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Tumino S, Mangano F, Bognanno M, Bordonaro S, Chessari G, De Angelis A, Avondo M. Effects of BLG polymorphism and dietary supplementation with carob pulp on ewe milk traits and fatty acid composition. ITALIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1080/1828051x.2023.2187713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Fabrizio Mangano
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Matteo Bognanno
- Dipartimento di Scienze e Tecnologie Agro-forestali e Ambientali, University of Reggio Calabria, Reggio Calabria, Italy
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Anna De Angelis
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Marcella Avondo
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
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Tumino S, Bognanno M, Chessari G, Tolone M, Bordonaro S, Mangano F, Marletta D, Avondo M. Polymorphisms at Candidate Genes for Fat Content and Fatty Acids Composition: Effects on Sheep Milk Production and Fatty Acid Profile Using Two Dietary Supplementations. Animals (Basel) 2023; 13:2533. [PMID: 37570341 PMCID: PMC10417724 DOI: 10.3390/ani13152533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
The nutritional value of sheep's milk and its derivatives is influenced by the lipid fraction, which is affected by diet and genetics. This study aimed to explore the genetic variations in the DGAT1 and SCD genes and assessed the impact of the DGAT1 genotype on milk quality in Valle del Belìce sheep, considering diet supplementation with carob pulp and barley grain. Among the potentially polymorphic sites, only DGAT1 g.127 C > A and SCD g.87 C > A showed variability. The DGAT1 genotype did not significantly impact milk yield and composition, except for higher urea content in the CA genotypes than in the CC ones. Carob pulp increased the milk fat content compared to barley grain. Genetic variation in DGAT1 was associated with changes in the milk fatty acid profile; specifically, the CA genotype exhibited higher levels of short-chain fatty acids and lower levels of polyunsaturated fatty acids compared to the CC genotype. Carob pulp supplementation increased saturated fatty acids and reduced unsaturated fractions, leading to milk with higher atherogenic and thrombogenic indices. No significant interaction was found between genotype and diet. This study provides insights into the genetic and dietary factors influencing sheep's milk composition. Further research is needed to understand the impact of these genetic variations on milk production and composition, as well as to determine optimal levels of carob pulp for improving fat percentage and promoting sustainable sheep breeding practices.
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Affiliation(s)
- Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Matteo Bognanno
- Dipartimento di Scienze e Tecnologie Agro-Forestali e Ambientali, University of Reggio Calabria, 89100 Reggio Calabria, Italy;
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Marco Tolone
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Fabrizio Mangano
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Marcella Avondo
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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Conte G, Palombo V, Serra A, Correddu F, D’Andrea M, Macciotta NPP, Mele M. Study of the Fatty Acid Profile of Milk in Different Sheep Breeds: Evaluation by Multivariate Factorial Analysis. Animals (Basel) 2022; 12:ani12060722. [PMID: 35327119 PMCID: PMC8944521 DOI: 10.3390/ani12060722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary The quality of milk is strongly influenced by its lipid profile. The increase in fats with nutraceutical properties at the expense of those negative for human health, has always been a goal to improve the functional properties of milk. To achieve this goal, it is essential to know the metabolism of the mammary gland and the relationship between the various lipid components. Much is known about bovine milk, while the aspect relating to the sheep species has not been developed. The present work aims to investigate the relationships between the various fatty acids in sheep’s milk through a multivariate approach, which can highlight the mammary role of lipid synthesis. Abstract A multivariate analysis was used to investigate the fatty acid (FA) profile in three different Italian sheep breeds: Comisana, Massese, and Sarda. A sample of 852 animals was considered: 118 Massese, 303 Comisana, 431 Sarda. Sarda sheep were divided into two groups, based on their breeding origin (298 and 133 reared in Sardinia and Tuscany, respectively). Sarda sheep, bred both in Sardinia and in Tuscany, were considered in different groups, both because in these two regions most of the sheep of this breed are reared, and because they differ in geographical characteristics and in the farming system. The individual milk FA composition of dairy ewes was analyzed with multivariate factor analysis. The extracted factors were representative of the following eight groups of fatty acids or functions: factor 1 (odd branched fatty acids and long-chain fatty acids), factor 2 (sn3_position), factor 3 (alternative biohydrogenation), factor 4 (SCD_1), factor 5 (SCD_2), factor 6 (SCD_3), factor 7 (fat secretion) and factor 8 (omega-3). A factor analysis suggested the presence of different metabolic pathways for de novo short- and medium-chain fatty acids and Δ9-desaturase products. The ANOVA of factor scores highlighted the significant effects of the breed. The results of the present study showed that breed is an important factor in defining the fatty acid profile of milk, combined with the effect of the diet. Breeds reared in the same farming system (Comisana, Massese and Sarda reared in Tuscany) showed significant differences for all the factors extracted. At the same time, we found differences between the Sarda sheep reared in Sardinia and Tuscany, two different regions of Italy.
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Affiliation(s)
- Giuseppe Conte
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (A.S.); (M.M.)
- Research Center of Nutraceutical and Food for Health, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Correspondence:
| | - Valentino Palombo
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via De Sanctis snc, 86100 Campobasso, Italy; (V.P.); (M.D.)
| | - Andrea Serra
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (A.S.); (M.M.)
- Research Center of Nutraceutical and Food for Health, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Fabio Correddu
- Department of Agriculture, University of Sassari, Via de Nicola 9, 07100 Sassari, Italy; (F.C.); (N.P.P.M.)
| | - Mariasilvia D’Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via De Sanctis snc, 86100 Campobasso, Italy; (V.P.); (M.D.)
| | | | - Marcello Mele
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (A.S.); (M.M.)
- Research Center of Nutraceutical and Food for Health, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Pecka-Kiełb E, Kowalewska-Łuczak I, Czerniawska-Piątkowska E, Króliczewska B. FASN, SCD1 and ANXA9 gene polymorphism as genetic predictors of the fatty acid profile of sheep milk. Sci Rep 2021; 11:23761. [PMID: 34887487 PMCID: PMC8660767 DOI: 10.1038/s41598-021-03186-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023] Open
Abstract
In this study, single nucleotide polymorphisms (SNPs) in the ANXA9 (annexin 9), FASN (fatty acid synthase) and SCD1 (stearoyl-CoA desaturase 1) genes were analyzed as factors influencing fatty acid profiles in milk from Zošľachtená valaška sheep. SNP in selected genes was identified using polymerase chain reaction (PCR) and restriction fragment length polymorphism (PCR–RFLP). The long-chain fatty acids profile in sheep milk was identified by gas chromatography. Statistical analysis of the SCD1/Cfr13I polymorphism showed that the milk of the homozygous AA animals was characterized by a lower (P < 0.05) share of C4:0, C6:0, C8:0, C10:0, C12:0, C14:0 in comparison to the homozygous CC sheep. The milk of heterozygous sheep was characterized by a higher (P < 0.05) proportion of C13:0 acid compared to the milk of sheep with the homozygous AA type. A higher (P < 0.05) level of saturated fatty acids (SFA) was found in the milk of CC genotype sheep compared to the AA genotype. Our results lead to the conclusion that the greatest changes were observed for the SCD1/Cfr13I polymorphism and the least significant ones for FASN/AciI. Moreover, it is the first evidence that milk from sheep with SCD1/Cfr13I polymorphism and the homozygous AA genotype showed the most desirable fatty acids profile.
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Affiliation(s)
- Ewa Pecka-Kiełb
- Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Norwida 31, 50-375, Wrocław, Poland.
| | - Inga Kowalewska-Łuczak
- Department of Genetics, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów Avenue 45, 79-311, Szczecin, Poland
| | - Ewa Czerniawska-Piątkowska
- Department of Ruminant Science, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Klemensa Janickiego 29, 71-270, Szczecin, Poland
| | - Bożena Króliczewska
- Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Norwida 31, 50-375, Wrocław, Poland
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Marina H, Pelayo R, Suárez-Vega A, Gutiérrez-Gil B, Esteban-Blanco C, Arranz JJ. Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds. J Dairy Sci 2021; 104:11850-11866. [PMID: 34454756 DOI: 10.3168/jds.2021-20510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
Abstract
This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.
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Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain.
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Pazzola M, Vacca GM, Paschino P, Bittante G, Dettori ML. Novel Genes Associated with Dairy Traits in Sarda Sheep. Animals (Basel) 2021; 11:ani11082207. [PMID: 34438665 PMCID: PMC8388407 DOI: 10.3390/ani11082207] [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: 06/21/2021] [Revised: 07/09/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of the present research was to analyze the variability of 45 SNPs from different genes involved in metabolism and innate immunity to perform an association analysis with the milk yield, composition and milk coagulation traits. A population of 1112 Sarda breed sheep was sampled. Genotyping was generated by a TaqMan Open ArrayTM. Thirty out of the 45 SNPs were polymorphic, and 12 displayed a minor allele frequency higher than 0.05. An association analysis showed that the variability at genes PRKAG3 and CD14 was significantly associated with the daily milk yield. The variability at PRKAG3 was also associated with the protein and casein content, somatic cell score and bacterial score. The variation at the PRKAA2 gene was associated with the milk lactose concentration. The SNPs at CD14 were also associated with the traditional milk coagulation properties, while the SNPs at GHR and GHRHR were associated with kSR, a derived coagulation parameter related to the rate of syneresis. The information provided here is new and increases our knowledge of genotype-phenotype interactions in sheep. Our findings might be useful in appropriate breeding schemes to be set up for the Sarda sheep breed, but these should be confirmed by further studies, possibly performed on independent populations.
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Affiliation(s)
- Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, SS, Italy; (M.P.); (P.P.); (M.L.D.)
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, SS, Italy; (M.P.); (P.P.); (M.L.D.)
- Correspondence: ; Tel.: +39-079229442
| | - Pietro Paschino
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, SS, Italy; (M.P.); (P.P.); (M.L.D.)
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Legnaro, PD, Italy;
| | - Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, SS, Italy; (M.P.); (P.P.); (M.L.D.)
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Brzáková M, Rychtářová J, Čítek J, Sztankóová Z. A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds. Animals (Basel) 2021; 11:ani11061796. [PMID: 34208578 PMCID: PMC8234603 DOI: 10.3390/ani11061796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
Milk production is influenced by many factors, including genetic and environmental factors and their interactions. Animal health, especially udder health, is usually evaluated by the number of somatic cells. The present study described the effect of polymorphisms in the ACACA, BTN1A1, LPL, and SCD genes on the daily milk yield, fat, and protein percentages and somatic cell count. In this study, 590 White Shorthaired (WSH) and Brown Shorthaired (BSH) goats were included. SNP genotyping was performed by PCR-RFLP and multiplex PCR followed by SNaPshot minisequencing analysis. The linear mixed model with repeated measurement was used to identify the genetic associations between the studied genes/SNPs and chosen traits. All selected genes were polymorphic in the tested goat populations and showed significant associations with milk traits. Only BTN1A1 (SNP g.599 A > G) showed a significant association with the somatic cell score. After Bonferroni correction, a significant effect of LPL g.300G > A on daily milk yield and fat percentage, LPL g.185G > T on protein percentage, and LPL G50C, SCD EX3_15G > A, and SCD EX3_68A > G on fat percentage was found. The importance of environmental factors, such as the herd-year effect, month of milking, and lactation order on all milk performance indicators was confirmed.
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Affiliation(s)
- Michaela Brzáková
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic;
- Correspondence: ; Tel.: +420-606-794059
| | - Jana Rychtářová
- Department of Biology of Reproduction, Institute of Animal Science, 104 00 Prague, Czech Republic;
| | - Jindřich Čítek
- Department of Genetics and Agricultural Biotechnologies, Faculty of Agriculture, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic;
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Zuzana Sztankóová
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic;
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Sztankoova Z, Borková M, Rychtářová J, Smolová J, Elich O, Švejcarová M, Brzáková M. The influence of lipoprotein lipase gene polymorphism in Czech East Friesian sheep on the fatty acid profile in milk and yoghurt drinks – a preliminary study. JOURNAL OF ANIMAL AND FEED SCIENCES 2021. [DOI: 10.22358/jafs/133804/2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Elucidating the processes and pathways enriched in buffalo sperm proteome in regulating semen quality. Cell Tissue Res 2020; 383:881-903. [PMID: 33151454 DOI: 10.1007/s00441-020-03303-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
Abstract
Sperm carries a reservoir of proteins regulating the molecular functions to attain functional competence. Semen samples collected from buffalo bulls were assessed for sperm functional attributes (n = 11) and proteome profiling (n = 6). Sperm proteins were extracted and profiled by employing LC-MS/MS. Overall, the buffalo sperm contained 1365 proteins, of which 458 were common between the groups. The unique proteins were 477 and 430 in good and poor quality semen, respectively. In the whole proteome of buffalo sperm, sexual reproduction with phosphatidylethanolamine-binding protein1 (PEBP1), fetuin-B (FETUB) and acrosin (ACR) was the most enriched (p = 8.44E-19) biological process, also with thermogenesis (p = 0.003), oocyte meiosis (p = 0.007) and vascular smooth muscle contraction (p = 0.009) apart from metabolic pathways. In good quality semen, mesenchyme migration (p = 1.24E-07) and morphogenesis (p = 0.001) were abundant biological processes. In good quality semen, the fluid shear stress (p = 0.01) and, in poor quality semen, valine, leucine and isoleucine degradation (p = 3.8E-05) pathways were enriched. In good quality semen, 7 proteins were significantly (p < 0.05) upregulated and 33 proteins were significantly (p < 0.05) downregulated. On validating the abundantly expressed sperm proteins, serine protease inhibitor Kazal-type 2-like (SPINK2; 2.17-fold) and neddylin (NEDD8; 1.13-fold) were upregulated and YBX2 was downregulated (0.41-fold) in good quality semen as compared with poor quality semen (1-fold). The present findings revealed the importance of sperm proteins in oocyte maturation, fertilization process and early embryonic development. The variations in the proteomic composition can be used as potential markers for the selection of breeding bulls.
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Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits. Animals (Basel) 2020; 10:ani10091542. [PMID: 32882861 PMCID: PMC7552124 DOI: 10.3390/ani10091542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 01/30/2023] Open
Abstract
Different studies have shown that polymorphisms in the sequence of genes coding for the milk proteins and milk fatty acids are associated with milk composition traits as well as with cheese-making traits. However, the lack of coincident results across sheep populations has prevented the use of this information in sheep breeding programs. The main objective of this study was to exploit the information derived from a total of 175 whole genome resequencing (WGR) datasets from 43 domestic sheep breeds and three wild sheep to evaluate the genetic diversity of 24 candidate genes for milk composition and identify genetic variants with a potential phenotypic effect. The functional annotation of the identified variants highlighted five single nucleotide polymorphisms (SNPs) predicted to have a high impact on the protein function and 42 missense SNPs with a putative deleterious effect. When comparing the allelic frequencies at these 47 polymorphisms with relevant functional effects between the genomes of Assaf and Churra sheep breeds, two missense deleterious variants were identified as potential markers associated to the milk composition differences found between the Churra and Assaf: XDH:92215727C>T and LALBA:137390760T>C. Future research is required to confirm the effect of the potential functionally relevant variants identified in the present study on milk composition and cheese-making traits.
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12
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Akhatayeva Z, Li H, Mao C, Cheng H, Zhang G, Jiang F, Meng X, Yao Y, Lan X, Song E, Zhang D. Detecting novel Indel variants within the GHR gene and their associations with growth traits in Luxi Blackhead sheep. Anim Biotechnol 2020; 33:214-222. [PMID: 32615865 DOI: 10.1080/10495398.2020.1784184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The growth hormone is important in the regulation of metabolism and energy homeostasis and acts through a growth hormone receptor (GHR). In this work, genetic variations within the ovine GHR gene were identified and tested for associations with body morphometric traits in Chinese Luxi Blackhead (LXBH) sheep. Novel deletion loci in the LXBH GHR gene included P2-del-23 bp and P8-del-23 bp indel variants. The polymorphic information content (PIC) was 0.329 in P2-del-23 bp and 0.257 in P8-del-23 bp. Moreover, both indel polymorphisms were not at Hardy-Weinberg equilibrium (p < 0.05) in the LXBH population. Statistical analyses revealed that the P2-del-23 bp and P8-del-23 bp indels were significantly associated (p < 0.05) with several growth traits in rams and ewes, including body weight, body height, chest depth, chest width, chest circumference, cannon circumference, paunch girth and hip width. Among the tested sheep, the body traits of those with genotype DD were superior to those with II and ID genotypes, suggesting that the 'D' allele was responsible for the positive effects on growth traits. Thus, these results indicate that the P2-del-23 bp and P8-del-23 bp indel sites and the DD genotype can be useful in marker-assisted selection in sheep.
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Affiliation(s)
- Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haixia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Cui Mao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haijian Cheng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Guoping Zhang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fugui Jiang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xianfeng Meng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuni Yao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Enliang Song
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Dongfu Zhang
- Shandong Liaocheng Luxi Blackhead Sheep Farm, Liaocheng, Shandong, China
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Marina H, Reverter A, Gutiérrez-Gil B, Alexandre PA, Porto-Neto LR, Suárez-Vega A, Li Y, Esteban-Blanco C, Arranz JJ. Gene Networks Driving Genetic Variation in Milk and Cheese-Making Traits of Spanish Assaf Sheep. Genes (Basel) 2020; 11:genes11070715. [PMID: 32605032 PMCID: PMC7397207 DOI: 10.3390/genes11070715] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 02/04/2023] Open
Abstract
Most of the milk produced by sheep is used for the production of high-quality cheese. Consequently, traits related to milk coagulation properties and cheese yield are economically important to the Spanish dairy industry. The present study aims to identify candidate genes and their regulators related to 14 milk and cheese-making traits and to develop a low-density panel of markers that could be used to predict an individual's genetic potential for cheese-making efficiency. In this study, we performed a combination of the classical genome-wide association study (GWAS) with a stepwise regression method and a pleiotropy analysis to determine the best combination of the variants located within the confidence intervals of the potential candidate genes that may explain the greatest genetic variance for milk and cheese-making traits. Two gene networks related to milk and cheese-making traits were created using the genomic relationship matrices built through a stepwise multiple regression approach. Several co-associated genes in these networks are involved in biological processes previously found to be associated with milk synthesis and cheese-making efficiency. The methodology applied in this study enabled the selection of a co-association network comprised of 374 variants located in the surrounding of genes showing a potential influence on milk synthesis and cheese-making efficiency.
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Affiliation(s)
- Héctor Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Pâmela Almeida Alexandre
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Yutao Li
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Juan-José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
- Correspondence: ; Tel.: +34-987-291-470
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14
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Abstract
The objective of the research reported in this research communication was the identification and association of single nucleotide polymorphisms (SNP) in the ovine DGAT1, FASN, SCD1 and ACAA2 genes with milk fat percentage and fatty acid (FA) content. Three consecutive monthly milk samplings were obtained from a total of 429 purebred Chios ewes during mid-lactation. Genotypic data were jointly analyzed with 1184 fat content and 37 718 FA percentage records using mixed models. The 3' untranslated region (UTR) of the DGAT1 gene and the 5' and 3'UTRs of the SCD1 gene appeared to be monomorphic. The FASN g.14777C>T SNP on exon 31 was associated with C13:0 and the ACAA2 g.2982T>C SNP on the 3'UTR was associated with C9:0, C11:0, C12:1 cis-9, C13:0 and the ω6/ω3 index, while fat percentage was not affected by the identified SNPs. The results could be useful for breeding programs aiming to improve the quality and nutritional value of ovine milk.
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15
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Cesarani A, Gaspa G, Correddu F, Cellesi M, Dimauro C, Macciotta N. Genomic selection of milk fatty acid composition in Sarda dairy sheep: Effect of different phenotypes and relationship matrices on heritability and breeding value accuracy. J Dairy Sci 2019; 102:3189-3203. [DOI: 10.3168/jds.2018-15333] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/13/2018] [Indexed: 01/21/2023]
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16
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Dettori ML, Pazzola M, Paschino P, Amills M, Vacca GM. Association between the GHR, GHRHR, and IGF1 gene polymorphisms and milk yield and quality traits in Sarda sheep. J Dairy Sci 2018; 101:9978-9986. [PMID: 30146276 DOI: 10.3168/jds.2018-14914] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/01/2018] [Indexed: 11/19/2022]
Abstract
The growth hormone receptor (GHR), the growth hormone releasing hormone receptor (GHRHR), and the insulin-like growth factor 1 (IGF1) genes are known to modulate growth, reproduction, and lactation traits in livestock. The aim of the current work was to investigate if the variation of the sheep GHR, GHRHR, and IGF1 genes is associated with milk yield and quality traits. Three hundred eighty dairy Sarda sheep were genotyped for 36 single nucleotide polymorphisms (SNP) mapping to these 3 loci, and records for milk yield and daily fat and protein yield, as well as for fat, protein, casein, lactose, and milk urea contents, pH, somatic cell score, logarithmic bacterial count, and milk energy were obtained. The linkage disequilibrium analysis was performed only for GHR, as both GHRHR and IGF1 had only 1 polymorphic SNP. Haplotype analysis revealed the existence of 7 haplotype blocks in GHR. Two haplotype blocks, including part of the intron 1 and the upstream region, were clearly separated from the remaining 5 blocks by SNP rs412986330, which may be a recombination hotspot. The latter 5 blocks were contiguous, spanning from intron 2 to exon 10. Statistical analysis revealed that the GHR polymorphism is significantly associated with milk traits for daily fat and protein yield and fat, milk urea, and lactose content. Moreover, variation in IGF1 was associated with milk protein and casein content. Data generated in this research provide new insights into the allelic effects of the ovine GHRHR, GHR, and IGF1 genes on milk production and quality traits, information that may be useful in gene-assisted selection programs.
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Affiliation(s)
- Maria L Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy.
| | - Pietro Paschino
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Giuseppe M Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
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SINGH KARANVEER, JAYAKUMAR S, DIXIT SP, MALIK ZS. SNPs association studies in promoter III of the acetyl coenzyme-A carboxylase-α gene (ACACA) in Munjal–A threatened sheep population of India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i7.81481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Armstrong E, Ciappesoni G, Iriarte W, Da Silva C, Macedo F, Navajas EA, Brito G, San Julián R, Gimeno D, Postiglioni A. Novel genetic polymorphisms associated with carcass traits in grazing Texel sheep. Meat Sci 2018; 145:202-208. [PMID: 29982074 DOI: 10.1016/j.meatsci.2018.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/11/2018] [Accepted: 06/12/2018] [Indexed: 11/26/2022]
Abstract
Improving meat production traits has increased its importance in sheep breeding. We report novel associations of SNP present in genes related to lipid metabolism and growth with several carcass traits in purebred Texel lambs. Expected progeny differences (EPD) predictions from 461 animals from the Central Progeny Testing of Texel breed in Uruguay were used for the association analysis. Live weights at different stages, ultrasound and post-mortem traits were analyzed. Markers in several genes were associated with growth, carcass and meat quality traits. Among others: PPARGC1A with valuable cuts weight, hot carcass weight and carcass fatness; DGAT1 with live weights, fat thickness, rib-eye area and shoulder weight; CAST with birth weight and fat thickness; GHR with birth weight and carcass fatness, and GHRHR with live weights and fat thickness. Genotypic effects ranged from 0.035 to 0.923 (DGAT1 vs. weaning weight) units of phenotypic SD. Most of the associations described are novel in sheep breeding, deserving further analyses.
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Affiliation(s)
- E Armstrong
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Av. Lasplaces 1550, Montevideo, Uruguay.
| | - G Ciappesoni
- Programa Nacional de Carne y Lana, Instituto de Investigación Agropecuaria, Las Brujas, Ruta 48 km. 10, Canelones, Uruguay
| | - W Iriarte
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Av. Lasplaces 1550, Montevideo, Uruguay
| | - C Da Silva
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Av. Lasplaces 1550, Montevideo, Uruguay
| | - F Macedo
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Av. Lasplaces 1550, Montevideo, Uruguay
| | - E A Navajas
- Unidad de Biotecnología, Instituto de Investigación Agropecuaria, Las Brujas, Ruta 48 km 10, Canelones, Uruguay
| | - G Brito
- Laboratorio de Calidad de la Canal y la Carne, Instituto de Investigación Agropecuaria, Ruta 5 km. 386, Tacuarembó, Uruguay
| | - R San Julián
- Laboratorio de Calidad de la Canal y la Carne, Instituto de Investigación Agropecuaria, Ruta 5 km. 386, Tacuarembó, Uruguay
| | - D Gimeno
- Área Investigación y Desarrollo, Secretariado Uruguayo de la Lana, Cno. Gral Servando Gomez 2408, Montevideo, Uruguay
| | - A Postiglioni
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Av. Lasplaces 1550, Montevideo, Uruguay
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Martin P, Palhière I, Maroteau C, Bardou P, Canale-Tabet K, Sarry J, Woloszyn F, Bertrand-Michel J, Racke I, Besir H, Rupp R, Tosser-Klopp G. A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content. Sci Rep 2017; 7:1872. [PMID: 28500343 PMCID: PMC5431851 DOI: 10.1038/s41598-017-02052-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/05/2017] [Indexed: 11/21/2022] Open
Abstract
The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.
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Affiliation(s)
- Pauline Martin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Cyrielle Maroteau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
- Division of Molecular and Clinical Medecine, School of Medecine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
- INRA, Sigenae, Castanet-Tolosan, France
| | - Kamila Canale-Tabet
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | | | - Ines Racke
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Hüseyin Besir
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
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Genetic parameters and genome-wide associations of twinning rate in a local breed, the Maremmana cattle. Animal 2017; 11:1660-1666. [PMID: 28219476 DOI: 10.1017/s1751731117000283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This study seeks to verify the feasibility of increasing twinning in a herd of the Italian autochtonous Maremmana breed. The data set included 1260 individuals born from 1963 to 2014, 527 males and 733 females, 402 of them calving at least once from 1983 through 2015. Breeding values for twinning were estimated by a single-trait linear animal model. However, since twinning is a dichotomous trait and the frequency of twins is far smaller than the frequency of single births, breeding values were also estimated by a single-trait animal threshold model. Heritability of twinning was 0.014±0.018 and 0.062±0.093 for the linear and the threshold models, respectively. Repeatability was 0.071±0.004 and 0.286± 0.012, respectively, for the two models. Genotyping with the Illumina BovineSNP54 BeadChip was performed for cows living on farm in 2012 (119 cows) and a genome-wide association analysis was performed on the corrected phenotype of all calving during the lifespan of each cow, using the GenABEL package in R and a three step GRAMMAR-GC approach. Genomic heritability, calculated from the genomic kinship matrix estimated through genomic marker data, was 0.29±0.021. The most significant detected single nucleotide polymorphisms (Hapmap22923-BTA-129564) was located in proximity of two genes, ARHGAP8 and TMEM200C, which might be potential functional candidates for twinning rate in cattle.
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21
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Crisà A, Ferrè F, Chillemi G, Moioli B. RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk. BMC Vet Res 2016; 12:264. [PMID: 27884183 PMCID: PMC5123407 DOI: 10.1186/s12917-016-0881-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/07/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism. RESULTS A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB). CONCLUSIONS To our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.
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Affiliation(s)
- Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy.
| | - Fabrizio Ferrè
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126, Bologna, Italy
| | - Giovanni Chillemi
- Applications and Innovation Department, CINECA, SCAI SuperComputing, Via dei Tizii 6, 00185, Rome, Italy
| | - Bianca Moioli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy
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22
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Wang H, Zhang L, Cao J, Wu M, Ma X, Liu Z, Liu R, Zhao F, Wei C, Du L. Genome-Wide Specific Selection in Three Domestic Sheep Breeds. PLoS One 2015; 10:e0128688. [PMID: 26083354 PMCID: PMC4471085 DOI: 10.1371/journal.pone.0128688] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/29/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. RESULTS We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study. CONCLUSIONS Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.
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Affiliation(s)
- Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Li Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Jiaxve Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Mingming Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Xiaomeng Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Zhen Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Ruizao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China, Beijing, China
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Association between single nucleotide polymorphisms (SNPs) and milk production traits in Italian Brown cattle. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Moioli B, Scatà MC, De Matteis G, Annicchiarico G, Catillo G, Napolitano F. The ACACA gene is a potential candidate gene for fat content in sheep milk. Anim Genet 2013; 44:601-3. [PMID: 23488977 DOI: 10.1111/age.12036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2013] [Indexed: 11/26/2022]
Abstract
No major gene has yet been reported in sheep that explains the variation of milk fat content. The coding region of the acetyl-CoA carboxylase alpha (ACACA) gene, which plays an important role in de novo fatty acid synthesis, had been investigated, but no non-synonymous mutations have been reported. In this study, the genomic regions encoding the three promoters of the ACACA gene were directly sequenced in 264 sheep of three different breeds, and 10 SNPs were identified. Allele frequencies of most SNPs significantly differed (P = 0.05-0.0001) between breeds. The SNPs that potentially altered either gene regulatory elements or putative binding sites of transcription factors were made evident through in silico analysis. The association analysis with milk traits, performed for one SNP of PIII (GenBank AJ292286, g.1330G>T), showed a significant allelic substitution effect (+0.33%, P < 0.0001 and +0.35%, P < 0.01) in the Altamurana and Gentile breeds respectively. Because this SNP was located in the binding site of the paired box protein transcription factors, which was shown to function as an efficient promoter element, and because PIII transcripts are expressed in the mammary gland, the SNP in PIII of the ACACA gene might affect the variation of fat content in sheep milk.
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Affiliation(s)
- B Moioli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via Salaria 31, Monterotondo, Italy.
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Moioli B, Contarini G, Pariset L, Marchitelli C, Crisà A, Catillo G, Napolitano F. Genetic variation of C18:1 and C18:2 isomers in sheep milk fat. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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