty acid synthase (FASN), caspase 2 (CASP2) and thyroglobulin (TG). Specifically, we obtained strong evidence of association signals for one SNP located at 51.3 Mb for FASN using Genome-wide Rapid Association Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approaches. Also, region-based association test identified multiple SNPs within FASN and ELOVL5 for C14:0. In addition, our result revealed that the effectiveness of genomic prediction for fatty acid composition using BayesB was slightly superior over GBLUP in Chinese Simmental cattle. CONCLUSIONS We identified several significantly associated regions and loci which can be considered as potential candidate markers for genomics-assisted breeding programs. Using multiple methods, our results revealed that FASN and ELOVL5 are associated with fatty acids with strong evidence. Our finding also suggested that it is feasible to perform genomic selection for fatty acids in Chinese Simmental cattle.
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21
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Oh DY, Lee JY, Jang JE, Lee SU. Genetic effects of sterol regulatory element binding proteins and fatty acid-binding protein4 on the fatty acid composition of Korean cattle (Hanwoo). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:160-166. [PMID: 27492349 PMCID: PMC5205601 DOI: 10.5713/ajas.16.0262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/25/2016] [Accepted: 08/03/2016] [Indexed: 11/27/2022]
Abstract
Objective This study identifies single-nucleotide polymorphisms (SNP) or gene combinations that affect the flavor and quality of Korean cattle (Hanwoo) by using the SNP Harvester method. Methods Four economic traits (oleic acid [C18:1], saturated fatty acids), monounsaturated fatty acids, and marbling score) were adjusted for environmental factors in order to focus solely on genetic effects. The SNP Harvester method was used to investigate gene combinations (two-way gene interactions) associated with these economic traits. Further, a multifactor dimensionality reduction method was used to identify superior genotypes in gene combinations. Results Table 3 to 4 show the analysis results for differences between superior genotypes and others for selected major gene combinations using the multifactor dimensionality reduction method. Environmental factors were adjusted for in order to evaluate only the genetic effect. Table 5 shows the adjustment effect by comparing the accuracy before and after correction in two-way gene interactions. Conclusion The g.3977-325 T>C and (g.2988 A>G, g.3977-325 T>C) combinations of fatty acid-binding protein4 were the superior gene, and the superior genotype combinations across all economic traits were the CC genotype at g.3977-325 T>C and the AACC, GACC, GGCC genotypes of (g.2988 A>G, g.3977-325 T>C).
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Affiliation(s)
- Dong-Yep Oh
- Livestock Research institute, Yeongju 750-871, Korea
| | - Jea-Young Lee
- Department of Statistics, Yeungnam University, Gyeongsan 712-749, Korea
| | - Ji-Eun Jang
- Department of Statistics, Yeungnam University, Gyeongsan 712-749, Korea
| | - Seung-Uk Lee
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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22
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Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of hepatic tissue in cattle. BMC Genomics 2016; 17:244. [PMID: 26984536 PMCID: PMC4794862 DOI: 10.1186/s12864-016-2578-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/08/2016] [Indexed: 12/12/2022] Open
Abstract
Background Compensatory growth (CG) is an accelerated growth phenomenon observed in animals upon re-alimentation following a period of dietary restriction. It is typically utilised in livestock systems to reduce feed costs during periods of reduced feed availability. The biochemical mechanisms controlling this phenomenon, however, are yet to be elucidated. This study aimed to uncover the molecular mechanisms regulating the hepatic expression of CG in cattle, utilising RNAseq. RNAseq was performed on hepatic tissue of bulls following 125 days of dietary restriction (RES) and again following 55 days of subsequent re-alimentation during which the animals exhibited significant CG. The data were compared with those of control animals offered the same diet on an ad libitum basis throughout (ADLIB). Elucidation of the molecular control of CG may yield critical information on genes and pathways which could be targeted as putative molecular biomarkers for the selection of animals with improved CG potential. Results Following a period of differential feeding, body-weight and liver weight were 161 and 4 kg higher, respectively, for ADLIB compared with RES animals. At this time RNAseq analysis of liver tissue revealed 1352 significantly differentially expressed genes (DEG) between the two treatments. DEGs indicated down-regulation of processes including nutrient transport, cell division and proliferation in RES. In addition, protein synthesis genes were up-regulated in RES following a period of restricted feeding. The subsequent 55 days of ad libitum feeding for both groups resulted in the body-weight difference reduced to 84 kg, with no difference in liver weight between treatment groups. At the end of 55 days of unrestricted feeding, 49 genes were differentially expressed between animals undergoing CG and their continuously fed counterparts. In particular, hepatic expression of cell proliferation and growth genes were greater in animals undergoing CG. Conclusions Greater expression of cell cycle and cell proliferation genes during CG was associated with a 100 % recovery of liver weight during re-alimentation. Additionally, an apparent up-regulation in capacity for cellular protein synthesis during restricted feeding may contribute to and sustain CG during re-alimentation. DEGs identified are potential candidate genes for the identification of biomarkers for CG, which may be incorporated into future breeding programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2578-5) contains supplementary material, which is available to authorized users.
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Yonekura S, Hirota S, Miyazaki H, Tokutake Y. Subcellular Localization and Polymorphism of Bovine FABP4 in Bovine Intramuscular Adipocytes. Anim Biotechnol 2016; 27:96-103. [DOI: 10.1080/10495398.2015.1102148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lee JY, Ha JJ, Park YS, Yi JK, Lee S, Mun S, Han K, Kim JJ, Kim HJ, Oh DY. Relationship between Single Nucleotide Polymorphisms in the Peroxisome Proliferator-Activated Receptor Gamma Gene and Fatty Acid Composition in Korean Native Cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:184-94. [PMID: 26732443 PMCID: PMC4698698 DOI: 10.5713/ajas.15.0502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/03/2015] [Accepted: 08/24/2015] [Indexed: 12/18/2022]
Abstract
The peroxisome proliferator-activated receptor gamma (PPARγ) gene plays an important role in the biosynthesis process controlled by a number of fatty acid transcription factors. This study investigates the relationships between 130 single-nucleotide polymorphisms (SNPs) in the PPARγ gene and the fatty acid composition of muscle fat in the commercial population of Korean native cattle. We identified 38 SNPs and verified relationships between 3 SNPs (g.1159-71208 A>G, g.42555-29812 G>A, and g.72362 G>T) and the fatty acid composition of commercial Korean native cattle (n = 513). Cattle with the AA genotype of g.1159-71208 A>G and the GG genotype of g.42555-29812 G>A and g.72362 G>T had higher levels of monounsaturated fatty acids and carcass traits (p<0.05). The results revealed that the 3 identified SNPs in the PPARγ gene affected fatty acid composition and carcass traits, suggesting that these 3 SNPs may improve the flavor and quality of beef in commercial Korean native cattle.
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Affiliation(s)
- Jea-Young Lee
- Livestock Research institute, Yeongju 750-871, Korea
| | - Jae-Jung Ha
- Livestock Research institute, Yeongju 750-871, Korea
| | - Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Hwaseong 445-760, Korea
| | - Jun-Koo Yi
- Livestock Research institute, Yeongju 750-871, Korea
| | - Seunguk Lee
- Biotechnology Research Center, The University of Tokyo, Bunkyo 113-8657, Tokyo
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea; DKU-Theragen institute for NGS analysis (DTiNa), Cheonan 330-714, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea; DKU-Theragen institute for NGS analysis (DTiNa), Cheonan 330-714, Korea
| | - J-J Kim
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
| | - Hyun-Ji Kim
- Livestock Research institute, Yeongju 750-871, Korea
| | - Dong-Yep Oh
- Livestock Research institute, Yeongju 750-871, Korea
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Chen L, Ekine-Dzivenu C, Vinsky M, Basarab J, Aalhus J, Dugan MER, Fitzsimmons C, Stothard P, Li C. Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle. BMC Genet 2015; 16:135. [PMID: 26589139 PMCID: PMC4654876 DOI: 10.1186/s12863-015-0290-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/30/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Identification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of beef fatty acid profiles through genomic selection and marker-assisted diet management. In this study, 81 and 83 fatty acid traits were measured in subcutaneous adipose (SQ) and longissimus lumborum muscle (LL), respectively, from 1366 purebred and crossbred beef steers and heifers that were genotyped on the Illumina BovineSNP50 Beadchip. The objective was to conduct genome-wide association studies (GWAS) for the fatty acid traits and to evaluate the accuracy of genomic prediction for fatty acid composition using genomic best linear unbiased prediction (GBLUP) and Bayesian methods. RESULTS In total, 302 and 360 significant SNPs spanning all autosomal chromosomes were identified to be associated with fatty acid composition in SQ and LL tissues, respectively. Proportions of total genetic variance explained by individual significant SNPs ranged from 0.03 to 11.06% in SQ, and from 0.005 to 24.28% in the LL muscle. Markers with relatively large effects were located near fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD), and thyroid hormone responsive (THRSP) genes. For the majority of the fatty acid traits studied, the accuracy of genomic prediction was relatively low (<0.40). Relatively high accuracies (> = 0.50) were achieved for 10:0, 12:0, 14:0, 15:0, 16:0, 9c-14:1, 12c-16:1, 13c-18:1, and health index (HI) in LL, and for 12:0, 14:0, 15:0, 10 t,12c-18:2, and 11 t,13c + 11c,13 t-18:2 in SQ. The Bayesian method performed similarly as GBLUP for most of the traits but substantially better for traits that were affected by SNPs of large effects as identified by GWAS. CONCLUSIONS Fatty acid composition in beef is influenced by a few host genes with major effects and many genes of smaller effects. With the current training population size and marker density, genomic prediction has the potential to predict the breeding values of fatty acid composition in beef cattle at a moderate to relatively high accuracy for fatty acids that have moderate to high heritability.
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Affiliation(s)
- Liuhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L 1 W1, Canada.
| | - Chinyere Ekine-Dzivenu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Michael Vinsky
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L 1 W1, Canada.
| | - John Basarab
- Lacombe Research Centre, Alberta Agriculture and Forestry, 6000 C & E Trail, Lacombe, AB, T4L 1 W1, Canada.
| | - Jennifer Aalhus
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L 1 W1, Canada.
| | - Mike E R Dugan
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L 1 W1, Canada.
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L 1 W1, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L 1 W1, Canada.
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Nishimaki T, Ibi T, Siqintuya, Kobayashi N, Matsuhashi T, Akiyama T, Yoshida E, Imai K, Matsui M, Uemura K, Eto H, Watanabe N, Fujita T, Saito Y, Komatsu T, Hoshiba H, Mannen H, Sasazaki S, Kunieda T. Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle. Anim Sci J 2015; 87:469-76. [PMID: 26249527 DOI: 10.1111/asj.12453] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 03/05/2015] [Accepted: 04/06/2015] [Indexed: 12/01/2022]
Abstract
Marker-assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.
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Affiliation(s)
- Takahiro Nishimaki
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Siqintuya
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Naohiko Kobayashi
- Gifu Prefectural Hida Region Livestock Hygiene Service Center, Takayama, Gifu, Japan
| | - Tamako Matsuhashi
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
| | - Takayuki Akiyama
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery, Asago, Hyogo, Japan
| | - Emi Yoshida
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery, Asago, Hyogo, Japan
| | - Kazumi Imai
- Hiroshima Prefectural Technology Research Institute, Health and Environment Center, Hiroshima, Japan
| | - Mayu Matsui
- Hiroshima Prefectural Technology Research Institute, Livestock Technology Research Center, Shobara, Hiroshima, Japan
| | - Keiichi Uemura
- Kagawa Prefecture Livestock Experiment Station, Kita-gun, Kagawa, Japan
| | - Hisayoshi Eto
- Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Livestock Research Division, Taketa, Oita, Japan
| | - Naoto Watanabe
- Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Livestock Research Division, Taketa, Oita, Japan
| | - Tatsuo Fujita
- Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Livestock Research Division, Taketa, Oita, Japan
| | - Yosuke Saito
- Miyagi Prefectural Livestock Experiment Station, Ohsaki, Miyagi, Japan
| | - Tomohiko Komatsu
- Yamagata Prefectural Animal Industrial Institute, Agricultural Research Center, Shinjo, Yamagata, Japan
| | - Hiroshi Hoshiba
- Cattle Breeding Development Institute of Kagoshima Prefecture, So, Kagoshima, Japan
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Shinji Sasazaki
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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Radke DW, Lee C. Adaptive potential of genomic structural variation in human and mammalian evolution. Brief Funct Genomics 2015; 14:358-68. [PMID: 26003631 DOI: 10.1093/bfgp/elv019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.
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Uemoto Y, Abe T, Tameoka N, Hasebe H, Inoue K, Nakajima H, Shoji N, Kobayashi M, Kobayashi E. Whole-genome association study for fatty acid composition of oleic acid in Japanese Black cattle. Anim Genet 2015; 42:141-8. [PMID: 20590532 DOI: 10.1111/j.1365-2052.2010.02088.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fatty acid composition, especially oleic acid (C18:1), plays an important role in the eating quality of meat in Japanese Black cattle. Therefore, the objective of this study was to identify loci associated with C18:1 in the intramuscular fat of the trapezius muscles in Japanese Black cattle using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. We also evaluated the relationship between C18:1 and three fatty acid synthesis genes, fatty acid synthase (FASN), stearoyl-CoA desaturase and sterol regulatory element-binding protein-1. In this experiment, we applied a mixed model and Genomic Control approach using selective genotyping to perform a genome-wide association study. A total of 160 animals (80 animals with higher values and 80 animals with lower values), selected from 3356 animals based on corrected phenotype, were genotyped using the Illumina BovineSNP50 BeadChip and three fatty acid synthesis genes, and the quality of these SNPs was assessed. In this study, a total of 38 955 SNPs, which included SNPs in the three fatty acid synthesis genes, were used, and the estimated inflation factor was 1.06. In the studied population, a total of 32 SNPs, including the FASN gene, had significant effects, and in particular 30 SNPs of all significant SNPs were located between 49 and 55 Mbp on chromosome 19. This study is one of the first genome-wide association studies for fatty acid composition in a cattle population using the recently released Illumina BovineSNP50 BeadChip.
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Affiliation(s)
- Y Uemoto
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan.Yamagata Prefectural Animal Industrial Institute, Agricultural Research Center, Shinjo, Yamagata 996-0041, Japan
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Dixit SP, Sivalingam J, Tyagi AK, Saroha V, Sharma A, Nagda RK. Association of novel SNPs in the candidate genes affecting caprine milk fatty acids related to human health. Meta Gene 2015; 4:45-56. [PMID: 25853060 PMCID: PMC4372655 DOI: 10.1016/j.mgene.2015.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 01/06/2015] [Accepted: 01/06/2015] [Indexed: 01/13/2023] Open
Abstract
In the present investigation, 618 milk samples of Sirohi breed of goat were collected, and analyzed for conjugated linoleic acid (CLA, C18:2) and other fatty acids. The CLA in studied goat milk samples was 4.87 mg/g of milk fat and C18:2 cis-9, trans-11 contributes 2.9 mg/g of milk fat and trans10 cis12 contributes 0.82 mg/g of milk fat. The saturated fatty acids in the milk accounted for 69.55% and unsaturated fatty acid accounted for 28.50%. The unsaturated fatty acid was constituted by monounsaturated fatty acid (24.57%) and polyunsaturated fatty acids (3.96%.). The major contribution (45.56%) in total fatty acid was of C12:0, C14:0 and C16:0. C18:0 and short chain ones (C4:0, C6:0, C8:0, and C10:0) have a neutral or cholesterol-decreasing effect. The DNA sequence analysis of the genes (DGAT1, SCAP, PPARG, OLR, FABP3 and PRL) in a random panel of 8 Sirohi goats revealed 38 SNPs across the targeted regions. Out of the studied SNPs (38) across these genes, 22 SNPs had significant effect on one or a group of fatty acids including CLA. The genotypes at these loci showed significant differences in the least square means of a particular fatty acid or a group of fatty acids including CLA and its isomers.
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Affiliation(s)
- S P Dixit
- National Bureau of Animal Genetic Resources, Karnal, Haryana, 131002, India
| | | | - A K Tyagi
- National Dairy Research Institute, Karnal, Haryana, 131002, India
| | - V Saroha
- National Bureau of Animal Genetic Resources, Karnal, Haryana, 131002, India
| | - A Sharma
- National Bureau of Animal Genetic Resources, Karnal, Haryana, 131002, India
| | - R K Nagda
- Rajasthan University of Veterinary and Animal Science, Vallabhnagar, Udaipur, Rajasthan, India
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30
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Hayakawa K, Sakamoto T, Ishii A, Yamaji K, Uemoto Y, Sasago N, Kobayashi E, Kobayashi N, Matsuhashi T, Maruyama S, Matsumoto H, Oyama K, Mannen H, Sasazaki S. The g.841G>C SNP of FASN gene is associated with fatty acid composition in beef cattle. Anim Sci J 2015; 86:737-46. [PMID: 25597874 DOI: 10.1111/asj.12357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/03/2014] [Indexed: 11/30/2022]
Abstract
The objective of the current study is to evaluate the association between fatty acid composition and fatty acid synthase gene polymorphisms as responsible mutations. For this purpose, we selected seven previously reported single nucleotide polymorphisms (SNPs) in FASN gene, including one within promoter region (g.841G>C) and six non-synonymous SNPs (g.8805C>T, g.13126C>T, g.15532A>C, g.16024A>G, g.16039C>T, g.17924A>G), and genotyped them in Japanese Black cattle. Genotyping results revealed that g.8805 C>T and g.17924 A>G were monomorphic loci. Genome-wide association analysis including the other five SNPs revealed that only g.841G>C showed significant associations with the percentages of C14:0, C14:1, C16:1 and C18:1 at 5% genome-wide significance level. In order to further evaluate the effect, we genotyped g.841G>C using additional three populations, including two Japanese Black populations and a Holstein cattle population. g.16024A>G was also genotyped and included in the analysis because it has been reported to be associated with fatty acid composition in Japanese Black cattle. In the result of analysis of variance, g.841G>C showed stronger effects on fatty acid percentage than those of g.16024A>G in all populations. These results suggested that g.841G>C would be a responsible mutation for fatty acid composition and contribute to production of high-grade beef as a selection marker in beef cattle.
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Affiliation(s)
- Kiri Hayakawa
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Takayuki Sakamoto
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Atsushi Ishii
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Keita Yamaji
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | | | - Nanae Sasago
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Eiji Kobayashi
- National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki, Japan
| | - Naohiko Kobayashi
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
| | - Tamako Matsuhashi
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
| | - Shin Maruyama
- Gifu Prefectural Livestock Research Institute, Takayama, Gifu, Japan
| | - Hirokazu Matsumoto
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai, Hyogo, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
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32
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Gotoh T, Takahashi H, Nishimura T, Kuchida K, Mannen H. Meat produced by Japanese Black cattle and Wagyu. Anim Front 2014. [DOI: 10.2527/af.2014-0033] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T. Gotoh
- Kuju Agricultural Research Center, Faculty of Agriculture, Kyushu University 8780201, Japan
| | - H. Takahashi
- Muscle Biology and Meat Science laboratory, Research Faculty of Agriculture, Hokkaido University, 060-8589, Japan
| | - T. Nishimura
- Obihiro University of Agriculture and Veterinary Medicine, 080-8555, Japan
| | - K. Kuchida
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, 657-8501, Japan
| | - H. Mannen
- Kuju Agricultural Research Center, Faculty of Agriculture, Kyushu University 8780201, Japan
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33
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Zhang HB, Wang MS, Wang ZS, Zhou AM, Zhang XM, Dong XW, Peng QH. Supplementation dietary zinc levels on growth performance, carcass traits, and intramuscular fat deposition in weaned piglets. Biol Trace Elem Res 2014; 161:69-77. [PMID: 25048402 DOI: 10.1007/s12011-014-0078-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/14/2014] [Indexed: 10/25/2022]
Abstract
This study was conducted to estimate dietary zinc (Zn) levels on growth performance, carcass traits, and intramuscular fat (IMF) deposition in weaned piglets. Sixty piglets were randomly divided into five groups, as follows: control (basal diet), Zn250, Zn380, Zn570, and Zn760 with supplementation of 250, 380, 570, and 760 mg Zn/kg of the basal diet, respectively. The final weight, average daily gain (ADG), gain/feed (G/F), lean meat percentage, fat meat percentage, lean eye area, backfat thickness, and IMF content were dose-dependently increased in all groups of Zn treatment. The serum total triglycerides (TG) and free fatty acid (FFA) were significantly higher in all Zn treatments than in the control. The enzyme activities of lipoprotein lipase (LPL), fatty acid synthase (FAS), and acetyl-CoA carboxylase (ACC) were markedly higher, while enzyme activities of hormone-sensitive lipase (HSL) and carnitine palmitoyltransferase-1 (CPT-1) were significantly lower in all Zn treatments than in the control. The messenger RNA (mRNA) levels of sterol regulatory element-binding protein 1 (SREBP-1), stearoyl-CoA desaturase (SCD), FAS, ACC, peroxisome proliferator-activated receptor γ (PPARγ), LPL, and adipocyte fatty acid-binding protein (A-FABP) were significantly higher, while the mRNA levels of CPT-1 and HSL were significantly lower in all Zn treatments compared with the control. These results indicated that high levels of Zn increased IMF accumulation by up-regulating intramuscular lipogenic and fatty acid transport gene expression and enzyme activities while down-regulating lipolytic gene expression and enzyme activities.
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Affiliation(s)
- H B Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Ya'an, 625014, China
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Rosse IDC, Steinberg RDS, Coimbra RS, Peixoto MGCD, Verneque RS, Machado MA, Fonseca CG, Carvalho MRS. Novel SNPs and INDEL polymorphisms in the 3'UTR of DGAT1 gene: in silico analyses and a possible association. Mol Biol Rep 2014; 41:4555-63. [PMID: 24676595 DOI: 10.1007/s11033-014-3326-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 02/26/2014] [Indexed: 12/24/2022]
Abstract
Diacylglycerol-O-acyltransferase (DGAT1) gene encodes the rate-limiting enzyme of triglyceride synthesis. A polymorphism in this gene, DGAT1 K232A, has been associated with milk production and composition in taurine breeds. However, this polymorphism is not a good tool for ascertaining the effects of this QTL in Bos indicus (Zebu), since the frequency of the DGAT1 232A allele is too low in these breeds. We sequenced the 3'-untranslated region of DGAT1 gene in a sample of bulls of the breeds Guzerá (Bos indicus) and Holstein (Bos taurus) and, using in silico analysis, we searched for genetic variation, evolutionary conservation, regulatory elements, and possible substitution effects. Six single nucleotide (SNPs) and one insertion-deletion (INDEL) polymorphisms were found in the Guzerá bulls. Additionally, we developed a preliminary association study, using this INDEL polymorphism as a genetic marker. A significant association was detected (P ≤ 0.05) between the INDEL (DGAT1 3'UTR INDEL) and the breeding values (BV) for protein, fat, and milk yields over a 305-day lactation period. The DGAT1 3' UTR INDEL genotype I/I (I, for insertion) was associated with lower BVs (-38.77 kg for milk, -1.86 kg for fat, and -1.48 kg for protein yields), when compared to the genotype I/D (D, for deletion). I/D genotype was lower D/D genotype (-34.98 kg milk, -1.73 kg fat, and -1.09 kg protein yields). This study reports the first polymorphism of DGAT1 3'UTR in the Guzerá breed, as well as its association with BV for milk protein, fat, and milk yields.
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Affiliation(s)
- Izinara da Cruz Rosse
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG, 31.270-901, Brazil
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Taniguchi M, Nakajima I, Chikuni K, Kojima M, Awata T, Mikawa S. MicroRNA-33b downregulates the differentiation and development of porcine preadipocytes. Mol Biol Rep 2014; 41:1081-90. [PMID: 24398549 PMCID: PMC3929038 DOI: 10.1007/s11033-013-2954-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 12/20/2013] [Indexed: 12/26/2022]
Abstract
Sterol regulatory element binding transcription factor (SREBF) is a key transcription regulator for lipid homeostasis. MicroRNA-33b (miR-33b) is embedded in intron 16 of porcine SREBF1 and is conserved among most mammals. Here, we investigated the effect of miR-33b on adipocyte differentiation and development in porcine subcutaneous pre-adipocytes (PSPA). PSPA were transiently transfected with miR-33b, and adipose differentiation was then induced. Delayed adipose differentiation and decreased lipid accumulation were observed in miR-33b-transfected PSPA. Computational predictions suggested that miR-33b may target early B cell factor 1 (EBF1), an adipocyte activator of lipogenesis regulators such as CCAAT-enhancer binding protein alpha (C/EBPα) and peroxisome proliferator-activated receptor gamma (PPARγ). Both gene and protein expression of EBF1 were downregulated in miR-33b-transfected PSPA, followed by considerable decreases in the expression of C/EBPα and PPARγ and their downstream lipogenic genes. However, miR-33b transfection did not markedly affect mRNA and protein expression of SREBF1. We also investigated differences in the expression of miR-33b and lipogenic genes in subcutaneous fat tissues between 5-month-old crossbred gilts derived from Landrace (lean-type) and Meishan (fatty-type) boars. Landrace-derived crossbred gilts expressed more miR-33b and less lipogenic genes than did gilts derived from Meishan. Our results suggest that miR-33b affected the differentiation and development of PSPA by attenuating the lipogenic gene expression cascade through EBF1 to C/EBPα and PPARγ. The differential expression of miR-33b observed in crossbred gilts may in part account for differences in lipogenic gene expression and the fat:lean ratio between pig breeds.
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Affiliation(s)
- Masaaki Taniguchi
- Animal Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
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Association between SREBP-1 gene expression in mammary gland and milk fat yield in Sarda breed sheep. Meta Gene 2013; 1:43-9. [PMID: 25606373 PMCID: PMC4205032 DOI: 10.1016/j.mgene.2013.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to examine the expression patterns of SREBP-1 gene in milk somatic cells and its association with milk fat yield during early lactation in Sarda breed sheep. A sample of 20 Sarda ewes, aged between 4 and 5 years, in their third to fourth lactation were chosen. From each ewe 28 days after lambing milk yield was measured, and a 160 ml milk sample for the RNA extraction and to test somatic cells count and lactose, fat and protein contents were collected. From the obtained RNA, total cDNA was synthesized and the quantitative PCR was performed. The fat, proteins and lactose content showed many differences among the animals, but these variations were no correlated with the milk yield. The SREBP-1 gene expression resulted higher in the high milk fat producing ewes. The correlation analysis showed that the SREBP-1 expression level is directly related to the amount of milk fat (g/die) (P < 0.001), while the total RNA obtained from each sample was found to be related to the somatic cells number (P < 0.001). Instead the expression of this gene showed no relations with the concentration of fat in milk. Our data highlight that in sheep SREBP-1 gene is expressed in the mammary gland during early lactation. Moreover, the positive relationship between SREBP-1 gene expression and the milk fat yield suggests that SREBP-1 gene is required for the lipid synthesis in the sheep mammary gland. We examined the SREBP-1 gene expression in milk somatic cell in the sheep. The expression of this gene is related with fat yield (g/die). Instead, no relationship was found between gene expression and milk fat concentration. A high SREBP-1 gene expression is necessary for the higher milk fat yield.
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Muñoz M, Fernández AI, Benítez R, Pena RN, Folch JM, Rodríguez MDC, Silió L, Alves E. Disentangling Two QTL on Porcine Chromosome 12 for Backfat Fatty Acid Composition. Anim Biotechnol 2013; 24:168-86. [DOI: 10.1080/10495398.2012.763130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Ishii A, Yamaji K, Uemoto Y, Sasago N, Kobayashi E, Kobayashi N, Matsuhashi T, Maruyama S, Matsumoto H, Sasazaki S, Mannen H. Genome-wide association study for fatty acid composition in Japanese Black cattle. Anim Sci J 2013; 84:675-82. [PMID: 23607548 DOI: 10.1111/asj.12063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/20/2013] [Indexed: 11/28/2022]
Abstract
Fatty acid composition is one of the important traits in beef. The aim of this study was to identify candidate genomic regions for fatty acid composition by genome-wide association study with 50 K single nucleotide polymorphism (SNP) array in Japanese Black cattle. A total of 461 individuals and 40 657 SNPs were used in this study. We applied genome-wide rapid association using mixed model and regression (GRAMMAR) and genomic control approaches to estimate the associations between genotypes and fatty acid composition. In addition, two SNPs in fatty acid synthase (FASN) (T1952A) and stearoyl-CoA desaturase (SCD) (V293A) genes were also genotyped. Association analysis revealed that 30 significant SNPs for several fatty acids (C14:0, C14:1, C16:1 and C18:1) were located in the BTA19 FASN gene located within this region but the FASN mutation had no significant effect on any traits. We also detected one significant SNP for C18:1 on BTA23 and two SNPs for C16:0 on BTA25. The region around 17 Mb on BTA26 harbored two significant SNPs for C14:1 and SNP in SCD in this region showed the strongest association with C14:1. This study demonstrated novel candidate regions in BTA19, 23 and 25 for fatty acid composition.
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Affiliation(s)
- Atsushi Ishii
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Association of bovine meat quality traits with genes included in the PPARG and PPARGC1A networks. Meat Sci 2013; 94:328-35. [PMID: 23567132 DOI: 10.1016/j.meatsci.2013.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 02/08/2013] [Accepted: 02/19/2013] [Indexed: 11/21/2022]
Abstract
Understanding which are the genetic variants underlying the nutritional and sensory properties of beef, enables improvement in meat quality. The aim of this study is to identify new molecular markers for meat quality through an association study using candidate genes included in the PPARG and PPARGC1A networks given their master role in coordinating metabolic adaptation in fat tissue, muscle and liver. Amongst the novel associations found in this study, selection of the positive marker variants of genes such as BCL3, LPL, PPARG, SCAP, and SCD will improve meat organoleptic characteristics and health by balancing the n-6 to n-3 fatty acid ratio in meat. Also previous results on GDF8 and DGAT1 were validated, and the novel ATF4, HNF4A and PPARGC1A associations, although slightly under the significance threshold, are consistent with their physiological roles. These data contribute insights into the complex gene-networks underlying economically important traits.
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40
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Han C, Vinsky M, Aldai N, Dugan M, McAllister T, Li C. Association analyses of DNA polymorphisms in bovine SREBP-1, LXRα, FADS1 genes with fatty acid composition in Canadian commercial crossbred beef steers. Meat Sci 2013; 93:429-36. [DOI: 10.1016/j.meatsci.2012.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/20/2012] [Accepted: 10/23/2012] [Indexed: 01/20/2023]
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41
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Recent developments in altering the fatty acid composition of ruminant-derived foods. Animal 2013; 7 Suppl 1:132-62. [DOI: 10.1017/s1751731112001681] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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42
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Matsumoto H, Shimizu Y, Tanaka A, Nogi T, Tabuchi I, Oyama K, Taniguchi M, Mannen H, Sasazaki S. The SNP in the promoter region of the bovine ELOVL5 gene influences economic traits including subcutaneous fat thickness. Mol Biol Rep 2012; 40:3231-7. [DOI: 10.1007/s11033-012-2398-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 12/17/2012] [Indexed: 12/31/2022]
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43
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Lee Y, Oh D, Lee J, La B, Yeo J. Novel single nucleotide polymorphisms of bovine SREBP1 gene is association with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo). Mol Biol Rep 2012; 40:247-54. [DOI: 10.1007/s11033-012-2055-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 10/02/2012] [Indexed: 11/30/2022]
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44
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Baeza MC, Corva PM, Soria LA, Pavan E, Rincon G, Medrano JF. Genetic variants in a lipid regulatory pathway as potential tools for improving the nutritional quality of grass-fed beef. Anim Genet 2012; 44:121-9. [DOI: 10.1111/j.1365-2052.2012.02386.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2012] [Indexed: 11/28/2022]
Affiliation(s)
- M. C. Baeza
- Departamento de Producción Animal, Facultad de Ciencias Agrarias, Unidad Integrada Balcarce; Universidad Nacional de Mar del Plata; Argentina
| | - P. M. Corva
- Departamento de Producción Animal, Facultad de Ciencias Agrarias, Unidad Integrada Balcarce; Universidad Nacional de Mar del Plata; Argentina
| | - L. A. Soria
- Cátedra de Genética, Facultad de Ciencias Veterinarias; Universidad de Buenos Aires; Argentina
| | - E. Pavan
- Estación Experimental Agropecuaria INTA Balcarce; Argentina
| | - G. Rincon
- Department of Animal Science; University of California; Davis CA USA
| | - J. F. Medrano
- Department of Animal Science; University of California; Davis CA USA
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45
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Manunza A, Zidi A, Fernández-Cabanás VM, Jordana J, Carrizosa J, Belaifa E, Urrutia B, Polvillo O, González-Redondo P, Amills M, Serradilla JM. Short Communication: An association analysis between one missense polymorphism at the SREBF1 gene and milk yield and composition traits in goats. CANADIAN JOURNAL OF ANIMAL SCIENCE 2012. [DOI: 10.4141/cjas2011-111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Manunza, A., Zidi, A., Fernández-Cabanás, V. M., Jordana, J., Carrizosa, J., Belaifa, E., Urrutia, B., Polvillo, O., González-Redondo, P., Amills, M. and Serradilla, J. M. 2012. Short Communication: An association analysis between one missense polymorphism at the SREBF1 gene and milk yield and composition traits in goats. Can. J. Anim. Sci. 92: 167–173. Sterol regulatory element binding transcription factor 1 (SREBF1) regulates the expression of genes involved in the biosynthesis of fatty acids and cholesterol. Herewith, we have sequenced the near-complete coding region and part of the 3′UTR of the goat SREBF1 gene. In doing so, we have detected a missense c.353C>T polymorphism causing a proline to leucine substitution at position 118 (P118L). An association analysis with milk composition traits recorded in Murciano-Granadina goats only revealed a statistical tendency linking SREBF1 genotype and milk omega-3 fatty acid content. The lack of significant associations suggests that the P118L substitution does not involve a functional change.
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Affiliation(s)
- A. Manunza
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - A. Zidi
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - V. M. Fernández-Cabanás
- Departamento de Ciencias Agroforestales, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Carretera Utrera, km. 1, 41013 Sevilla, Spain
| | - J. Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - J. Carrizosa
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA). Estación Sericícola, 30150-La Alberca, Murcia, Spain
| | - E. Belaifa
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - B. Urrutia
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA). Estación Sericícola, 30150-La Alberca, Murcia, Spain
| | - O. Polvillo
- Departamento de Ciencias Agroforestales, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Carretera Utrera, km. 1, 41013 Sevilla, Spain
| | - P. González-Redondo
- Departamento de Ciencias Agroforestales, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Carretera Utrera, km. 1, 41013 Sevilla, Spain
| | - M. Amills
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - J. M. Serradilla
- Departamento de Producción Animal, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
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MANNEN H. Genes Associated with Fatty Acid Composition of Beef. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2012. [DOI: 10.3136/fstr.18.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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47
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Cecchinato A, Ribeca C, Maurmayr A, Penasa M, De Marchi M, Macciotta N, Mele M, Secchiari P, Pagnacco G, Bittante G. Short communication: Effects of β-lactoglobulin, stearoyl-coenzyme A desaturase 1, and sterol regulatory element binding protein gene allelic variants on milk production, composition, acidity, and coagulation properties of Brown Swiss cows. J Dairy Sci 2012; 95:450-4. [DOI: 10.3168/jds.2011-4581] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 09/22/2011] [Indexed: 11/19/2022]
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48
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Barendse W. Haplotype analysis improved evidence for candidate genes for intramuscular fat percentage from a genome wide association study of cattle. PLoS One 2011; 6:e29601. [PMID: 22216329 PMCID: PMC3247274 DOI: 10.1371/journal.pone.0029601] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Accepted: 12/01/2011] [Indexed: 11/23/2022] Open
Abstract
In genome wide association studies (GWAS), haplotype analyses of SNP data are neglected in favour of single point analysis of associations. In a recent GWAS, we found that none of the known candidate genes for intramuscular fat (IMF) had been identified. In this study, data from the GWAS for these candidate genes were re-analysed as haplotypes. First, we confirmed that the methodology would find evidence for association between haplotypes in candidate genes of the calpain-calpastatin complex and musculus longissimus lumborum peak force (LLPF), because these genes had been confirmed through single point analysis in the GWAS. Then, for intramuscular fat percent (IMF), we found significant partial haplotype substitution effects for the genes ADIPOQ and CXCR4, as well as suggestive associations to the genes CEBPA, FASN, and CAPN1. Haplotypes for these genes explained 80% more of the phenotypic variance compared to the best single SNP. For some genes the analyses suggested that there was more than one causative mutation in some genes, or confirmed that some causative mutations are limited to particular subgroups of a species. Fitting the SNPs and their interactions simultaneously explained a similar amount of the phenotypic variance compared to haplotype analyses. Haplotype analysis is a neglected part of the suite of tools used to analyse GWAS data, would be a useful method to extract more information from these data sets, and may contribute to reducing the missing heritability problem.
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Affiliation(s)
- William Barendse
- Cooperative Research Centre for Beef Genetic Technologies, Commonwealth Scientific and Industrial Research Organization, St. Lucia, Queensland, Australia.
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49
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Kuchtík J, Zapletal D, Šustová K. Chemical and physical characteristics of lamb meat related to crossbreeding of Romanov ewes with Suffolk and Charollais sires. Meat Sci 2011; 90:426-30. [PMID: 21945053 DOI: 10.1016/j.meatsci.2011.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/22/2011] [Accepted: 08/30/2011] [Indexed: 10/17/2022]
Abstract
The aim was to evaluate the effects of crossbreeding Romanov (RO) ewes with Suffolk (SF) and Charollais (CH) sires on the chemicophysical characteristics and FA profile of the Quadriceps femoris muscle (QFM) in lambs fattened under organic conditions. The experimental animals were male lamb twins of two different crossbreds; CH 50 RO 50 and SF 50 RO 50. Lambs were slaughtered at an average live weight of 31kg. CH 50 RO 50 displayed higher contents of dry matter and intramuscular fat of the QFM. A lower pH value of CH 50 RO 50 was reflected in an increase of WHC. Meat of SF 50 RO 50 lambs had more lightness (L*) and yellowness (b*). The CH 50 RO 50 genotype showed a significantly higher proportion of C18:3n-3cis and n-3 PUFA than the SF 50 RO 50 genotype. The genotype also affected the Δ(9)-desaturase (16) index.
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Affiliation(s)
- Jan Kuchtík
- Department of Animal Breeding, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
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50
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KANEDA M, LIN BZ, SASAZAKI S, OYAMA K, MANNEN H. Allele frequencies of gene polymorphisms related to economic traits in Bos taurus and Bos indicus cattle breeds. Anim Sci J 2011; 82:717-21. [DOI: 10.1111/j.1740-0929.2011.00910.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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