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Giannuzzi D, Mota LFM, Pegolo S, Tagliapietra F, Schiavon S, Gallo L, Marsan PA, Trevisi E, Cecchinato A. Prediction of detailed blood metabolic profile using milk infrared spectra and machine learning methods in dairy cattle. J Dairy Sci 2023; 106:3321-3344. [PMID: 37028959 DOI: 10.3168/jds.2022-22454] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/14/2022] [Indexed: 04/09/2023]
Abstract
The adoption of preventive management decisions is crucial to dealing with metabolic impairments in dairy cattle. Various serum metabolites are known to be useful indicators of the health status of cows. In this study, we used milk Fourier-transform mid-infrared (FTIR) spectra and various machine learning (ML) algorithms to develop prediction equations for a panel of 29 blood metabolites, including those related to energy metabolism, liver function/hepatic damage, oxidative stress, inflammation/innate immunity, and minerals. For most traits, the data set comprised observations from 1,204 Holstein-Friesian dairy cows belonging to 5 herds. An exception was represented by β-hydroxybutyrate prediction, which contained observations from 2,701 multibreed cows pertaining to 33 herds. The best predictive model was developed using an automatic ML algorithm that tested various methods, including elastic net, distributed random forest, gradient boosting machine, artificial neural network, and stacking ensemble. These ML predictions were compared with partial least squares regression, the most commonly used method for FTIR prediction of blood traits. Performance of each model was evaluated using 2 cross-validation (CV) scenarios: 5-fold random (CVr) and herd-out (CVh). We also tested the best model's ability to classify values precisely in the 2 extreme tails, namely, the 25th (Q25) and 75th (Q75) percentiles (true-positive prediction scenario). Compared with partial least squares regression, ML algorithms achieved more accurate performance. Specifically, elastic net increased the R2 value from 5% to 75% for CVr and 2% to 139% for CVh, whereas the stacking ensemble increased the R2 value from 4% to 70% for CVr and 4% to 150% for CVh. Considering the best model, with the CVr scenario, good prediction accuracies were obtained for glucose (R2 = 0.81), urea (R2 = 0.73), albumin (R2 = 0.75), total reactive oxygen metabolites (R2 = 0.79), total thiol groups (R2 = 0.76), ceruloplasmin (R2 = 0.74), total proteins (R2 = 0.81), globulins (R2 = 0.87), and Na (R2 = 0.72). Good prediction accuracy in classifying extreme values was achieved for glucose (Q25 = 70.8%, Q75 = 69.9%), albumin (Q25 = 72.3%), total reactive oxygen metabolites (Q25 = 75.1%, Q75 = 74%), thiol groups (Q75 = 70.4%), total proteins (Q25 = 72.4%, Q75 = 77.2.%), globulins (Q25 = 74.8%, Q75 = 81.5%), and haptoglobin (Q75 = 74.4%). In conclusion, our study shows that FTIR spectra can be used to predict blood metabolites with relatively good accuracy, depending on trait, and are a promising tool for large-scale monitoring.
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Affiliation(s)
- Diana Giannuzzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy.
| | - Lucio Flavio Macedo Mota
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Franco Tagliapietra
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Luigi Gallo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Nutrition (DIANA) and the Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food and Environmental Sciences, Catholic University of the Sacred Heart, 29122, Piacenza, Italy; Nutrigenomics and Proteomics Research Center, Catholic University of the Sacred Heart, 29122, Piacenza, Italy
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition (DIANA) and the Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food and Environmental Sciences, Catholic University of the Sacred Heart, 29122, Piacenza, Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
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Dall’Asta M, Barbato M, Rocchetti G, Rossi F, Lucini L, Marsan PA, Colli L. Nutrigenomics: an underestimated contribution to the functional role of polyphenols. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100880] [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] [Indexed: 11/16/2022]
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Capra E, Toschi P, Del Corvo M, Lazzari B, Stella A, Williams JL, Loi P, Ajmone Marsan P. Short Communication: Maternal undernutrition during peri-conceptional period affects whole genome ovine muscle methylation in adult offspring. J Anim Sci 2022; 100:6586878. [PMID: 35580043 DOI: 10.1093/jas/skac180] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Experimental and epidemiological studies suggest that maternal nutritional status during early pregnancy, including the period around the time of conception, may induce long-lasting epigenetic changes in the offspring. However, this remains largely unexplored in livestock. Therefore, the objective of this study was to evaluate if modification of the maternal diet of sheep (CTR: control; UND: 50% undernutrition) during the peri-conceptional period (42 days in total: -14/+28 from mating), would impact CpG methylation in muscle tissue (Longissimus dorsi) of adult offspring (11.5 months old). Reduced Representation Bisulfite Sequencing (RRBS), identified 262 (Edge-R, FDR<0.05) and 686 (Logistic Regression, FDR <0.001) differentially methylated regions (DMRs) between the UND and CTR groups. Gene ontology (GO) analysis identified genes related to development, functions of the muscular system and steroid hormone receptor activity within the DMRs. The data reported here show that nutritional stress during early pregnancy leads to epigenetic modifications in the muscle of the resulting offspring, with possible implications for cardiac dysfunction, muscle physiology and meat production.
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Affiliation(s)
- Emanuele Capra
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Einstein 26900 Lodi, Italy
| | - Paola Toschi
- Department. of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Marcello Del Corvo
- Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Emilia Parmense 84, 29122, Piacenza, Italy
| | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Einstein 26900 Lodi, Italy
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Einstein 26900 Lodi, Italy
| | - John Lewis Williams
- Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Emilia Parmense 84, 29122, Piacenza, Italy.,Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Pasqualino Loi
- Laboratory of Experimental Embryology, Faculty of Veterinary Medicine, University of Teramo, Via R. Balzarini 1, 64100, Teramo, Italy
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Emilia Parmense 84, 29122, Piacenza, Italy
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Giannuzzi D, Toscano A, Pegolo S, Gallo L, Tagliapietra F, Mele M, Minuti A, Trevisi E, Ajmone Marsan P, Schiavon S, Cecchinato A. Associations between Milk Fatty Acid Profile and Body Condition Score, Ultrasound Hepatic Measurements and Blood Metabolites in Holstein Cows. Animals (Basel) 2022; 12:ani12091202. [PMID: 35565628 PMCID: PMC9104722 DOI: 10.3390/ani12091202] [Citation(s) in RCA: 2] [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: 03/18/2022] [Revised: 04/22/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023] Open
Abstract
Dairy cows have high incidences of metabolic disturbances, which often lead to disease, having a subsequent significant impact on productivity and reproductive performance. As the milk fatty acid (FA) profile represents a fingerprint of the cow’s nutritional and metabolic status, it could be a suitable indicator of metabolic status at the cow level. In this study, we obtained milk FA profile and a set of metabolic indicators (body condition score, ultrasound liver measurements, and 29 hematochemical parameters) from 297 Holstein–Friesian cows. First, we applied a multivariate factor analysis to detect latent structure among the milk FAs. We then explored the associations between these new synthetic variables and the morphometric, ultrasonographic and hematic indicators of immune and metabolic status. Significant associations were exhibited by the odd-chain FAs, which were inversely associated with β-hydroxybutyrate and ceruloplasmin, and positively associated with glucose, albumin, and γ-glutamyl transferase. Short-chain FAs were inversely related to predicted triacylglycerol liver content. Rumen biohydrogenation intermediates were associated with glucose, cholesterol, and albumin. These results offer new insights into the potential use of milk FAs as indicators of variations in energy and nutritional metabolism in early lactating dairy cows.
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Affiliation(s)
- Diana Giannuzzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
- Correspondence:
| | - Alessandro Toscano
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
| | - Luigi Gallo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
| | - Franco Tagliapietra
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
| | - Marcello Mele
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, 56124 Pisa, Italy;
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition (DIANA), The Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (A.M.); (E.T.); (P.A.M.)
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition (DIANA), The Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (A.M.); (E.T.); (P.A.M.)
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Nutrition (DIANA), The Romeo and Enrica Invernizzi Research Center for Sustainable Dairy Production (CREI), Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (A.M.); (E.T.); (P.A.M.)
- Nutrigenomics and Proteomics Research Center, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, 35020 Legnaro, Italy; (A.T.); (S.P.); (L.G.); (F.T.); (S.S.); (A.C.)
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Cortellari M, Bionda A, Negro A, Frattini S, Mastrangelo S, Somenzi E, Lasagna E, Sarti FM, Ciani E, Ciampolini R, Marletta D, Liotta L, Ajmone Marsan P, Pilla F, Colli L, Talenti A, Crepaldi P. Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems. Genet Sel Evol 2021; 53:92. [PMID: 34895134 PMCID: PMC8666052 DOI: 10.1186/s12711-021-00685-4] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00685-4.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Elisa Somenzi
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | | | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
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Giannuzzi D, Tessari R, Pegolo S, Fiore E, Gianesella M, Trevisi E, Ajmone Marsan P, Premi M, Piccioli-Cappelli F, Tagliapietra F, Gallo L, Schiavon S, Bittante G, Cecchinato A. Associations between ultrasound measurements and hematochemical parameters for the assessment of liver metabolic status in Holstein-Friesian cows. Sci Rep 2021; 11:16314. [PMID: 34381105 PMCID: PMC8357813 DOI: 10.1038/s41598-021-95538-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/24/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022] Open
Abstract
Metabolic disorders, including hepatic lipidosis and ketosis, severely affect animal health status and welfare with a large economic burden in dairy herds. The gold standard for diagnosing hepatic lipidosis is the liver biopsy, which is impractical and invasive for the screening at farm level. Ultrasound (US) imaging is a promising technique for identifying liver dysfunction, but standardized specifications in physiological conditions are needed. Herein, we described the features of four US measurements, namely the liver predicted triacylglycerol (pTAG) content, liver depth (LD), and portal vein area (PVA) and depth (PVD) and we investigated their associations with a set of hematochemical (HC) indicators in 342 clinically healthy Holstein Friesian dairy cows. Liver pTAG content was negatively associated with hematocrit and positively with globulin, whereas PVA was negatively associated with thiol group levels, and LD positively with ceruloplasmin. We found significant interactions between some HC parameters and parity: in particular, creatinine, thiol groups and globulin for PVA, and aspartate aminotransferase, paraoxonase and ceruloplasmin for PVD. This study offers new insights on variations in liver function occurring after calving and pave the way for the potential use of minimally invasive techniques for prompt detection of metabolic disorders in dairy herds.
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Affiliation(s)
- Diana Giannuzzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
| | - Rossella Tessari
- Department of Animal Medicine, Productions and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy.
| | - Enrico Fiore
- Department of Animal Medicine, Productions and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Matteo Gianesella
- Department of Animal Medicine, Productions and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy.,Nutrigenomics and Proteomics Research Center (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Michele Premi
- Department of Animal Science, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fiorenzo Piccioli-Cappelli
- Department of Animal Science, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Franco Tagliapietra
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
| | - Luigi Gallo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
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7
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Toschi P, Capra E, Anzalone DA, Lazzari B, Turri F, Pizzi F, Scapolo PA, Stella A, Williams JL, Ajmone Marsan P, Loi P. Maternal peri-conceptional undernourishment perturbs offspring sperm methylome. Reproduction 2021; 159:513-523. [PMID: 32103819 DOI: 10.1530/rep-19-0549] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/06/2020] [Indexed: 11/08/2022]
Abstract
The genotype of an organism is stable throughout its life; however, its epigenome is dynamic and can be altered in response to environmental factors, such as diet. Inheritance of acquired epigenetic modifications by the next generation occurs through the germline, although the precise mechanisms remain to be elucidated. Here, we used a sheep model to evaluate if modification of the maternal diet (CTR; control, UND: undernutrition; FA: undernutrition and folic acid supplementation) during the peri-conceptional period affects the genome-wide methylation status of the gametes of male offspring. Sperm DNA methylation, measured by Reduced Representation Bisulfite Sequencing (RRBS), identified Differentially Methylated Regions (DMR) in offspring that experienced in utero undernutrition, both in UND (244) and FA (240), compared with CTR. Gene ontology (GO) analysis identified DMRs in categories related to sperm function, therefore we investigated whether the fertilizing capacity of the semen from the three groups differed in an in vitro fertilization assay. Spermatozoa from the undernourished groups showed lower motility and sperm chromatin structure abnormalities, represented by a higher percentage of DNA fragmentation and an increased number of immature cells, compared with CTR. While good quality blastocysts were obtained from all three groups, the proportion of embryos reaching the blastocyst stage was reduced in the UND vs CTR, an effect partially rescued by the FA treatment. The data reported here show that nutritional stress during early pregnancy leads to epigenetic modifications in the semen of the resulting offspring, the effects of which in next generation remain to be elucidated.
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Affiliation(s)
- Paola Toschi
- Laboratory of Experimental Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Emanuele Capra
- Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | - Debora A Anzalone
- Laboratory of Experimental Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Barbara Lazzari
- Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | - Federica Turri
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | - Flavia Pizzi
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | - Pier A Scapolo
- Laboratory of Experimental Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Pasqualino Loi
- Laboratory of Experimental Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
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Persichilli C, Senczuk G, Pasqualino L, Anzalone DA, Negrini R, Ajmone Marsan P, Colli L, Pilla F, Mastrangelo S. Genome-wide diversity of Pagliarola sheep residual population and its conservation implication. Italian Journal of Animal Science 2021. [DOI: 10.1080/1828051x.2021.1970033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Christian Persichilli
- Dipartimento di Agraria, Ambientale e Scienze dell’alimentazione, University of Molise, Campobasso, Italy
| | - Gabriele Senczuk
- Dipartimento di Agraria, Ambientale e Scienze dell’alimentazione, University of Molise, Campobasso, Italy
| | - Loi Pasqualino
- Facoltà di Veterinaria, University of Teramo, Campobasso, Italy
| | | | - Riccardo Negrini
- Department of Animal Science Food and Nutrition, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paolo Ajmone Marsan
- Department of Animal Science Food and Nutrition, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Department of Animal Science Food and Nutrition, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento di Agraria, Ambientale e Scienze dell’alimentazione, University of Molise, Campobasso, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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9
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Palombo V, Pegolo S, Conte G, Cesarani A, Macciotta NPP, Stefanon B, Ajmone Marsan P, Mele M, Cecchinato A, D'Andrea M. Genomic prediction for latent variables related to milk fatty acid composition in Holstein, Simmental and Brown Swiss dairy cattle breeds. J Anim Breed Genet 2020; 138:389-402. [PMID: 33331079 DOI: 10.1111/jbg.12532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/17/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022]
Abstract
Genomic selection (GS) reports on milk fatty acid (FA) profiles have been published quite recently and are still few despite this trait represents the most important aspect of milk nutritional and sensory quality. Reasons for this can be found in the high costs of phenotype recording but also in issues related to its nature of complex trait constituted by multiple genetically correlated variables with low heritabilities. One possible strategy to deal with such constraint is represented by the use of dimension reduction methods. We analysed 40 individual FAs from Italian Brown Swiss, Holstein and Simmental milk through multivariate factor analysis (MFA) to study the genetics of milk FA-related latent variables (factors) and assess their potential use in breeding. A total of nine factors were obtained, and their genetic parameters were inferred under a Bayesian framework using two statistical approaches: the classical pedigree best linear unbiased prediction (ABLUP) and the single-step genomic BLUP (ssGBLUP). The resulting factorial solutions were able to represent groups of FAs with common origin and function and can be considered concise pathway-level phenotypes. The heritability (h2 ) values showed relevant variations across different factors in each breed (0.03 ≤ h2 ≤ 0.38). The accuracies of breeding values predicted were low to high, ranging from 0.13 to 0.72 and from 0.18 to 0.74 considering the pedigree and the genomic model, respectively. The gain in accuracy in genetic prediction due to the addition of genomic information was ~30% and ~5% in validation and training groups respectively, confirming the contribution of genomic information in yielding more accurate predictions compared to the traditional ABLUP methodology. Our results suggest that MFA in combination with GS can be a valuable tool in dairy cattle breeding and deserves to be further investigated for use in future breeding programs to improve cow's milk FA-related traits.
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Affiliation(s)
- Valentino Palombo
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Sara Pegolo
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente (DAFNAE), Università di Padova, Padova, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Pisa, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, Sezione Scienze Zootecniche, Università degli Studi di Sassari, Sassari, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | | | - Bruno Stefanon
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, Università di Udine, Udine, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, degli Alimenti e della Nutrizione - DIANA e Centro di Ricerca Nutrigenomica e Proteomica - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Pisa, Italy
| | - Alessio Cecchinato
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente (DAFNAE), Università di Padova, Padova, Italy
| | - Mariasilvia D'Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
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10
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Del Corvo M, Bongiorni S, Stefanon B, Sgorlon S, Valentini A, Ajmone Marsan P, Chillemi G. Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk. Genes (Basel) 2020; 11:genes11080850. [PMID: 32722461 PMCID: PMC7464205 DOI: 10.3390/genes11080850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.
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Affiliation(s)
- Marcello Del Corvo
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
- Istituto di Biologia e BiotecnologiaAgraria, Consiglio Nazionale delle Ricerche, 20133 Milan, Italy
- Correspondence:
| | - Silvia Bongiorni
- Department of Ecological and Biological sciences DEB, University of Tuscia, 01100 Viterbo, Italy;
| | - Bruno Stefanon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Sandy Sgorlon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
| | - Paolo Ajmone Marsan
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, 70126 Bari, Italy
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11
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Palombo V, Conte G, Mele M, Macciotta NPP, Stefanon B, Marsan PA, D'Andrea M. Use of multivariate factor analysis of detailed milk fatty acid profile to perform a genome-wide association study in Italian Simmental and Italian Holstein. J Appl Genet 2020; 61:451-463. [PMID: 32578141 DOI: 10.1007/s13353-020-00568-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/15/2019] [Revised: 01/20/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
Milk fatty acid (FA) profile is a clear example of complex and multiple correlated traits whose genetic basis is difficult to assess. Although genome-wide association (GWA) studies have been successful in the identification of significant genetic variants for complex traits, when correlated phenotypes are analysed separately, the outcomes are difficult to compare and interpret in a metabolic context. Here, we performed a multivariate factor analysis (MFA) on Italian Simmental and Italian Holstein milk fat profiles to extract latent unobserved factors able to explain correlation structure and common metabolic function among different FAs. Individual factor scores obtained by MFA were used to perform a single-SNP based GWA. In both breeds, MFA was able to extract ten latent factors with specific biological meaning, notably: de novo synthesis, desaturation activity and biohydrogenation. The GWA result confirmed the increased power of joint association analysis on multiple correlated traits and allowed us to identify major candidate genes with well-documented function consistent with the metabolic classification of factors obtained, such as DGAT1, FASN and SCD.
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Affiliation(s)
- Valentino Palombo
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, via De Sanctis snc, 86100, Campobasso, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Nicolò Pietro Paolo Macciotta
- Dipartimento di Agraria, Sezione Scienze Zootecniche, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Bruno Stefanon
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, Università di Udine, via delle Scienze, 208, 33100, Udine, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali degli Alimenti e della Nutrizione - DIANA e Centro di Ricerca Nutrigenomica e Proteomica - PRONUTRIGEN, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Mariasilvia D'Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, via De Sanctis snc, 86100, Campobasso, Italy.
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12
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Barbato M, Reichel MP, Passamonti M, Low WY, Colli L, Tearle R, Williams JL, Ajmone Marsan P. A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel. PLoS One 2020; 15:e0231162. [PMID: 32271816 PMCID: PMC7145104 DOI: 10.1371/journal.pone.0231162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/28/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.
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Affiliation(s)
- Mario Barbato
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
| | - Michael P. Reichel
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Matilde Passamonti
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Licia Colli
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rick Tearle
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - John L. Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
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13
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Summer A, Di Frangia F, Ajmone Marsan P, De Noni I, Malacarne M. Occurrence, biological properties and potential effects on human health of β-casomorphin 7: Current knowledge and concerns. Crit Rev Food Sci Nutr 2020; 60:3705-3723. [PMID: 32033519 DOI: 10.1080/10408398.2019.1707157] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genetic variant A1 of bovine β-casein (β-Cn) presents a His residue at a position 67 of the mature protein. This feature makes the Ile66-His67 bond more vulnerable to enzymatic cleavage, determining the release of the peptide β-Cn f(60-66), named β-casomorphin 7 (BCM7). BCM7 is an opioid-agonist for μ receptors, and it has been hypothesized to be involved in the development of different non-transmissible diseases in humans. In the last decade, studies have provided additional results on the potential health impact of β-Cn A1 and BCM7. These studies, here reviewed, highlighted a relation between the consumption of β-Cn A1 (and its derivative BCM7) and the increase of inflammatory response as well as discomfort at the gastrointestinal level. Conversely, the role of BCM7 and the effects of ingestion of β-Cn A1 on the onset or worsening of other non-transmissible diseases as caused or favored by still need proof of evidence. Overall, the reviewed literature demonstrates that the "β-Cn A1/BCM7 issue" remains an intriguing but not exhaustively explained topic in human nutrition. On this basis, policies in favor of breeding for β-Cn variants not releasing BCM7 and consumption of "A1-like" milk appear not yet sound for a healthier and safer nutrition.
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Affiliation(s)
- Andrea Summer
- Department of Veterinary Sciences, Università di Parma, Parma, Italy
| | | | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Nutrition (DIANA) and Nutrigenomics and Proteomics Research Center (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ivano De Noni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Massimo Malacarne
- Department of Veterinary Sciences, Università di Parma, Parma, Italy
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14
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Mastrangelo S, Ciani E, Ajmone Marsan P, Bagnato A, Battaglini L, Bozzi R, Carta A, Catillo G, Cassandro M, Casu S, Ciampolini R, Crepaldi P, D'Andrea M, Di Gerlando R, Fontanesi L, Longeri M, Macciotta NP, Mantovani R, Marletta D, Matassino D, Mele M, Pagnacco G, Pieramati C, Portolano B, Sarti FM, Tolone M, Pilla F. Conservation status and historical relatedness of Italian cattle breeds. Genet Sel Evol 2018; 50:35. [PMID: 29940848 PMCID: PMC6019226 DOI: 10.1186/s12711-018-0406-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 10/12/2017] [Accepted: 06/11/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
| | | | - Alessandro Bagnato
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095, Grugliasco, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, University of Firenze, 50144, Florence, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015, Monterotondo, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100, Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e tecnologie Agroalimentari, University of Bologna, 40127, Bologna, Italy
| | - Maria Longeri
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione, Ambiente, University of Catania, 95125, Catania, Italy
| | - Donato Matassino
- Divulgazione e Applicazione di Biotecniche Innovative, Consorzio per la Sperimentazione, 82100, Benevento, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, 56124, Pisa, Italy
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Camillo Pieramati
- Dipartimento di Medicina Veterinaria, University of Perugia, 06126, Perugia, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari, Ambientali, University of Perugia, 06121, Perugia, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, University of Molise, 86100, Campobasso, Italy.,Centro Risorse Bio-Culturali e Sviluppo Locale, University of Molise, 86100, Campobasso, Italy
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15
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Capra E, Lazzari B, Frattini S, Chessa S, Coizet B, Talenti A, Castiglioni B, Marsan PA, Crepaldi P, Pagnacco G, Williams JL, Stella A. Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus. BMC Genomics 2018; 19:417. [PMID: 29848285 PMCID: PMC5977473 DOI: 10.1186/s12864-018-4767-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 07/03/2017] [Accepted: 05/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Molecular regulation of the hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in the fine tuning of seasonal estrus in Capra hircus. Noncoding RNAs (ncRNAs) are emerging as key regulators in sexual development and mammalian reproduction. In order to identify ncRNAs and to assess their expression patterns, along the HPG axis, we sequenced ncRNA libraries from hypothalamus, pituitary and ovary of three goats. Results Among the medium length noncoding RNAs (mncRNAs) identified, small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs) were found to be more abundant in ovary and hypothalamus, respectively. The observed GC content was representative for different classes of ncRNAs, allowing the identification of a tRNA-derived RNA fragments (tRFs) subclass, which had a peak distribution around 32–38% GC content in the hypothalamus. Differences observed among organs confirmed the specificity of microRNA (miRNA) profiles for each organ system. Conclusions Data on ncRNAs in organs constituting the HPG axis will contribute to understanding their role in the physiological regulation of reproduction in goats. Electronic supplementary material The online version of this article (10.1186/s12864-018-4767-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.,Parco Tecnologico Padano, Lodi, Italy
| | - Stefano Frattini
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Stefania Chessa
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Beatrice Coizet
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Giulio Pagnacco
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.,Parco Tecnologico Padano, Lodi, Italy.,Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy. .,Parco Tecnologico Padano, Lodi, Italy.
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16
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Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, Sarti FM, Lasagna E, Panella F, Achilli A. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One 2018; 13:e0192567. [PMID: 29462170 PMCID: PMC5819780 DOI: 10.1371/journal.pone.0192567] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 10/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. METHODOLOGY The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. CONCLUSION The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.
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Affiliation(s)
- Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- * E-mail: (HL); (AA)
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Emine Sahin
- Korkuteli Vocational School, University of Akdeniz, Antalya, Turkey
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail: (HL); (AA)
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17
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Namous H, Peñagaricano F, Del Corvo M, Capra E, Thomas DL, Stella A, Williams JL, Marsan PA, Khatib H. Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy. BMC Genomics 2018; 19:123. [PMID: 29409445 PMCID: PMC5801776 DOI: 10.1186/s12864-018-4509-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets altered the transcriptome of fetal tissues. However, the mechanisms underlying transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle that generate the methyl group donor, SAM. Therefore, in the present study, we tested whether different maternal diets during pregnancy would alter the DNA methylation and gene expression patterns in fetal tissues. RESULTS Pregnant ewes were randomly divided into two groups which received either hay or corn diet from mid-gestation (day 67 ± 5) until day 131 ± 1 when fetuses were collected by necropsy. A total of 1516 fetal longissimus dorsi (LD) tissues were used for DNA methylation analysis and gene expression profiling. Whole genome DNA methylation using methyl-binding domain enrichment analysis revealed 60 differentially methylated regions (DMRs) between hay and corn fetuses with 39 DMRs more highly methylated in the hay fetuses vs. 21 DMRs more highly methylated in the corn fetuses. Three DMRs (LPAR3, PLIN5-PLIN4, and the differential methylation of a novel lincRNA) were validated using bisulfite sequencing. These DMRs were associated with differential gene expression. Additionally, significant DNA methylation differences were found at the single CpG level. Integrative methylome and transcriptome analysis revealed an association between gene expression and inter-/intragenic methylated regions. Furthermore, intragenic DMRs were found to be associated with expression of neighboring genes. CONCLUSIONS The findings of this study imply that maternal diet from mid- to late-gestation can shape the epigenome and the transcriptome of fetal tissues, and putatively affect phenotypes of the lambs.
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Affiliation(s)
- Hadjer Namous
- Department of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI 53706 USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida Genetics Institute, University of Florida, Florida, USA
| | - Marcello Del Corvo
- Institute of Zootechnics and PRONUTRIGEN Research Center, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - David L. Thomas
- Department of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI 53706 USA
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Institute of Zootechnics and PRONUTRIGEN Research Center, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI 53706 USA
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18
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Chillemi G, Bongiorni S, Gioiosa S, Flati T, Castrignanò T, Milanesi M, Ajmone Marsan P, Valentini A. Missense mutations of NCPAG gene affect calving ease in Piedmontese cattle: preliminary evidences. Italian Journal of Animal Science 2017. [DOI: 10.1080/1828051x.2017.1370362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Giovanni Chillemi
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
| | - Silvia Bongiorni
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Viterbo, Italy
| | - Silvia Gioiosa
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Tiziano Flati
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Tiziana Castrignanò
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
| | - Marco Milanesi
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza (PC), Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza (PC), Italy
| | - Alessio Valentini
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Viterbo, Italy
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19
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Periasamy K, Vahidi S, Silva P, Faruque M, Naqvi A, Basar M, Cao J, Zhao S, Thuy LT, Pichler R, Podesta MG, Shamsuddin M, Boettcher P, Garcia JF, Han JL, Marsan PA, Diallo A, Viljoen GJ. Mapping molecular diversity of indigenous goat genetic resources of Asia. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.035] [Citation(s) in RCA: 10] [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: 01/25/2023]
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20
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Pulina G, Francesconi AHD, Stefanon B, Sevi A, Calamari L, Lacetera N, Dell’Orto V, Pilla F, Ajmone Marsan P, Mele M, Rossi F, Bertoni G, Crovetto GM, Ronchi B. Sustainable ruminant production to help feed the planet. Italian Journal of Animal Science 2016. [DOI: 10.1080/1828051x.2016.1260500] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Giuseppe Pulina
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | | | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Agostino Sevi
- Dipartimento di Scienze Agrarie, degli Alimenti e dell’Ambiente, University of Foggia, Foggia, Italy
| | - Luigi Calamari
- Istituto di Zootecnica, University Cattolica del Sacro Cuore, Piacenza, Italy
| | - Nicola Lacetera
- Dipartimento di Scienze Agrarie e Forestali, University of Tuscia, Viterbo, Italy
| | - Vittorio Dell’Orto
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milano, Milan, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura Ambiente Alimenti, University of Molise, Campobasso, Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, University Cattolica del Sacro Cuore, Piacenza, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy
| | - Filippo Rossi
- Istituto di Scienze degli Alimenti e della Nutrizione, University Cattolica del Sacro Cuore, Piacenza, Italy
| | - Giuseppe Bertoni
- Istituto di Zootecnica, University Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Bruno Ronchi
- Dipartimento di Scienze Agrarie e Forestali, University of Tuscia, Viterbo, Italy
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21
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Sorbolini S, Gaspa G, Steri R, Dimauro C, Cellesi M, Stella A, Marras G, Marsan PA, Valentini A, Macciotta NPP. Use of canonical discriminant analysis to study signatures of selection in cattle. Genet Sel Evol 2016; 48:58. [PMID: 27521154 PMCID: PMC4983034 DOI: 10.1186/s12711-016-0236-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 01/26/2016] [Accepted: 08/01/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Cattle include a large number of breeds that are characterized by marked phenotypic differences and thus constitute a valuable model to study genome evolution in response to processes such as selection and domestication. Detection of "signatures of selection" is a useful approach to study the evolutionary pressures experienced throughout history. In the present study, signatures of selection were investigated in five cattle breeds farmed in Italy using a multivariate approach. METHODS A total of 4094 bulls from five breeds with different production aptitudes (two dairy breeds: Italian Holstein and Italian Brown Swiss; two beef breeds: Piemontese and Marchigiana; and one dual purpose breed: Italian Simmental) were genotyped using the Illumina BovineSNP50 v.1 beadchip. Canonical discriminant analysis was carried out on the matrix of single nucleotide polymorphisms (SNP) genotyping data, separately for each chromosome. Scores for each canonical variable were calculated and then plotted in the canonical space to quantify the distance between breeds. SNPs for which the correlation with the canonical variable was in the 99th percentile for a specific chromosome were considered to be significantly associated with that variable. Results were compared with those obtained using an FST-based approach. RESULTS Based on the results of the canonical discriminant analysis, a large number of signatures of selection were detected, among which several had strong signals in genomic regions that harbour genes known to have an impact on production and morphological bovine traits, including MSTN, LCT, GHR, SCD, NCAPG, KIT, and ASIP. Moreover, new putative candidate genes were identified, such as GCK, B3GALNT1, MGAT1, GALNTL1, PRNP, and PRND. Similar results were obtained with the FST-based approach. CONCLUSIONS The use of canonical discriminant analysis on 50 K SNP genotypes allowed the extraction of new variables that maximize the separation between breeds. This approach is quite straightforward, it can compare more than two groups simultaneously, and relative distances between breeds can be visualized. The genes that were highlighted in the canonical discriminant analysis were in concordance with those obtained using the FST index.
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Affiliation(s)
- Silvia Sorbolini
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Giustino Gaspa
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Roberto Steri
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via Salaria 31, 00015, Monterotondo, Italy
| | - Corrado Dimauro
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Massimo Cellesi
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | | | | | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Alessio Valentini
- Dipartimento per l'Innovazione dei Sistemi Biologici Agroalimentari e Forestali DIBAF, Università della Tuscia, Viterbo, Italy
| | - Nicolò Pietro Paolo Macciotta
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy.
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22
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Loi P, Toschi P, Zacchini F, Ptak G, Scapolo PA, Capra E, Stella A, Marsan PA, Williams JL. Synergies between assisted reproduction technologies and functional genomics. Genet Sel Evol 2016; 48:53. [PMID: 27481215 PMCID: PMC4968447 DOI: 10.1186/s12711-016-0231-z] [Citation(s) in RCA: 10] [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] [Received: 02/29/2016] [Accepted: 07/15/2016] [Indexed: 12/17/2022] Open
Abstract
This review, is a synopsis of advanced reproductive technologies in farm animals, including the discussion of their limiting factors as revealed by the study of offspring derived from embryos produced in vitro and through cloning. These studies show that the problems of epigenetic mis-programming, which were reported in the initial stages of assisted reproduction, still persist. The importance of whole-genome analyses, including the methylome and transcriptome, in improving embryo biotechnologies in farm animals, are discussed. Genome editing approaches for the improvement of economically-relevant traits in farm animals are also described. Efficient farm animal embryo biotechnologies, including cloning and the most recent technologies such as genome editing, will effectively complement the latest strategies to accelerate genetic improvement of farm animals.
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Affiliation(s)
- Pasqualino Loi
- Laboratory of Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy.
| | - Paola Toschi
- Laboratory of Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Federica Zacchini
- Laboratory of Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy.,Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postepu 36A, Jastrzębiec, 05-552, Magdalenka, Poland
| | - Grazyna Ptak
- Laboratory of Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy.,Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postepu 36A, Jastrzębiec, 05-552, Magdalenka, Poland.,National Research Institute of Animal Production 1, Krakowska Street, 32-083, Balice n/Kraków, Poland
| | - Pier A Scapolo
- Laboratory of Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Emanuele Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council, 26900, Lodi, Italy
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council, 26900, Lodi, Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Proteomic and Nutrigenomic Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
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23
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Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SMF, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P, Achilli A. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015; 16:1115. [PMID: 26714643 PMCID: PMC4696231 DOI: 10.1186/s12864-015-2342-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [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: 06/30/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023] Open
Abstract
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Pellecchia
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Marcin Rzepus
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Wahid Zamani
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. .,Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran.
| | - Saeid Naderi
- Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran.
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. .,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK.
| | | | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.
| | - Ettore Randi
- Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. .,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark.
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Hamid Reza Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran.
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece.
| | - Frédéric Boyer
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - François Pompanon
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
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Chessa S, Nicolazzi EL, Nicoloso L, Negrini R, Marino R, Vicario D, Ajmone Marsan P, Valentini A, Stefanon B. Analysis of candidate SNPs affecting milk and functional traits in the dual-purpose Italian Simmental cattle. Livest Sci 2015. [DOI: 10.1016/j.livsci.2014.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic "footprints" in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.
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Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Saif Agha
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland Department of Animal Science, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Licia Colli
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - James W Kijas
- CSIRO Livestock Industries, St Lucia, Brisbane, Qld, Australia
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Mancini G, Gargani M, Chillemi G, Nicolazzi EL, Marsan PA, Valentini A, Pariset L. Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel. Mol Biol Rep 2014; 41:957-65. [PMID: 24442315 PMCID: PMC3929051 DOI: 10.1007/s11033-013-2940-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 11/05/2012] [Accepted: 12/20/2013] [Indexed: 01/16/2023]
Abstract
In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.
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Affiliation(s)
- Giordano Mancini
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, 01100, Viterbo, Italy
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Ajmone Marsan P, Cocconcelli PS, Masoero F, Miggiano G, Morelli L, Moro D, Rossi F, Sckokai P, Trevisi E. Food for Healthy Living and Active Ageing. Stud Health Technol Inform 2014; 203:32-43. [PMID: 26630510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The link between diet and health has been recognized since the Grecian period; as Hippocrates said, "Let food be your medicine and medicine be your food". Although the primary goals of diet are meeting nutritional requirements and providing energy, there is increasing awareness that a correct and balanced diet may prevent the insurgence of diet-related pathologies and/or improve well-being and life expectancy, also reflecting on the ageing process. Research on the interaction among nutrients, gut microbiota and host metabolism is presently unravelling the molecular mechanisms underlying the positive and negative effects of traditional diets on health and ageing, providing useful information for the design of innovative foods targeting specific needs and segments of the population. The food supply chain plays a key role in ensuring quality and safety through both comprehensive quality management and inspection systems and a focused innovation process mainly devoted to the creation of functional foods. However, innovation and scientific development pose a problem of information asymmetry towards final consumers; thus, regulatory aspects and private and public communication strategies must be efficiently developed.
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Affiliation(s)
- Paolo Ajmone Marsan
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Pier Sandro Cocconcelli
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Francesco Masoero
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Giacinto Miggiano
- Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore
| | - Lorenzo Morelli
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Daniele Moro
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Filippo Rossi
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Paolo Sckokai
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Erminio Trevisi
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
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28
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Minuti A, Patrone V, Giuberti G, Spigno G, Pietri A, Battilani P, Ajmone Marsan P. Nutrition and Ageing. Stud Health Technol Inform 2014; 203:112-121. [PMID: 26630518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The world elderly population is rapidly increasing. This demographic change represents a new challenge for the society and demands for a multisectorial intervention to promote a long, healthy, and active life span. Between the factors that contribute in fostering a long healthy life, the nutritional regime plays a central role and is recognized as a major factor in the onset of chronic diseases. A better understanding of the interaction between nutrition and ageing is essential to unravel the mechanisms responsible for these positive/negative effects and to identify diet components promoting the quality of life in the old age and to contribute to the prevention of late-life disabilities. At Università Cattolica del Sacro Cuore, the research activity in food science is focusing on four main objectives: food quality, food safety, functional foods and diet balancing. These objectives are the target of multidisciplinary ongoing and future research activities for a better understanding of the link between diet and ageing. Briefly, the different activities are addressed to the study of the following subjects: the most relevant factors affecting food choices and habits of old aged persons; the effects of long term low dose supplementation of conjugated linoleic acid in mouse; the use of low glycemic index and high resistant starch foods to prevent diabetes and obesity; the adjuvant effect of food bacteria for vaccination; the role of food ingredients in disease; the immunosuppression effect of mycotoxins, and its relevance in ageing people; the production of sustainable and natural antioxidant ingredients to encourage a healthy diet. Our research projects emphasize an holistic and integrated approach that, by bringing together complementary research groups, can combine the collective expertise and thus provide a comprehensive assessment of the role of nutrition in healthy ageing people.
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Affiliation(s)
- Andrea Minuti
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Vania Patrone
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Gianluca Giuberti
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Giorgia Spigno
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Amedeo Pietri
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Paola Battilani
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
| | - Paolo Ajmone Marsan
- Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore
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29
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Mariotti M, Valentini A, Marsan PA, Pariset L. Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation. ACTA ACUST UNITED AC 2013; 24:577-83. [DOI: 10.3109/19401736.2013.770493] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Taberlet P, Zimmermann NE, Englisch T, Tribsch A, Holderegger R, Alvarez N, Niklfeld H, Coldea G, Mirek Z, Moilanen A, Ahlmer W, Marsan PA, Bona E, Bovio M, Choler P, Cieślak E, Colli L, Cristea V, Dalmas J, Frajman B, Garraud L, Gaudeul M, Gielly L, Gutermann W, Jogan N, Kagalo AA, Korbecka G, Küpfer P, Lequette B, Letz DR, Manel S, Mansion G, Marhold K, Martini F, Negrini R, Niño F, Paun O, Pellecchia M, Perico G, Piękoś‐Mirkowa H, Prosser F, Puşcaş M, Ronikier M, Scheuerer M, Schneeweiss GM, Schönswetter P, Schratt‐Ehrendorfer L, Schüpfer F, Selvaggi A, Steinmann K, Thiel‐Egenter C, Loo M, Winkler M, Wohlgemuth T, Wraber T, Gugerli F. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecol Lett 2012; 15:1439-48. [DOI: 10.1111/ele.12004] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Taberlet
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Niklaus E. Zimmermann
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Thorsten Englisch
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Andreas Tribsch
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Nadir Alvarez
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Harald Niklfeld
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Gheorghe Coldea
- Institute of Biological Research Str. Republicii nr. 48 400015 Cluj‐Napoca Romania
| | - Zbigniew Mirek
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Atte Moilanen
- Department of Biosciences P.O. Box 65 (Biocenter III) FI‐00014 University of Helsinki Finland
| | - Wolfgang Ahlmer
- University of Regensburg Institute of Botany 93040 Regensburg Germany
| | - Paolo Ajmone Marsan
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Enzo Bona
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Maurizio Bovio
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Philippe Choler
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Elżbieta Cieślak
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Licia Colli
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | | | - Jean‐Pierre Dalmas
- Conservatoire Botanique National Alpin ‐ CBNA Domaine de Charance 05000 Gap France
| | - Božo Frajman
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Luc Garraud
- Conservatoire Botanique National Alpin ‐ CBNA Domaine de Charance 05000 Gap France
| | - Myriam Gaudeul
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Ludovic Gielly
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Walter Gutermann
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Nejc Jogan
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Alexander A. Kagalo
- Institute of Ecology of the Carpathians N.A.S. of Ukraine 4 Kozelnitska str. 79026 Lviv Ukraine
| | - Grażyna Korbecka
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Philippe Küpfer
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Benoît Lequette
- Parc national du Mercantour 23 rue d'Italie, BP 1316 06006 Nice Cedex 1 France
| | - Dominik Roman Letz
- Institute of Botany of Slovak Academy of Sciences Department of Vascular Plant Taxonomy Dúbravská cesta 9 845 23 Bratislava Slovakia
| | - Stéphanie Manel
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Guilhem Mansion
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Karol Marhold
- Institute of Botany of Slovak Academy of Sciences Department of Vascular Plant Taxonomy Dúbravská cesta 9 845 23 Bratislava Slovakia
| | - Fabrizio Martini
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Riccardo Negrini
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Fernando Niño
- Medias‐France/IRD CNES ‐ BPi 2102, 18, Av. Edouard Belin F‐31401 Toulouse Cedex 9 France
| | - Ovidiu Paun
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Marco Pellecchia
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Giovanni Perico
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | | | | | - Mihai Puşcaş
- Babes‐Bolyai University 400015 Cluj‐Napoca Romania
| | - Michał Ronikier
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Martin Scheuerer
- University of Regensburg Institute of Botany 93040 Regensburg Germany
| | | | - Peter Schönswetter
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | | | - Fanny Schüpfer
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Alberto Selvaggi
- Istituto per le Piante da Legno e l'Ambiente c.so Casale, 476 10132 Torino Italy
| | - Katharina Steinmann
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Conny Thiel‐Egenter
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Marcela Loo
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Manuela Winkler
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Thomas Wohlgemuth
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Tone Wraber
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
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Pariset L, Mariotti M, Gargani M, Joost S, Negrini R, Perez T, Bruford M, Ajmone Marsan P, Valentini A. Genetic diversity of sheep breeds from Albania, Greece, and Italy assessed by mitochondrial DNA and nuclear polymorphisms (SNPs). ScientificWorldJournal 2011; 11:1641-59. [PMID: 22125424 PMCID: PMC3201683 DOI: 10.1100/2011/186342] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/30/2011] [Accepted: 08/08/2011] [Indexed: 11/17/2022] Open
Abstract
We employed mtDNA and nuclear SNPs to investigate the genetic diversity of sheep breeds of three countries of the Mediterranean basin: Albania, Greece, and Italy. In total, 154 unique mtDNA haplotypes were detected by means of D-loop sequence analysis. The major nucleotide diversity was observed in Albania. We identified haplogroups, A, B, and C in Albanian and Greek samples, while Italian individuals clustered in groups A and B. In general, the data show a pattern reflecting old migrations that occurred in postneolithic and historical times. PCA analysis on SNP data differentiated breeds with good correspondence to geographical locations. This could reflect geographical isolation, selection operated by local sheep farmers, and different flock management and breed admixture that occurred in the last centuries.
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Affiliation(s)
- Lorraine Pariset
- Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, 01100 Viterbo, Italy.
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Pariset L, Joost S, Marsan PA, Valentini A. Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genet 2009; 10:7. [PMID: 19228375 PMCID: PMC2663570 DOI: 10.1186/1471-2156-10-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [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: 08/10/2008] [Accepted: 02/19/2009] [Indexed: 01/18/2023] Open
Abstract
Background In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring. Results The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the identification of the same three loci involved in milk and meat quality data by using the two methods, while the FST based method identified 3 more loci as under selection sweep in the breeds examined. Conclusion Data appear congruent by using the two methods for FST values exceeding the 99% confidence limits. The methods of FST and SAM can independently detect signatures of selection and therefore can reduce the probability of finding false positives if employed together. The outlier loci identified in this study could indicate adaptive variation in the analysed species, characterized by a large range of climatic conditions in the rearing areas and by a history of intense trade, that implies plasticity in adapting to new environments.
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Affiliation(s)
- Lorraine Pariset
- Dipartimento di Produzioni Animali, Università della Tuscia, Viterbo, Italy.
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Marchitelli C, Savarese MC, Crisà A, Nardone A, Marsan PA, Valentini A. Double muscling in Marchigiana beef breed is caused by a stop codon in the third exon of myostatin gene. Mamm Genome 2003; 14:392-5. [PMID: 12879361 DOI: 10.1007/s00335-002-2176-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [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: 02/15/2002] [Accepted: 02/06/2003] [Indexed: 10/26/2022]
Abstract
Double muscling is a partially recessive trait present in some beef breeds. It shows a high frequency in some breeds, while in others the frequency is low, and double-muscled individuals are rare. The double muscling is caused by an allelic series of mutations that cause a loss of function of the myostatin gene ( GDF8). We describe here a new mutation in the myostatin gene in Marchigiana breed, a typical beef breed of Central Italy, in which rare double-muscling individuals have been described. A PCR product of the third exon was sequenced in subjects phenotypically showing double muscling, and a G > T transversion was discovered that introduces a premature stop codon. The variant found adds to the large series of mutations present in cattle, and particularly to the only two causative of double muscling in the third exon. A PCR-RFLP test is described for the rapid and effective identification of both heterozygous and homozygous subjects. It was applied to a larger survey carried on the same and also in two other beef breeds, Chianina and Romagnola. Further individuals carrying the new variant were found in Marchigiana, but none in the other breeds. The results may be important for a better comprehension of the role of myostatin in muscular development, for commercial use and for the inference of phylogeny of this gene.
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Affiliation(s)
- Cinzia Marchitelli
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy.
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