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Huuki H, Vilkki J, Vanhatalo A, Tapio I. Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health. Front Microbiol 2024; 15:1353874. [PMID: 38505558 PMCID: PMC10949896 DOI: 10.3389/fmicb.2024.1353874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12 months. The treatment group (T-group) received adult cow fresh rumen liquid inoculum during the pre-weaning period, while the control group did not (C-group). The effects of inoculum were assessed on calf gut health and as microbial seeding route into the hindgut. The early rumen modulation had no effect on age-related fecal microbiota development. The fecal bacterial community evolved gradually following dietary changes and categorized into pre-weaning and post-weaning communities. Bacterial richness increased with age and stabilized at month 9, while between-sample variation reduced in post-weaning samples. Archaeal load in fecal samples increased after month 4, while archaeal richness increased and stabilized in both groups by month 9. Between-sample similarity was higher during the pre-weaning period, with increased dissimilarity from month 4 onward. Anaerobic fungi were detected in feces at month 4, with richness peaking at month 7. Before month 6, fungal community composition distinctly differed from mature communities. When colostrum, calf rumen, and donor inoculum were evaluated as seeding sources for hindgut colonization, the calf's own rumen was identified as the primary seeding source for fecal bacteria and fungi. Colostrum was a source for several bacteria detected in feces, but these were of temporary importance until weaning. The donor inoculum had limited impact on gut health as diarrhea rates were similar between the T-group and C-group. In conclusion, early-life microbiota modulation shows potential in ruminant development. However, a more targeted approach with bacteria adapted to the hindgut environment may be necessary to modulate hindgut effectively. This research contributes to our understanding of the complex relationship between gut microbiota and calf health and growth.
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Affiliation(s)
- Hanna Huuki
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Johanna Vilkki
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Aila Vanhatalo
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ilma Tapio
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Iso-Touru T, Panitz F, Fischer D, Kyläniemi MK, Taponen S, Tabell J, Virta A, Vilkki J. Genes and pathways revealed by whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge. Vet Res 2024; 55:13. [PMID: 38303095 PMCID: PMC10835992 DOI: 10.1186/s13567-024-01269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Mastitis, inflammation of the mammary gland, is the costliest disease in dairy cattle and a major animal welfare concern. Mastitis is usually caused by bacteria, of which staphylococci, streptococci and Escherichia coli are most frequently isolated from bovine mastitis. Bacteria activate the mammary immune system in variable ways, thereby influencing the severity of the disease. Escherichia coli is a common cause of mastitis in cattle causing both subclinical and clinical mastitis. Understanding of the molecular mechanisms that activate and regulate the host response would be central to effective prevention of mastitis and breeding of cows more resistant to mastitis. We used primary bovine mammary epithelial cell cultures extracted noninvasively from bovine milk samples to monitor the cellular responses to Escherichia coli challenge. Differences in gene expression between control and challenged cells were studied by total RNA-sequencing at two time points post-challenge. In total, 150 and 440 (Padj < 0.05) differentially expressed genes were identified at 3 h and 24 h post-challenge, respectively. The differentially expressed genes were mostly upregulated at 3 h (141/150) and 24 h (424/440) post-challenge. Our results are in line with known effects of E. coli infection, with a strong early inflammatory response mediated by pathogen receptor families. Among the most significantly enriched early KEGG pathways were the TNF signalling pathway, the cytokine-cytokine receptor interaction, and the NF-kappa B signalling pathway. At 24 h post-challenge, most significantly enriched were the Influenza A, the NOD-like receptor signalling, and the IL-17 signaling pathway.
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Affiliation(s)
- Terhi Iso-Touru
- Natural Resources Institute Finland (Luke), Jokioinen, Finland.
| | - Frank Panitz
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Minna K Kyläniemi
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Suvi Taponen
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Jonna Tabell
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Anneli Virta
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Johanna Vilkki
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Huuki H, Tapio M, Mäntysaari P, Negussie E, Ahvenjärvi S, Vilkki J, Vanhatalo A, Tapio I. Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions. Front Microbiol 2022; 13:983823. [PMID: 36425044 PMCID: PMC9679419 DOI: 10.3389/fmicb.2022.983823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 09/29/2023] Open
Abstract
Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray-Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow's 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.
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Affiliation(s)
- Hanna Huuki
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Miika Tapio
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Päivi Mäntysaari
- Production Systems, Animal Nutrition, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Enyew Negussie
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Seppo Ahvenjärvi
- Production Systems, Animal Nutrition, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Johanna Vilkki
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Aila Vanhatalo
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ilma Tapio
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Huuki H, Ahvenjärvi S, Lidauer P, Popova M, Vilkki J, Vanhatalo A, Tapio I. Fresh Rumen Liquid Inoculant Enhances the Rumen Microbial Community Establishment in Pre-weaned Dairy Calves. Front Microbiol 2022; 12:758395. [PMID: 35095788 PMCID: PMC8790516 DOI: 10.3389/fmicb.2021.758395] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/30/2021] [Indexed: 02/01/2023] Open
Abstract
The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inoculum from an adult cow, provided to calves during the pre-weaning period, influences the establishment of rumen bacterial, archaeal, fungal, and ciliate protozoan communities in monozygotic twin calves (n = 6 pairs). The calves were divided into treatment (T-group) and control (C-group) groups, where the T-group received fresh rumen liquid as an oral inoculum during a 2-8-week period. The C-group was not inoculated. The rumen microbial community composition was determined using bacterial and archaeal 16S ribosomal RNA (rRNA) gene, protozoal 18S rRNA gene, and fungal ITS1 region amplicon sequencing. Animal weight gain and feed intake were monitored throughout the experiment. The T-group tended to have a higher concentrate intake (Treatment: p < 0.08) and had a significantly higher weekly weight gain (Treatment: p < 0.05), but no significant difference in volatile fatty acid concentrations between the groups was observed. In the T-group, the inoculum stimulated the earlier establishment of mature rumen-related bacterial taxa, affecting significant differences between the groups until 6 weeks of age. The inoculum also increased the archaeal operational taxonomic unit (OTU) diversity (Treatment: p < 0.05) but did not affect the archaeal quantity. Archaeal communities differed significantly between groups until week 4 (p = 0.02). Due to the inoculum, ciliate protozoa were detected in the T-group in week 2, while the C-group remained defaunated until 6 weeks of age. In week 8, Eremoplastron dilobum was the dominant ciliate protozoa in the C-group and Isotricha sp. in the T-group, respectively. The Shannon diversity of rumen anaerobic fungi reduced with age (Week: p < 0.01), and community establishment was influenced by a change of diet and potential interaction with other rumen microorganisms. Our results indicate that an adult cow rumen liquid inoculum enhanced the maturation of bacterial and archaeal communities in pre-weaning calves' rumen, whereas its effect on eukaryotic communities was less clear and requires further investigation.
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Affiliation(s)
- Hanna Huuki
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Seppo Ahvenjärvi
- Production Systems, Animal Nutrition, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Paula Lidauer
- Production Systems, Welfare of Farmed Animals, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR 1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Johanna Vilkki
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Aila Vanhatalo
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ilma Tapio
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Bayat A, Razzaghi A, Sari M, Kairenius P, Tröscher A, Trevisi E, Vilkki J. The effect of dietary rumen-protected trans-10,cis-12 conjugated linoleic acid or a milk fat-depressing diet on energy metabolism, inflammation, and oxidative stress of dairy cows in early lactation. J Dairy Sci 2022; 105:3032-3048. [DOI: 10.3168/jds.2021-20543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/08/2021] [Indexed: 01/04/2023]
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Bayat AR, Vilkki J, Razzaghi A, Leskinen H, Kettunen H, Khurana R, Brand T, Ahvenjärvi S. Evaluating the effects of high-oil rapeseed cake or natural additives on methane emissions and performance of dairy cows. J Dairy Sci 2021; 105:1211-1224. [PMID: 34799103 DOI: 10.3168/jds.2021-20537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/30/2021] [Indexed: 01/13/2023]
Abstract
We evaluated the potential of feeding high-oil rapeseed cake or natural additives as rumen modifiers on enteric methane (CH4) emissions, nutrient utilization, performance, and milk fatty acid (FA) profile of dairy cows. Eight Nordic Red dairy cows averaging (mean ± SD) 81 ± 21 d in milk and 41.0 ± 1.9 kg of milk yield at the beginning of the study were randomly assigned to a replicated 4 × 4 Latin square design with 21-d periods. Treatments comprised grass silage-based diets (45:55 forage to concentrate ratio on dry matter basis) including (1) control containing 19.3% rapeseed meal (CON), (2) CON with full replacement of rapeseed meal with rapeseed cake (RSC), (3) supplementation of CON with 50 g/d of yeast hydrolysate product plus coniferous resin acid-based compound (YHR), and (4) supplementation of CON with 20 g/d of combination of garlic-citrus extract and essential oils in a pellet (GCE). Apparent total-tract digestibility was measured using total collection of feces, and CH4 emissions were measured in respiratory chambers on 4 consecutive days. Data collected during d 17 and 21 in each period were used for ANOVA analysis using a mixed model. Treatments did not affect dry matter intake (DMI), whereas feeding RSC increased crude protein and ether extract digestibility compared with the other diets. Emissions of CH4 per day, per kilogram of DMI, and per kilogram of energy-corrected milk, and gross energy intake were lower for RSC compared with other diets. We found no effect of YHR on daily CH4 emissions, whereas CH4 yield (g of CH4/kg of DMI or as percentage of gross energy intake) decreased with GCE compared with CON. Treatments did not influence energy balance. Further, RSC reduced the proportion of N intake excreted in feces, and YHR improved N balance compared with CON diet. Feeding RSC resulted in greatest yields of milk and energy-corrected milk, and feed efficiency. Relative to the CON diet, RSC decreased saturated FA by 10% in milk fat by increasing cis-monounsaturated FA but also increased the proportion of trans FA. Proportion of odd- and branched-chain FA increased with GCE and YHR compared with CON. We conclude that replacing rapeseed meal by rapeseed cake decreased CH4 emissions, whereas YHR or GCE had no effect on CH4 emissions in this study.
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Affiliation(s)
- A R Bayat
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland.
| | - J Vilkki
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland
| | - A Razzaghi
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland
| | - H Leskinen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland
| | - H Kettunen
- Hankkija Oy, Peltokuumolantie 4, 05801 Hyvinkää, Finland
| | - R Khurana
- Mootral SA, Z.A. La Pièce 1 - A5, 1180 Rolle, Switzerland
| | - T Brand
- Mootral SA, Z.A. La Pièce 1 - A5, 1180 Rolle, Switzerland
| | - S Ahvenjärvi
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland
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Darabighane B, Tapio I, Ventto L, Kairenius P, Stefański T, Leskinen H, Shingfield KJ, Vilkki J, Bayat AR. Effects of Starch Level and a Mixture of Sunflower and Fish Oils on Nutrient Intake and Digestibility, Rumen Fermentation, and Ruminal Methane Emissions in Dairy Cows. Animals (Basel) 2021; 11:1310. [PMID: 34063184 PMCID: PMC8147431 DOI: 10.3390/ani11051310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 02/01/2023] Open
Abstract
Four multiparous dairy cows were used in a 4 × 4 Latin square to examine how starch level and oil mixture impact dry matter (DM) intake and digestibility, milk yield and composition, rumen fermentation, ruminal methane (CH4) emissions, and microbial diversity. Experimental treatments comprised high (HS) or low (LS) levels of starch containing 0 or 30 g of a mixture of sunflower and fish oils (2:1 w/w) per kg diet DM (LSO and HSO, respectively). Intake of DM did not differ between cows fed LS and HS diets while oil supplementation reduced DM intake. Dietary treatments did not affect milk and energy corrected milk yields. There was a tendency to have a lower milk fat concentration due to HSO compared with other treatments. Both high starch level and oil supplementation increased digestibility of gross energy. Cows receiving HS diets had higher levels of total rumen VFA while acetate was lower than LS without any differences in rumen pH, or ruminal CH4 emissions. Although dietary oil supplementation had no impact on rumen fermentation, decreased CH4 emissions (g/day and g/kg milk) were observed with a concomitant increase in Anoplodinium-Diplodinium sp. and Epidinium sp. but a decrease in Christensenellaceae, Ruminococcus sp., Methanobrevibacter ruminantium and Mbb. gottschalkii clades.
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Affiliation(s)
- Babak Darabighane
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
| | - Ilma Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland;
| | - Laura Ventto
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
| | - Piia Kairenius
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
| | - Tomasz Stefański
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
| | - Heidi Leskinen
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
| | - Kevin J. Shingfield
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
| | - Johanna Vilkki
- Research and Customer Relationships, Service Groups, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland;
| | - Ali-Reza Bayat
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland; (B.D.); (L.V.); (P.K.); (T.S.); (H.L.); (K.J.S.)
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Wallace RJ, Sasson G, Garnsworthy PC, Tapio I, Gregson E, Bani P, Huhtanen P, Bayat AR, Strozzi F, Biscarini F, Snelling TJ, Saunders N, Potterton SL, Craigon J, Minuti A, Trevisi E, Callegari ML, Cappelli FP, Cabezas-Garcia EH, Vilkki J, Pinares-Patino C, Fliegerová KO, Mrázek J, Sechovcová H, Kopečný J, Bonin A, Boyer F, Taberlet P, Kokou F, Halperin E, Williams JL, Shingfield KJ, Mizrahi I. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci Adv 2019; 5:eaav8391. [PMID: 31281883 PMCID: PMC6609165 DOI: 10.1126/sciadv.aav8391] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/30/2019] [Indexed: 05/19/2023]
Abstract
A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.
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Affiliation(s)
- R. John Wallace
- The Rowett Institute, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, UK
- Corresponding author. (R.J.W.); (I.M.)
| | - Goor Sasson
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Philip C. Garnsworthy
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Ilma Tapio
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Emma Gregson
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Paolo Bani
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Pekka Huhtanen
- Swedish University of Agricultural Sciences, Department of Agriculture for Northern Sweden, S-90 183 Umeå, Sweden
| | - Ali R. Bayat
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | | | | | - Timothy J. Snelling
- The Rowett Institute, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, UK
| | - Neil Saunders
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Sarah L. Potterton
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - James Craigon
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Maria L. Callegari
- Institute of Microbiology, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Fiorenzo Piccioli Cappelli
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Edward H. Cabezas-Garcia
- Swedish University of Agricultural Sciences, Department of Agriculture for Northern Sweden, S-90 183 Umeå, Sweden
| | - Johanna Vilkki
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Cesar Pinares-Patino
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Kateřina O. Fliegerová
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Hana Sechovcová
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France
| | - Fotini Kokou
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Eran Halperin
- Departments of Computer Science, Computational Medicine, Human Genetics, and Anesthesiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Kevin J. Shingfield
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- Corresponding author. (R.J.W.); (I.M.)
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Leskinen H, Ventto L, Kairenius P, Shingfield KJ, Vilkki J. Temporal changes in milk fatty acid composition during diet-induced milk fat depression in lactating cows. J Dairy Sci 2019; 102:5148-5160. [PMID: 30904304 DOI: 10.3168/jds.2018-15860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/29/2019] [Indexed: 12/19/2022]
Abstract
Diet-induced milk fat depression (MFD) in lactating cows has been attributed to alterations in ruminal lipid metabolism leading to the formation of specific fatty acid (FA) biohydrogenation intermediates that directly inhibit milk fat synthesis. However, the mechanisms responsible for decreased lipid synthesis in the mammary gland over time are not well defined. The aim of this study was to evaluate the effect of diet on milk FA composition and milk fat production over time, especially during MFD, and explore the associations between MFD and FA biohydrogenation intermediates in omasal digesta and milk. Four lactating Finnish Ayrshire cows used in a 4 × 4 Latin square with a 2 × 2 factorial arrangement of treatments and 35-d experimental periods were fed diets formulated to cause differences in ruminal and mammary lipid metabolism. Treatments consisted of an iso-nitrogenous total mixed ration based on grass silage with a forage to concentrate ratio of 65:35 or 35:65 without added oil, or with sunflower oil at 50 g/kg of diet dry matter. The high-concentrate diet with sunflower oil (HSO) induced a 2-stage drop in milk fat synthesis that was accompanied by specific temporal changes in the milk FA composition. The MFD on HSO was associated especially with trans-10 18:1 and also with trans-9,cis-11 conjugated linoleic acid (CLA) in milk and omasal digesta across all diets and was accompanied by the appearance of trans-10,cis-15 18:2. Trans-10,cis-12 CLA was increased in HSO, but milk fat secretion was not associated with omasal or milk trans-10,cis-12 CLA. The temporal changes in milk fat content and yield and milk FA composition reflect the shift from the predominant ruminal biohydrogenation pathway to an alternative pathway. The ambiguous role of trans-10,cis-12 CLA suggests that trans-10 18:1, trans-9,cis-11 CLA and trans-10,cis-15 18:2 or additional mechanisms contributed to the diet-induced MFD in lactating cows.
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Affiliation(s)
- H Leskinen
- Milk Production, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.
| | - L Ventto
- Milk Production, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - P Kairenius
- Milk Production, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - K J Shingfield
- Milk Production, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - J Vilkki
- Animal Genetics, Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
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10
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Qin N, Bayat AR, Trevisi E, Minuti A, Kairenius P, Viitala S, Mutikainen M, Leskinen H, Elo K, Kokkonen T, Vilkki J. Dietary supplement of conjugated linoleic acids or polyunsaturated fatty acids suppressed the mobilization of body fat reserves in dairy cows at early lactation through different pathways. J Dairy Sci 2018; 101:7954-7970. [PMID: 29960784 DOI: 10.3168/jds.2017-14298] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/08/2018] [Indexed: 01/25/2023]
Abstract
To investigate the metabolic changes in the adipose tissue (AT) of dairy cows under milk fat depression (MFD), 30 cows were randomly allocated to a control diet, a conjugated linoleic acid (CLA)-supplemented diet, or a high-starch diet supplemented with a mixture of sunflower and fish oil (2:1; as HSO diet) from 1 to 112 d in milk. Performance of animals, milk yield, milk composition, energy balance, and blood metabolites were measured during lactation. Quantitative PCR analyses were conducted on the AT samples collected at wk 3 and 15 of lactation. The CLA and HSO diets considerably depressed milk fat yield and milk fat content at both wk 3 and 15 in the absence of significant changes in milk protein and lactose contents. In addition, the HSO diet lowered milk yield at wk 15 and decreased dry matter intake of cows from wk 3 to 15. Compared with the control, both CLA and HSO groups showed reduced body weight loss, improved energy balance, and decreased plasma concentrations of nonesterified fatty acids and β-hydroxybutyrate at early lactation. The gene expression analyses reflected suppressed lipolysis in AT of the CLA and HSO groups compared with the control at wk 3, as suggested by the downregulation of hormone-sensitive lipase and fatty acid binding protein 4 and the upregulation of perilipin 2. In addition, the HSO diet promoted lipogenesis in AT at wk 15 through the upregulation of 1-acylglycerol-3-phosphate O-acyltransferase 2, mitochondrial glycerol-3-phosphate acyltransferase, perilipin 2, and peroxisome proliferator-activated receptor γ. The CLA diet likely regulated insulin sensitivity in AT as it upregulated the transcription of various genes involved in insulin signaling, inflammatory responses, and ceramide metabolism, including protein kinase B2, nuclear factor κ B1, toll-like receptor 4, caveolin 1, serine palmitoyltransferase long chain base subunit 1, and N-acylsphingosine amidohydrolase 1. In contrast, the HSO diet resulted in little or no change in the pathways relevant to insulin sensitivity. In conclusion, the CLA and HSO diets induced a shift in energy partitioning toward AT instead of mammary gland during lactation through the regulation of different pathways.
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Affiliation(s)
- Nanbing Qin
- Department of Agricultural Sciences, PO Box 28, FI-00014 University of Helsinki, Finland
| | - Ali-Reza Bayat
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 20123 Milan, Italy
| | - Andrea Minuti
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 20123 Milan, Italy
| | - Piia Kairenius
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Sirja Viitala
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Mervi Mutikainen
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Heidi Leskinen
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Kari Elo
- Department of Agricultural Sciences, PO Box 28, FI-00014 University of Helsinki, Finland
| | - Tuomo Kokkonen
- Department of Agricultural Sciences, PO Box 28, FI-00014 University of Helsinki, Finland
| | - Johanna Vilkki
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland.
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11
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Tuiskula-Haavisto M, Honkatukia M, Dunn IC, Bain MM, De Koning DJ, Preisinger R, Schmutz M, Arango J, Fischer D, Vilkki J. Validated quantitative trait loci for eggshell quality in experimental and commercial laying hens. Anim Genet 2018; 49:329-333. [PMID: 29797511 DOI: 10.1111/age.12671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2018] [Indexed: 01/07/2023]
Abstract
Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker-assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow implementation of measurements integrating a number of shell parameters that are difficult to measure. In this study, we selected the most promising autosomal quantitative trait loci (QTL) affecting eggshell quality on chromosomes 2, 3, 6 and 14 from earlier experiments and we extended the F2 population to include 1599 F2 females. The study was repeated on two commercial populations: Lohmann Tierzucht Rhode Island Red line (n = 692 females) and a Hy-Line White Plymouth Rock line (n = 290 progeny tested males). We analyzed the selected autosomal QTL regions on the three populations with SNP markers at 4-13 SNPs/Mb density. QTL for eggshell quality were replicated on all studied regions in the F2 population. New QTL were detected for eggshell color on chromosomes 3 and 6. Marker associations with eggshell quality traits were validated in the tested commercial lines on chromosomes 2, 3 and 6, thus paving the way for marker-assisted selection for improved eggshell quality.
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Affiliation(s)
- M Tuiskula-Haavisto
- Natural Resources Institute Finland (Luke), Production Systems, FI-31600, Jokioinen, Finland
| | - M Honkatukia
- Natural Resources Institute Finland (Luke), Production Systems, FI-31600, Jokioinen, Finland
| | - I C Dunn
- Avian Biology the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - M M Bain
- College of Medical, Veterinary and Life Sciences (MVLS), IBAHCM, University of Glasgow, University Avenue, Glasgow G128QQ, UK
| | - D J De Koning
- Swedish University of Agricultural Sciences, Almas Allé 8, 75507, Uppsala, Sweden
| | - R Preisinger
- Lohmann Tierzucht GmbH, Am Seedeich 9-11, 27472, Cuxhaven, Germany
| | - M Schmutz
- Lohmann Tierzucht GmbH, Am Seedeich 9-11, 27472, Cuxhaven, Germany
| | - J Arango
- Hy-Line International, PO Box 310, Dallas Center, IA, 50063, USA
| | - D Fischer
- Natural Resources Institute Finland (Luke), Production Systems, FI-31600, Jokioinen, Finland
| | - J Vilkki
- Natural Resources Institute Finland (Luke), Production Systems, FI-31600, Jokioinen, Finland
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12
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Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nat Genet 2018; 50:362-367. [PMID: 29459679 DOI: 10.1038/s41588-018-0056-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/03/2018] [Indexed: 11/09/2022]
Abstract
Stature is affected by many polymorphisms of small effect in humans 1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10-8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP-seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
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Affiliation(s)
- Aniek C Bouwman
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Hans D Daetwyler
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Amanda J Chamberlain
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Carla Hurtado Ponce
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Simon Boitard
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Marlies Dolezal
- Platform of Bioinformatics and Statistics, University of Veterinary Medicine, Vienna, Austria
| | - Hubert Pausch
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany.,Animal Genomics, ETH Zurich, Zurich, Switzerland
| | - Rasmus F Brøndum
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Phil J Bowman
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Bo Thomsen
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | - Min Wang
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Anna A E Vinkhuyzen
- University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland, Australia.,University of Queensland, Queensland Brain Institute, St Lucia, Queensland, Australia
| | - Frank Panitz
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Christian Bendixen
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Lars-Erik Holm
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Allice, Paris, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | | | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Aurelien Capitan
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Allice, Paris, France
| | - Thierry Tribout
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Anne Barbat
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Pascal Croiseau
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | | | | | - Christy Vander Jagt
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | | | - Anna Bieber
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Deirdre C Purfield
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
| | - Reiner Emmerling
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Poing, Germany
| | - Kay-Uwe Götz
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Poing, Germany
| | | | | | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, USA
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science/Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Mike E Goddard
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Ben J Hayes
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia. .,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia.
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13
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Bayat A, Tapio I, Vilkki J, Shingfield K, Leskinen H. Plant oil supplements reduce methane emissions and improve milk fatty acid composition in dairy cows fed grass silage-based diets without affecting milk yield. J Dairy Sci 2018; 101:1136-1151. [DOI: 10.3168/jds.2017-13545] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/13/2017] [Indexed: 01/07/2023]
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14
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Mesbah-Uddin M, Guldbrandtsen B, Iso-Touru T, Vilkki J, De Koning DJ, Boichard D, Lund MS, Sahana G. Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. DNA Res 2017; 25:49-59. [PMID: 28985340 PMCID: PMC5824824 DOI: 10.1093/dnares/dsx037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/18/2017] [Indexed: 01/10/2023] Open
Abstract
Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp–773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10−6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10−22, 2.06 × 10−22, 7.01 × 10−6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher’s P-value = 8.91 × 10−10 and 7.4 × 10−11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.
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Affiliation(s)
- Md Mesbah-Uddin
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark.,Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | - Terhi Iso-Touru
- Green Technology, Natural Resources Institute Finland, FI-31600 Jokioinen, Finland
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland, FI-31600 Jokioinen, Finland
| | - Dirk-Jan De Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750?07 Uppsala, Sweden
| | - Didier Boichard
- Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mogens Sandø Lund
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | - Goutam Sahana
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
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15
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Bayat AR, Ventto L, Kairenius P, Stefański T, Leskinen H, Tapio I, Negussie E, Vilkki J, Shingfield KJ. Dietary forage to concentrate ratio and sunflower oil supplement alter rumen fermentation, ruminal methane emissions, and nutrient utilization in lactating cows. Transl Anim Sci 2017; 1:277-286. [PMID: 32704652 PMCID: PMC7205341 DOI: 10.2527/tas2017.0032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/10/2017] [Indexed: 11/13/2022] Open
Abstract
The effects of supplementing high- or low-concentrate diets with sunflower oil (SO) on rumen fermentation, nutrient utilization, and ruminal methane (CH4) emissions in lactating cows were examined. Four multiparous Nordic Red dairy cows fitted with rumen cannulae were used in a 4 × 4 Latin square with a 2 × 2 factorial arrangement of treatments and 35-d periods. Experimental treatments comprised iso-nitrogenous total mixed rations based on grass silage with forage to concentrate ratio of 65:35 or 35:65 supplemented with 0 or 50 g/kg diet DM of SO. Apparent ruminal OM and starch digestibility was greater (P < 0.05) with high- than low-concentrate diets but was unaffected by SO. Inclusion of SO in high-concentrate diet decreased (P ≤ 0.05) apparent total tract OM, fiber, and GE, and apparent ruminal fiber digestibility. High-concentrate diets and SO shifted (P < 0.05) fiber digestion from rumen to the hindgut. High-concentrate diet resulted in a lower rumen pH and elevated total rumen VFA concentration compared with low-concentrate diet, whereas SO increased rumen pH and decreased rumen VFA concentration when included in high-, but not low-concentrate diet (P < 0.05 for interaction). High-concentrate diet reduced rumen ammonia-N (P < 0.01) and molar proportion of acetate to propionate (P < 0.01), and decreased (P < 0.05) ruminal CH4 emissions when expressed as g/d or g/kg OM digested in the rumen. With both low- and high-concentrate diets, SO reduced (P < 0.05) daily emissions of CH4 as g/d or g/kg OM digested in the rumen, but SO reduced CH4 emissions expressed as g/kg OM intake, OM digested in total digestive tract, energy-corrected milk or % of GE intake only with low-concentrate diet (P ≤ 0.05 for interaction). In conclusion, replacing grass silage with concentrates led to a reduction in daily ruminal CH4 emissions that were accompanied by a shift in rumen fermentation toward the synthesis of propionate, and decreases in rumen pH and fiber digestion. Sunflower oil was effective in reducing daily CH4 emissions in lactating cows which was accompanied by a noticeable lower feed intake with high- but not low-concentrate diet. Overall the effects of SO and greater proportion of concentrates in the diet on daily CH4 emissions were additive but the additivity declined or vanished when different indices of CH4 emission intensity were considered. Consequently, SO was more effective in reducing CH4 emissions when low-concentrate diet was fed.
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Affiliation(s)
- A R Bayat
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - L Ventto
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - P Kairenius
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - T Stefański
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - H Leskinen
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - I Tapio
- Animal Genomics, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - E Negussie
- Biometrical Genetics, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - J Vilkki
- Animal Genomics, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - K J Shingfield
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
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16
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Tapio I, Fischer D, Blasco L, Tapio M, Wallace RJ, Bayat AR, Ventto L, Kahala M, Negussie E, Shingfield KJ, Vilkki J. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PLoS One 2017; 12:e0180260. [PMID: 28704445 PMCID: PMC5509137 DOI: 10.1371/journal.pone.0180260] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/13/2017] [Indexed: 01/05/2023] Open
Abstract
The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions.
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Affiliation(s)
- Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
- * E-mail:
| | - Daniel Fischer
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Lucia Blasco
- Bio-based business and industry, Natural Resources Institute Finland, Jokioinen, Finland
| | - Miika Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - R. John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Ali R. Bayat
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Laura Ventto
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Minna Kahala
- Bio-based business and industry, Natural Resources Institute Finland, Jokioinen, Finland
| | - Enyew Negussie
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Kevin J. Shingfield
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
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17
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Fischer D, Honkatukia M, Tuiskula-Haavisto M, Nordhausen K, Cavero D, Preisinger R, Vilkki J. Subgroup detection in genotype data using invariant coordinate selection. BMC Bioinformatics 2017; 18:173. [PMID: 28302061 PMCID: PMC5356247 DOI: 10.1186/s12859-017-1589-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/09/2017] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be found in the analyst's toolbox and hence are only rarely applied. RESULTS We present a modern dimension reduction method called 'Invariant Coordinate Selection' (ICS) and its application to high-throughput genotype data. The more commonly known Independent Component Analysis (ICA) is in this framework just a special case of ICS. We use ICS on both, a simulated and a real dataset to demonstrate first some deficiencies of PCA and how ICS is capable to recover the correct subgroups within the simulated data. Second, we apply the ICS method on a chicken dataset and also detect there two subgroups. These subgroups are then further investigated with respect to their genotype to provide further evidence of the biological relevance of the detected subgroup division. Further, we compare the performance of ICS also to five other popular dimension reduction methods. CONCLUSION The ICS method was able to detect subgroups in data where the PCA fails to detect anything. Hence, we promote the application of ICS to high-throughput genotype data in addition to the established PCA. Especially in statistical programming environments like e.g. R, its application does not add any computational burden to the analysis pipeline.
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Affiliation(s)
- Daniel Fischer
- Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland
| | - Mervi Honkatukia
- Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland
| | | | - Klaus Nordhausen
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- University of Tampere, School of Health Sciences, Medisiinarinkatu 3, Tampere, 33014 Finland
| | - David Cavero
- Lohmann Tierzucht GmbH, Am Seedeich 9-11, Cuxhaven, 27454 Germany
| | | | - Johanna Vilkki
- Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland
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18
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Vilkki J, Fischer D, Tapio I, Ahvenjärvi S, Shingfield KJ. 1105 ADSA®-EAAP speaker exchange presentation: Effect of rumen content exchange on gene expression in rumen epithelium of lactating cows. J Anim Sci 2016. [DOI: 10.2527/jam2016-1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Iso-Touru T, Tapio M, Vilkki J, Kiseleva T, Ammosov I, Ivanova Z, Popov R, Ozerov M, Kantanen J. Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe. Anim Genet 2016; 47:647-657. [DOI: 10.1111/age.12473] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
Affiliation(s)
- T. Iso-Touru
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - M. Tapio
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - J. Vilkki
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - T. Kiseleva
- All-Russian Research Institute for Farm Animal Genetics and Breeding; Russian Academy of Sciences; 55-a Moskovskoe Shosse St. Petersburg-Pushkin 199601 Russia
| | - I. Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region; Batagay-Alyta 678580 The Sakha Republic (Yakutsk) Russia
| | - Z. Ivanova
- Yakutian Research Institute of Agriculture; Yakutsk Sakha 677007 Russia
| | - R. Popov
- Yakutian Research Institute of Agriculture; Yakutsk Sakha 677007 Russia
| | - M. Ozerov
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
- Department of Biology; University of Turku; Turku 20014 Finland
| | - J. Kantanen
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
- Department of Environmental and Biological Sciences; University of Eastern Finland; PO Box 1627 Kuopio 70211 Finland
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Vilkki J, Fischer D, Tapio I, Shingfield KJ. P3010 Effect of rumen content exchange on gene expression in rumen epithelium of lactating cows. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement456x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Niemi M, Sajantila A, Vilkki J. Temporal variation in coat colour (genotypes) supports major changes in the Nordic cattle population after Iron Age. Anim Genet 2016; 47:495-8. [PMID: 27297978 DOI: 10.1111/age.12445] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2016] [Indexed: 11/29/2022]
Abstract
Variation in coat colour genotypes of archaeological cattle samples from Finland was studied by sequencing 69 base pairs of the extension locus (melanocortin 1-receptor, MC1R) targeting both a transition and a deletion defining the three main alleles, such as dominant black (E(D) ), wild type (E(+) ) and recessive red (e). The 69-bp MC1R sequence was successfully analysed from 23 ancient (1000-1800 AD) samples. All three main alleles and genotype combinations were detected with allele frequencies of 0.26, 0.17 and 0.57 for E(D) , E(+) and e respectively. Recessive red and dominant black alleles were detected in both sexes. According to the best of our knowledge, this is the first ancient DNA study defining all three main MC1R alleles. Observed MC1R alleles are in agreement with calculated phenotype frequencies from historical sources. The division of ancient Finnish cattle population into modern Finnish breeds with settled colours was dated to the 20th century. From the existing genotyped populations in Europe (43 breeds, n = 2360), the closest match to ancient MC1R genotype frequencies was with the Norwegian native multicoloured breeds. In combined published genotype data of ancient (n = 147) and genotypes and phenotypes of modern Nordic cattle (n = 738), MC1R allele frequencies showed temporal changes similar to neutral mitochondrial DNA and Y-chromosomal haplotypes analysed earlier. All three markers indicate major change in genotypes in Nordic cattle from the Late Iron Age to the Medieval period followed by slower change through the historical periods until the present.
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Affiliation(s)
- M Niemi
- Department of Forensic Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,Green technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland
| | - A Sajantila
- Department of Forensic Medicine, University of Helsinki, FI-00014, Helsinki, Finland
| | - J Vilkki
- Green technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland
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22
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Leskinen H, Viitala S, Mutikainen M, Kairenius P, Tapio I, Taponen J, Bernard L, Vilkki J, Shingfield KJ. Ruminal Infusions of Cobalt EDTA Modify Milk Fatty Acid Composition via Decreases in Fatty Acid Desaturation and Altered Gene Expression in the Mammary Gland of Lactating Cows. J Nutr 2016; 146:976-85. [PMID: 27075908 DOI: 10.3945/jn.115.226100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/01/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Intravenous or ruminal infusion of lithium salt of cobalt EDTA (Co-EDTA) or cobalt-acetate alters milk fat composition in cattle, but the mechanisms involved are not known. OBJECTIVE The present study evaluated the effect of ruminal Co-EDTA infusion on milk FA composition, mammary lipid metabolism, and mammary lipogenic gene expression. METHODS For the experiment, 4 cows in midlactation and fitted with rumen cannulae were used in a 4 × 4 Latin square with 28-d periods. Co-EDTA was administered in the rumen to supply 0, 1.5, 3.0, or 4.5 g Co/d over an 18-d interval with a 10-d washout between experimental periods. Milk production was recorded daily, and milk FA composition was determined on alternate days. Mammary tissue was biopsied on day 16, and arteriovenous differences of circulating lipid fractions and FA uptake across the mammary gland were measured on day 18. RESULTS Co-EDTA had no effect on intake, proportions of rumen volatile FA, or milk production but caused dose-dependent changes in milk FA composition. Alterations in milk fat composition were evident within 3 d of infusion and characterized by linear or quadratic decreases (P < 0.05) in FAs containing a cis-9 double bond, an increase in 4:0 and 16:0, and linear decreases in milk 8:0, 10:0, 12:0, and 14:0 concentrations. Co-EDTA progressively decreased (P < 0.05) the stearoyl-CoA desaturase (SCD)-catalyzed desaturation of FAs in the mammary gland by up to 72% but had no effect on mammary SCD1 mRNA or SCD protein abundance. Changes in milk FA composition were accompanied by altered expression of specific genes involved in de novo FA and triacylglycerol synthesis. CONCLUSION Ruminal infusion of Co-EDTA alters milk FA composition in cattle via a mechanism that involves decreases in the desaturation of FAs synthesized de novo or extracted from blood and alterations in mammary lipogenic gene expression, without affecting milk fat yield.
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Affiliation(s)
- Heidi Leskinen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Sirja Viitala
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Mervi Mutikainen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Piia Kairenius
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ilma Tapio
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Juhani Taponen
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Laurence Bernard
- Adipose Tissue and Milk Lipid Laboratory, Herbivore Research Unit, INRA-Theix, Saint-Genès-Champanelle, France; and
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Kevin J Shingfield
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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Sahana G, Iso-Touru T, Wu X, Nielsen US, de Koning DJ, Lund MS, Vilkki J, Guldbrandtsen B. A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle. Genet Sel Evol 2016; 48:35. [PMID: 27091210 PMCID: PMC4835938 DOI: 10.1186/s12711-016-0215-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/11/2016] [Indexed: 11/24/2022] Open
Abstract
Background A whole-genome association study of 4631 progeny-tested Nordic Red dairy cattle bulls using imputed next-generation sequencing data revealed a major quantitative trait locus (QTL) that affects birth index (BI) on Bos taurus autosome (BTA) 23. We analyzed this QTL to identify which of the component traits of BI are affected and understand its molecular basis. Results A genome-wide scan of BI in Nordic Red dairy cattle detected major QTL on BTA6, 14 and 23. The strongest associated single nucleotide polymorphism (SNP) on BTA23 was located at 13,313,896 bp with \documentclass[12pt]{minimal}
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\begin{document}$$- \log_{10} ({\text{p}}) = 50.63$$\end{document}-log10(p)=50.63. Analyses of component traits showed that the QTL had a large effect on stillbirth. Based on the 10 most strongly associated SNPs with stillbirth, we constructed a haplotype. Among this haplotype’s alleles, HAPQTL had a large negative effect on stillbirth. No animals were found to be homozygous for HAPQTL. Analysis of stillbirth records that were categorized by carrier status for HAPQTL of the sire and maternal grandsire suggested that this haplotype had a recessive mode of inheritance. Illumina BovineHD BeadChip genotypes and genotype intensity data indicated a chromosomal deletion between 12.28 and 12.81 Mbp on BTA23. An independent set of Illumina Bovine50k BeadChip genotypes identified a recessive lethal haplotype that spanned the deleted region. Conclusions A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0215-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Goutam Sahana
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.
| | - Terhi Iso-Touru
- Natural Resources Institute Finland, 31600, Jokioinen, Finland
| | - Xiaoping Wu
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | | | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Mogens Sandø Lund
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Johanna Vilkki
- Natural Resources Institute Finland, 31600, Jokioinen, Finland
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
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24
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Iso-Touru T, Sahana G, Guldbrandtsen B, Lund MS, Vilkki J. Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants. BMC Genet 2016; 17:55. [PMID: 27006194 PMCID: PMC4804490 DOI: 10.1186/s12863-016-0363-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/17/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health traits offers a great opportunity to study production traits and identify causal variants behind them. In this study, we used whole genome sequence level data from 4280 progeny tested Nordic Red Cattle bulls to scan the genome for loci affecting milk, fat and protein yields. RESULTS Using a genome-wise significance threshold, regions on Bos taurus chromosomes 5, 14, 23, 25 and 26 were associated with fat yield. Regions on chromosomes 5, 14, 16, 19, 20 and 25 were associated with milk yield and chromosomes 5, 14 and 25 had regions associated with protein yield. Significantly associated variations were found in 227 genes for fat yield, 72 genes for milk yield and 30 genes for protein yield. Ingenuity Pathway Analysis was used to identify networks connecting these genes displaying significant hits. When compared to previously mapped genomic regions associated with fertility, significantly associated variations were found in 5 genes common for fat yield and fertility, thus linking these two traits via biological networks. CONCLUSION This is the first time when whole genome sequence data is utilized to study genomic regions affecting milk production in the Nordic Red Cattle population. Sequence level data offers the possibility to study quantitative traits in detail but still cannot unambiguously reveal which of the associated variations is causative. Linkage disequilibrium creates difficulties to pinpoint the causative genes and variations. One solution to overcome these difficulties is the identification of the functional gene networks and pathways to reveal important interacting genes as candidates for the observed effects. This information on target genomic regions may be exploited to improve genomic prediction.
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Affiliation(s)
- T Iso-Touru
- Animal Genomics, Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland.
| | - G Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - B Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - M S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - J Vilkki
- Animal Genomics, Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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25
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Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PLoS One 2016; 11:e0151220. [PMID: 26986467 PMCID: PMC4795602 DOI: 10.1371/journal.pone.0151220] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/23/2016] [Indexed: 11/19/2022] Open
Abstract
Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.
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Affiliation(s)
- Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | | | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS, Grenoble, France
| | - Daniel Fischer
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Ali R. Bayat
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | | | - Timothy J. Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - R. John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
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Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol 2015; 16:57. [PMID: 25854118 PMCID: PMC4373242 DOI: 10.1186/s13059-015-0622-4] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
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27
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Sironen A, Fischer D, Laiho A, Gyenesei A, Vilkki J. A recent L1 insertion withinSPEF2gene is associated with changes inPRLRexpression in sow reproductive organs. Anim Genet 2014; 45:500-7. [DOI: 10.1111/age.12153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2014] [Indexed: 12/01/2022]
Affiliation(s)
- A. Sironen
- Agrifood Research Finland; MTT; Biotechnology and Food Research, Genomics; FI-36100 Jokioinen Finland
| | - D. Fischer
- Agrifood Research Finland; MTT; Biotechnology and Food Research, Genomics; FI-36100 Jokioinen Finland
| | - A. Laiho
- The Finnish Microarray and Sequencing Centre; Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Tykistökatu 6 FI-20520 Turku Finland
| | - A. Gyenesei
- The Finnish Microarray and Sequencing Centre; Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Tykistökatu 6 FI-20520 Turku Finland
| | - J. Vilkki
- Agrifood Research Finland; MTT; Biotechnology and Food Research, Genomics; FI-36100 Jokioinen Finland
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28
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Kadri NK, Sahana G, Charlier C, Iso-Touru T, Guldbrandtsen B, Karim L, Nielsen US, Panitz F, Aamand GP, Schulman N, Georges M, Vilkki J, Lund MS, Druet T. A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock. PLoS Genet 2014; 10:e1004049. [PMID: 24391517 PMCID: PMC3879169 DOI: 10.1371/journal.pgen.1004049] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/04/2013] [Indexed: 12/02/2022] Open
Abstract
In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has concomitantly severely declined. It is generally assumed that this reduction is primarily due to the negative energy balance of high-producing cows at the peak of lactation. We herein describe the fine-mapping of a major fertility QTL in Nordic Red cattle, and identify a 660-kb deletion encompassing four genes as the causative variant. We show that the deletion is a recessive embryonically lethal mutation. This probably results from the loss of RNASEH2B, which is known to cause embryonic death in mice. Despite its dramatic effect on fertility, 13%, 23% and 32% of the animals carry the deletion in Danish, Swedish and Finnish Red Cattle, respectively. To explain this, we searched for favorable effects on other traits and found that the deletion has strong positive effects on milk yield. This study demonstrates that embryonic lethal mutations account for a non-negligible fraction of the decline in fertility of domestic cattle, and that associated positive effects on milk yield may account for part of the negative genetic correlation. Our study adds to the evidence that structural variants contribute to animal phenotypic variation, and that balancing selection might be more common in livestock species than previously appreciated. We report the identification of a large deletion encompassing four genes and the demonstration of its negative effect on fertility in Nordic Red dairy cattle. We show that this deletion is recessively lethal (homozygous embryos die) and therefore, when carrier cows are mated to carrier bulls, there is a high risk of embryonic mortality. As a result, chances of insemination failure are higher for such matings. Surprisingly, despite its negative effect, the deletion is frequent in Nordic Red cattle. We show that this high frequency may be a consequence of the fact that the deletion is associated with increased milk production and therefore selected for. Due to increased levels of inbreeding resulting from the widespread use of artificial insemination, such recessive lethal alleles may account for a non-negligible fraction of the reduction in fertility observed in cattle.
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Affiliation(s)
- Naveen Kumar Kadri
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- * E-mail: (GS); (TD)
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Terhi Iso-Touru
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Frank Panitz
- Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Nina Schulman
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Johanna Vilkki
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- * E-mail: (GS); (TD)
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Laine VN, Herczeg G, Shikano T, Vilkki J, Merilä J. QTL analysis of behavior in nine-spined sticklebacks (Pungitius pungitius). Behav Genet 2013; 44:77-88. [PMID: 24190427 DOI: 10.1007/s10519-013-9624-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 10/12/2013] [Indexed: 11/25/2022]
Abstract
The genetic architecture of behavioral traits is yet relatively poorly understood in most non-model organisms. Using an F2-intercross (n = 283 offspring) between behaviorally divergent nine-spined stickleback (Pungitius pungitius) populations, we tested for and explored the genetic basis of different behavioral traits with the aid of quantitative trait locus (QTL) analyses based on 226 microsatellite markers. The behaviors were analyzed both separately (viz. feeding activity, risk-taking and exploration) and combined in order to map composite behavioral type. Two significant QTL-explaining on average 6 % of the phenotypic variance-were detected for composite behavioral type on the experiment-wide level, located on linkage groups 3 and 8. In addition, several suggestive QTL located on six other linkage groups were detected on the chromosome-wide level. Apart from providing evidence for the genetic basis of behavioral variation, the results provide a good starting point for finer-scale analyses of genetic factors influencing behavioral variation in the nine-spined stickleback.
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Affiliation(s)
- Veronika N Laine
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland,
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Laine VN, Shikano T, Herczeg G, Vilkki J, Merilä J. Quantitative trait loci for growth and body size in the nine-spined sticklebackPungitius pungitiusL. Mol Ecol 2013; 22:5861-76. [DOI: 10.1111/mec.12526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/06/2013] [Accepted: 09/11/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Veronika N. Laine
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku 20014 Finland
| | - Takahito Shikano
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki PO Box 65 00014 Finland
| | - Gábor Herczeg
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki PO Box 65 00014 Finland
- Behavioural Ecology Group; Department of Systematic Zoology and Ecology; Eötvös Loránd University; Pázmány Péter sétány 1/C 1117 Budapest Hungary
| | | | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki PO Box 65 00014 Finland
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Fliegerova K, Tapio I, Bonin A, Mrazek J, Callegari ML, Bani P, Bayat A, Vilkki J, Kopečný J, Shingfield KJ, Boyer F, Coissac E, Taberlet P, Wallace RJ. Effect of DNA extraction and sample preservation method on rumen bacterial population. Anaerobe 2013; 29:80-4. [PMID: 24125910 DOI: 10.1016/j.anaerobe.2013.09.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/12/2013] [Accepted: 09/30/2013] [Indexed: 12/15/2022]
Abstract
The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P < 0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P < 0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile.
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Affiliation(s)
- Katerina Fliegerova
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic.
| | - Ilma Tapio
- MTT Agrifood Research Finland, Animal Genomics, FI-31600 Jokioinen, Finland
| | - Aurelie Bonin
- Laboratoire d'Ecologie Alpine, CNRS, 2233 rue de la Piscine, 38041 Grenoble, France
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | | | - Paolo Bani
- Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Alireza Bayat
- MTT Agrifood Research Finland, Animal Nutrition and Nutrigenomics, FI-31600 Jokioinen, Finland
| | - Johanna Vilkki
- MTT Agrifood Research Finland, Animal Genomics, FI-31600 Jokioinen, Finland
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Kevin J Shingfield
- MTT Agrifood Research Finland, Animal Nutrition and Nutrigenomics, FI-31600 Jokioinen, Finland
| | - Frederic Boyer
- Laboratoire d'Ecologie Alpine, CNRS, 2233 rue de la Piscine, 38041 Grenoble, France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine, CNRS, 2233 rue de la Piscine, 38041 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS, 2233 rue de la Piscine, 38041 Grenoble, France
| | - R John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, United Kingdom
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Honkatukia M, Tuiskula-Haavisto M, Arango J, Tabell J, Schmutz M, Preisinger R, Vilkki J. QTL mapping of egg albumen quality in egg layers. Genet Sel Evol 2013; 45:31. [PMID: 23953064 PMCID: PMC3847062 DOI: 10.1186/1297-9686-45-31] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 07/13/2013] [Indexed: 12/01/2022] Open
Abstract
Background A fresh, good quality egg has a firm and gelatinous albumen that anchors the yolk and restricts growth of microbiological pathogens. As the egg ages, the gel-like structure collapses, resulting in thin and runny albumen. Occasionally thin albumen is found in a fresh egg, giving the impression of a low quality product. A mapping population consisting of 1599 F2 hens from a cross between White Rock and Rhode Island Red lines was set up, to identify loci controlling albumen quality. The phenotype for albumen quality was evaluated by albumen height and in Haugh units (HU) measured on three consecutive eggs from each F2 hen at the age of 40 weeks. For the fine-mapping analysis, albumen height and HU were used simultaneously to eliminate contribution of the egg size to the phenotype. Results Linkage analysis in a small population of seven half-sib families (668 F2) with 162 microsatellite markers spread across 27 chromosomes revealed two genome-wide significant regions with additive effects for HU on chromosomes 7 and Z. In addition, two putative genome-wide quantitative trait loci (QTL) regions were identified on chromosomes 4 and 26. The QTL effects ranged from 2 to 4% of the phenotypic variance. The genome-wide significant QTL regions on chromosomes 7 and Z were selected for fine-mapping in the full set composed of 16 half-sib families. In addition, their existence was confirmed by an association analysis in an independent commercial Hy-Line pure line. Conclusions We identified four chicken genomic regions that affect albumen quality. Our results also suggest that genes that affect albumen quality act both directly and indirectly through several different mechanisms. For instance, the QTL regions on both fine-mapped chromosomes 7 and Z overlapped with a previously reported QTL for eggshell quality, indicating that eggshell membranes may play a role in albumen quality.
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Khatun M, Sørensen P, Jørgensen HBH, Sahana G, Sørensen LP, Lund MS, Ingvartsen KL, Buitenhuis AJ, Vilkki J, Bjerring M, Thomasen JR, Røntved CM. Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on the disease phenotypes of dairy cows with experimentally induced Escherichia coli mastitis. J Dairy Sci 2013; 96:1820-33. [PMID: 23357017 DOI: 10.3168/jds.2012-5528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 11/28/2012] [Indexed: 01/08/2023]
Abstract
Several quantitative trait loci (QTL) affecting mastitis incidence and mastitis-related traits such as somatic cell score exist in dairy cows. Previously, QTL haplotypes associated with susceptibility to Escherichia coli mastitis in Nordic Holstein-Friesian (HF) cows were identified on Bos taurus autosome 9. In the present study, we induced experimental E. coli mastitis in Danish HF cows to investigate the effect of 2 E. coli mastitis-associated QTL haplotypes on the cows' disease phenotypes and recovery in early lactation. Thirty-two cows were divided in 2 groups bearing haplotypes with either low (HL) or high (HH) susceptibility to E. coli. In addition, biopsies (liver and udder) were collected from half of the cows (n=16), resulting in a 2 × 2 factorial design, with haplotype being one factor (HL vs. HH) and biopsy being the other factor (biopsies vs. no biopsies). Each cow was inoculated with a low E. coli dose (20 to 40 cfu) in one front quarter at time 0 h. Liver biopsies were collected at -144, 12, 24, and 192 h; udder biopsies were collected at 24h and 192 h post-E. coli inoculation. The clinical parameters: feed intake, milk yield, body temperature, heart rate, respiration rate, rumen motility; and the paraclinical parameters: bacterial counts, somatic cell count (SCC), and milk amyloid A levels in milk; and white blood cell count, polymorphonuclear neutrophilic leukocyte (PMNL) count, and serum amyloid A levels in blood were recorded at different time points post-E. coli inoculation. Escherichia coli inoculation changed the clinical and paraclinical parameters in all cows except one that was not infected. Clinically, the HH group tended to have higher body temperature and heart rate than the HL group did. Paraclinically, the HL group had faster PMNL recruitment and SCC recovery than the HH group did. However, we also found interactions between the effects of haplotype and biopsy for body temperature, heart rate, and PMNL. In conclusion, when challenged with E. coli mastitis, HF cows with the specific Bos taurus autosome 9-located QTL haplotypes were associated with differences in leukocyte kinetics, with low-susceptibility cows having faster blood PMNL recruitment and SCC recovery and a tendency for a milder clinical response than the high-susceptibility cows did.
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Affiliation(s)
- M Khatun
- Department of Animal Science, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, PO Box 50, DK-8300 Tjele, Denmark
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Korhonen K, Julkunen H, Kananen K, Bredbacka P, Tiirikka T, Räty M, Vartia K, Kaimio I, Kontinen A, Halmekytö M, Vilkki J, Peippo J, Lindeberg H. The effect of ascorbic acid during biopsy and cryopreservation on viability of bovine embryos produced in vivo. Theriogenology 2012; 77:201-5. [DOI: 10.1016/j.theriogenology.2011.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 07/05/2011] [Accepted: 07/25/2011] [Indexed: 11/16/2022]
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Sironen A, Uimari P, Venhoranta H, Andersson M, Vilkki J. An exonic insertion within Tex14 gene causes spermatogenic arrest in pigs. BMC Genomics 2011; 12:591. [PMID: 22136159 PMCID: PMC3248578 DOI: 10.1186/1471-2164-12-591] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 12/02/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific events in sperm development. Sperm development is a complex process, where diploid spermatogonia develop into haploid, highly specialized spermatozoa. Correct expression and function of various genes and their protein products are required for production of fertile sperm. We have identified an infertility defect in Finnish Yorkshire boars caused by spermatogenic arrest. The aim of this study was to locate the disease associated region using genome wide screen with the PorcineSNP60 Beadchip and identify the causal mutation by candidate gene approach. RESULTS In the Finnish Yorkshire pig population the spermatogenic arrest (SA) defect appears to be of genetic origin and causes severe degeneration of germ cells and total absence of spermatozoa. Genome wide scan with the PorcineSNP60 Beadchip localized the SA defect to porcine chromosome 12 in a 2 Mbp region. Sequencing of a candidate gene Tex14 revealed a 51 bp insertion within exon 27, which caused differential splicing of the exon and created a premature translation stop codon. The expression of Tex14 was markedly down regulated in the testis of a SA affected boar compared to control boars and no protein product was identified by Western blotting. The SA insertion sequence was also found within intron 27 in all analyzed animals, thus the insertion appears to be a possible duplication event. CONCLUSION In this study we report the identification of a causal mutation for infertility caused by spermatogenic arrest at an early meiotic phase. Our results highlight the role of TEX14 specifically in spermatogenesis and the importance of specific genomic remodeling events as causes for inherited defects.
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Affiliation(s)
- Anu Sironen
- Agrifood Research Finland, MTT, Biotechnology and Food Research, Genomics, FI-36100 Jokioinen, Finland.
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Sironen A, Uimari P, Iso-Touru T, Vilkki J. L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire population. J Anim Breed Genet 2011; 129:92-7. [PMID: 22394230 DOI: 10.1111/j.1439-0388.2011.00977.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Immotile, short-tail sperm defect (ISTS) expanded in the Finnish Yorkshire population in the end of 1990s. The causal mutation for this defect is a recent L1 insertion within the SPEF2 gene in chromosome 16. Even though all homozygous boars are eliminated from the population because of infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established. To elucidate the associated effects of the ISTS defect on production traits, we have investigated the association of the L1 insertion and PRLR haplotype with reproduction traits in the Finnish Yorkshire population. Two data sets including 357 sows and 491 AI-boars were genotyped for the presence of the L1 insertion and analysed for association with reproduction traits. A Proc Mixed procedure (SAS Inc) and a software package for analysing multivariate mixed models (DMU) were used to study the effect of polymorphisms on reproduction traits. The L1-insertion within SPEF2 gene was associated with litter size in the first parity. The SPEF2 gene is located adjacent to a candidate gene for litter size in the pig, PRLR. Haplotypes within PRLR exon 10 were analysed in data set of 93 AI-boars for the association with reproduction traits. However, no associations were detected within the analysed data set indicating that PRLR sequence variants are not the causal cause for the identified effect on litter size.
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Affiliation(s)
- A Sironen
- Agrifood Research Finland, MTT, Biotechnology and Food Research, Genomics, Jokioinen, Finland.
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Honkatukia M, Tuiskula-Haavisto M, Ahola V, Uimari P, Schmutz M, Preisinger R, Cavero D, Vennerström P, Arango J, O'Sullivan N, Fulton J, Vilkki J. Mapping of QTL affecting incidence of blood and meat inclusions in egg layers. BMC Genet 2011; 12:55. [PMID: 21668941 PMCID: PMC3145579 DOI: 10.1186/1471-2156-12-55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 06/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. RESULTS Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL) affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. CONCLUSIONS There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s) in chickens.
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Affiliation(s)
- Mervi Honkatukia
- Biotechnology and Food Research, MTT, Jokioinen, 31600, Finland.
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Cano JM, Li MH, Laurila A, Vilkki J, Merilä J. First-generation linkage map for the common frog Rana temporaria reveals sex-linkage group. Heredity (Edinb) 2011; 107:530-6. [PMID: 21587305 DOI: 10.1038/hdy.2011.39] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The common frog (Rana temporaria) has become a model species in the fields of ecology and evolutionary biology. However, lack of genomic resources has been limiting utility of this species for detailed evolutionary genetic studies. Using a set of 107 informative microsatellite markers genotyped in a large full-sib family (800 F1 offspring), we created the first linkage map for this species. This partial map-distributed over 15 linkage groups-has a total length of 1698.8 cM. In line with the fact that males are the heterogametic sex in this species and a reduction of recombination is expected, we observed a lower recombination rate in the males (map length: 1371.5 cM) as compared with females (2089.8 cM). Furthermore, three loci previously documented to be sex-linked (that is, carrying male-specific alleles) in adults from the wild mapped to the same linkage group. The linkage map described in this study is one of the densest ones available for amphibians. The discovery of a sex linkage group in Rana temporaria, as well as other regions with strongly reduced male recombination rates, should help to uncover the genetic underpinnings of the sex-determination system in this species. As the number of linkage groups found (n=15) is quite close to the actual number of chromosomes (n=13), the map should provide a useful resource for further evolutionary, ecological and conservation genetic work in this and other closely related species.
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Affiliation(s)
- J M Cano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland.
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Sironen A, Uimari P, Nagy S, Paku S, Andersson M, Vilkki J. Knobbed acrosome defect is associated with a region containing the genes STK17b and HECW2 on porcine chromosome 15. BMC Genomics 2010; 11:699. [PMID: 21143916 PMCID: PMC3016419 DOI: 10.1186/1471-2164-11-699] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 12/09/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific events in sperm development. Correct condensation of the sperm head and development of the acrosome are required for fertile sperm. In the Finnish Yorkshire pig population a knobbed acrosome defect (KAD) has been reported which appears to be of genetic origin. In previous studies we have shown that a large number of affected spermatozoa have a cystic swelling anterior to the apical part of the acrosome. RESULTS Characterization of the knobbed acrosome affected sperm revealed that both the acrosomal granules and chromatin are affected. This type of KAD appears to be a previously unknown and serious form of the defect. A genome wide scan with PorcineSNP60 Genotyping BeadChip defined the KAD associated region within 0.7 Mbp on porcine chromosome 15. Two genes, STK17b and HECW2, located within this region were sequenced. The expression of these genes appeared comparable in KA-affected and control boars. The known function of HECW2 in acrosome development highlighted this gene as a good candidate responsible for the KAD. One nonsynonymous SNP was identified within the HECW2 gene. However, as this mutation was found in homozygous state in individuals with normal sperm, this is not likely to be the causal mutation. CONCLUSIONS In this study we identified two candidate genes for a severe defect affecting both the sperm acrosome and chromatin that causes infertility. One of these genes, HECW2, plays an important role in ubiquitination, a prerequisite for chromatin remodelling and acrosome formation, highlighting the involvement of this gene in the knobbed acrosome defect and male infertility.
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Affiliation(s)
- Anu Sironen
- Agrifood Research Finland, MTT, Biotechnology and Food Research, Genomics, FI-36100 Jokioinen, Finland.
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Tuiskula-Haavisto M, Honkatukia M, Preisinger R, Schmutz M, de Koning DJ, Wei WH, Vilkki J. Quantitative trait loci affecting eggshell traits in an F(2) population. Anim Genet 2010; 42:293-9. [PMID: 21054450 DOI: 10.1111/j.1365-2052.2010.02131.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Good eggshell quality is important for both table egg quality and chicken reproductive performance. Weak eggshells cause economic losses in all production steps. Poor eggshell quality also poses increased risk for Salmonella infections. Eggshell quality has been a difficult trait to improve by traditional breeding, as it can be measured only for females and it is difficult and expensive to measure. Breeding for improved shell quality may therefore benefit from the use of marker-assisted selection. In an effort to find markers linked to eggshell quality, we have used an F(2) population of 668 females to map quantitative trait loci (QTL) affecting eggshell traits (eggshell deformation, breaking force, weight). By using 160 microsatellite markers on 27 chromosomes, we found 11 genome-wide and 15 suggestive QTL for shell traits measured at different times during production. Loci affecting the deformation were found on chromosomes 1, 2, 6, 10, 14 and Z. Loci affecting the breaking force were detected on chromosomes 2, 3, 10, 12 and Z. Loci affecting the shell weight were detected on chromosomes 6, 12, 24 and Z. Each QTL explains between 1.5% and 4.6% of the phenotypic variance, adding up to 10-15% of total phenotypic variance explained for the different traits. No epistatic effects were observed between loci affecting eggshell traits. Because the effects for quality are mainly additive, these results provide a basis for further characterization of the loci to identify closely linked markers to be used in marker-assisted selection.
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Affiliation(s)
- M Tuiskula-Haavisto
- MTT Agrifood Research Finland, Biotechnology and Food Research, 31600 Jokioinen, Finland.
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Sironen AI, Uimari P, Serenius T, Mote B, Rothschild M, Vilkki J. Effect of polymorphisms in candidate genes on reproduction traits in Finnish pig populations1. J Anim Sci 2010; 88:821-7. [DOI: 10.2527/jas.2009-2426] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sironen A, Hansen J, Thomsen B, Andersson M, Vilkki J, Toppari J, Kotaja N. Expression of SPEF2 during mouse spermatogenesis and identification of IFT20 as an interacting protein. Biol Reprod 2009; 82:580-90. [PMID: 19889948 DOI: 10.1095/biolreprod.108.074971] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
SPEF2 is expressed in all ciliated cells and is essential for correct sperm tail development and male fertility. We have previously identified a mutation within the SPEF2 gene as the cause for infertility because of immotile and malformed sperm tails in pigs. This mutation in pigs alters the testis-specific long SPEF2 isoform and exclusively affects the sperm tail development. In infertile boars, axonemal and all accessory structures of the sperm tail are affected; thus, SPEF2 seems to participate in the organization of these structures. In the present study, we have investigated the expression of SPEF2 during mouse spermatogenesis. SPEF2 mRNA and protein products appear to be localized both in germ cells and in Sertoli cells. In differentiating germ cells, SPEF2 protein is localized in the Golgi complex, manchette, basal body, and midpiece of the sperm tail. In mature murine sperm, SPEF2 is present in the distal part of the sperm tail midpiece. Using yeast two-hybrid assay and coimmunoprecipitation experiments, we identified an interaction between SPEF2 and the intraflagellar transport protein IFT20 in the testis. Furthermore, these two proteins colocalize in differentiating male germ cells. These results support the crucial importance of SPEF2 in sperm differentiation and involvement of SPEF2 in structuring of the sperm tail.
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Affiliation(s)
- Anu Sironen
- Biotechnology and Food Research, Animal Genomics, MTT Agrifood Research Finland, Jokioinen, Finland
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43
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Iso-Touru T, Kantanen J, Li MH, Gizejewski Z, Vilkki J. Divergent evolution in the cytoplasmic domains of PRLR and GHR genes in Artiodactyla. BMC Evol Biol 2009; 9:172. [PMID: 19622175 PMCID: PMC2720954 DOI: 10.1186/1471-2148-9-172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 07/22/2009] [Indexed: 11/10/2022] Open
Abstract
Background Prolactin receptor (PRLR) and growth hormone receptor (GHR) belong to the large superfamily of class 1 cytokine receptors. Both of them have been identified as candidate genes affecting key quantitative traits, like growth and reproduction in livestock. We have previously studied the molecular anatomy of the cytoplasmic domain of GHR in different cattle breeds and artiodactyl species. In this study we have analysed the corresponding cytoplasmic signalling region of PRLR. Results We sequenced PRLR gene exon 10, coding for the major part of the cytoplasmic domain, from cattle, American bison, European bison, yak, sheep, pig and wild boar individuals. We found different patterns of variation in the two receptors within and between ruminants and pigs. Pigs and bison species have no variation within GHR exon 10, but show high haplotype diversity for the PRLR exon 10. In cattle, PRLR shows lower diversity than GHR. The Bovinae PRLR haplotype network fits better the known phylogenetic relationships between the species than that of the GHR, where differences within cattle breeds are larger than between the different species in the subfamily. By comparison with the wild boar haplotypes, a high number of subsequent nonsynonymous substitutions seem to have accumulated in the pig PRLR exon 10 after domestication. Conclusion Both genes affect a multitude of traits that have been targets of selection after domestication. The genes seem to have responded differently to different selection pressures imposed by human artificial selection. The results suggest possible effects of selective sweeps in GHR before domestication in the pig lineage or species divergence in the Bison lineage. The PRLR results may be explained by strong directional selection in pigs or functional switching.
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Affiliation(s)
- Terhi Iso-Touru
- Biotechnology and Food Research, MTT Agrifood Research Finland,Jokioinen, Finland.
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Kantanen J, Edwards CJ, Bradley DG, Viinalass H, Thessler S, Ivanova Z, Kiselyova T, Cinkulov M, Popov R, Stojanović S, Ammosov I, Vilkki J. Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus). Heredity (Edinb) 2009; 103:404-15. [PMID: 19603063 DOI: 10.1038/hdy.2009.68] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.
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Affiliation(s)
- J Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland.
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Hastings N, Fernandez A, Lund MS, Sahana G, Thomsen B, Schulman N, Williams JL, Andersson-Eklund L, Viinalass H, Vilkki J. The discovery of QTL for mastitis resistance in Nordic dairy cattle. Vet Immunol Immunopathol 2009. [DOI: 10.1016/j.vetimm.2008.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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46
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Kopp C, Sironen A, Ijäs R, Taponen J, Vilkki J, Sukura A, Andersson M. Infertile Boars with Knobbed and Immotile Short-tail Sperm Defects in the Finnish Yorkshire Breed. Reprod Domest Anim 2008; 43:690-5. [DOI: 10.1111/j.1439-0531.2007.00971.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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47
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Varvio SL, Iso-Touru T, Kantanen J, Viitala S, Tapio I, Mäki-Tanila A, Zerabruk M, Vilkki J. Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus. Proc Biol Sci 2008; 275:1525-34. [PMID: 18381258 DOI: 10.1098/rspb.2008.0181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Quantitative trait loci (QTL) studies have indicated growth hormone receptor (GHR) as a candidate gene affecting cattle milk yield and composition. In order to characterize genetic variation at GHR in cattle, we studied European and East African breeds with different histories of selection, and Bos grunniens, Ovis aries, Sus scrofa, Bison bison and Rangifer tarandus as references. We sequenced most of the cytoplasmic domain (900 bp of exon 10), 89 bp of exon 8, including the putative causative mutation for the QTL effect, and 390 bp of intron 8 for comparison. In the cytoplasmic domain, seven synonymous and seven non-synonymous single nucleotide polymorphisms (SNP) were identified in cattle. Three non-synonymous SNPs were found in sheep and one synonymous SNP in yak, while other studied species were monomorphic. Three major haplotypes were observed, one unique to African breeds, one unique to European breeds and one shared. Bison and yak haplotypes are derivatives of the European haplotype lineage. Most of the exon 10 non-synonymous cattle SNPs appear at phylogenetically highly conserved sites. The polymorphisms in exon 10 cluster around a ruminant-specific tyrosine residue, suggesting that this site may act as an additional signalling domain of GHR in ruminants. Alternative explanations for the persistent polymorphism include balancing selection, hitch-hiking, pleiotropic or sexually antagonistic fitness effects or relaxed functional constraints.
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Affiliation(s)
- S-L Varvio
- Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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48
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Sahana G, Lund MS, Andersson-Eklund L, Hastings N, Fernandez A, Iso-Touru T, Thomsen B, Viitala S, Sørensen P, Williams JL, Vilkki J. Fine-mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds. Anim Genet 2008; 39:354-62. [PMID: 18462482 PMCID: PMC2655356 DOI: 10.1111/j.1365-2052.2008.01729.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical mastitis to be mapped to a small interval (<1 cM) between the markers BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9.
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Affiliation(s)
- G Sahana
- Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Research Centre Foulum, DK-8830 Tjele, Denmark.
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Li MH, Tapio I, Vilkki J, Ivanova Z, Kiselyova T, Marzanov N, Cinkulov M, Stojanović S, Ammosov I, Popov R, Kantanen J. The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation. Mol Ecol 2007; 16:3839-53. [PMID: 17850550 DOI: 10.1111/j.1365-294x.2007.03437.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for approximately 90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of 'genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization.
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Affiliation(s)
- Meng-Hua Li
- Biotechnology and Food Research, MTT Agrifood Research Finland, FIN-31600 Jokioinen, Finland
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Lund M, Sahana G, Andersson-Eklund L, Hastings N, Fernandez A, Schulman N, Thomsen B, Viitala S, Williams J, Sabry A, Viinalass H, Vilkki J. Joint Analysis of Quantitative Trait Loci for Clinical Mastitis and Somatic Cell Score on Five Chromosomes in Three Nordic Dairy Cattle Breeds. J Dairy Sci 2007; 90:5282-90. [DOI: 10.3168/jds.2007-0177] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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