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Pauciullo A, Gaspa G, Zhang Y, Liu Q, Cosenza G. CSN1S1, CSN3 and LPL: Three Validated Gene Polymorphisms Useful for More Sustainable Dairy Production in the Mediterranean River Buffalo. Animals (Basel) 2024; 14:1414. [PMID: 38791632 PMCID: PMC11117199 DOI: 10.3390/ani14101414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The search for DNA polymorphisms useful for the genetic improvement of dairy farm animals has spanned more than 40 years, yielding relevant findings in cattle for milk traits, where the best combination of alleles for dairy processing has been found in casein genes and in DGAT1. Nowadays, similar results have not yet been reached in river buffaloes, despite the availability of advanced genomic technologies and accurate phenotype records. The aim of the present study was to investigate and validate the effect of four single nucleotide polymorphisms (SNP) in the CSN1S1, CSN3, SCD and LPL genes on seven milk traits in a larger buffalo population. These SNPs have previously been reported to be associated with, or affect, dairy traits in smaller populations often belonging to one farm. A total of 800 buffaloes were genotyped. The following traits were individually recorded, monthly, throughout each whole lactation period from 2010 to 2021: daily milk yield (dMY, kg), protein yield (dPY, kg) and fat yield (dFY, kg), fat and protein contents (dFP, % and dPP, %), somatic cell count (SCC, 103 cell/mL) and urea (mg/dL). A total of 15,742 individual milk test day records (2496 lactations) were available for 680 buffalo cows, with 3.6 ± 1.7 parities (from 1 to 13) and an average of 6.1 ± 1.2 test day records per lactation. Three out four SNPs in the CSN1S1, CSN3 and LPL genes were associated with at least one of analyzed traits. In particular, the CSN1S1 (AJ005430:c.578C>T) gave favorable associations with all yield traits (dMY, p = 0.022; dPY, p = 0.014; dFY, p = 0.029) and somatic cell score (SCS, p = 0.032). The CSN3 (HQ677596: c.536C>T) was positively associated with SCS (p = 0.005) and milk urea (p = 0.04). Favorable effects on daily milk yield (dMY, p = 0.028), fat (dFP, p = 0.027) and protein (dPP, p = 0.050) percentages were observed for the LPL. Conversely, the SCD did not show any association with milk traits. This is the first example of a confirmation study carried out in the Mediterranean river buffalo for genes of economic interest in the dairy field, and it represents a very important indication for the preselection of young bulls destined for breeding programs aimed at more sustainable dairy production.
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Affiliation(s)
- Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Giustino Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qingyou Liu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Gianfranco Cosenza
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
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2
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Du X, Sun Y, Fu T, Gao T, Zhang T. Research Progress and Applications of Bovine Genome in the Tribe Bovini. Genes (Basel) 2024; 15:509. [PMID: 38674443 PMCID: PMC11050176 DOI: 10.3390/genes15040509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.
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Affiliation(s)
- Xingjie Du
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yu Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tianliu Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Singh A, Malla WA, Kumar A, Jain A, Thakur MS, Khare V, Tiwari SP. Review: genetic background of milk fatty acid synthesis in bovines. Trop Anim Health Prod 2023; 55:328. [PMID: 37749432 DOI: 10.1007/s11250-023-03754-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
Milk fat composition is an important trait for the dairy industry as it directly influences the nutritional and technological properties of milk and other dairy products. The synthesis of milk fat is a complex process regulated by a network of genes. Thus, understanding the genetic variation and molecular mechanisms regulating milk fat synthesis will help to improve the nutritional quality of dairy products. In this review, we provide an overview of milk fat synthesis in bovines along with the candidate genes involved in the pathway. We also discuss de novo synthesis of fatty acids (ACSS, ACACA, FASN), uptake of FAs (FATP, FAT, LPL), intracellular activation and channelling of FAs (ACSL, FABP), elongation (EVOLV6), desaturation (SCD, FADS), formation of triglycerides (GPAM, AGPAT, LIPIN, DGAT), and milk lipid secretion (BTN1A1, XDH, PLIN2). The genetic variability of individual fatty acids will help to develop selection strategies for obtaining a healthier milk fat profile in bovines. Thus, this review will offer a potential understanding of the molecular mechanisms that regulate milk fat synthesis in bovines.
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Affiliation(s)
- Akansha Singh
- College of Veterinary Science and Animal Husbandry, NDVSU, Jabalpur, M.P, 482001, India.
| | - Waseem Akram Malla
- ICMR-National Institute of Malaria Research, Field Unit Guwahati, Assam, 781022, India
| | - Amit Kumar
- ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - Asit Jain
- College of Veterinary Science and Animal Husbandry, NDVSU, Jabalpur, M.P, 482001, India
| | - Mohan Singh Thakur
- College of Veterinary Science and Animal Husbandry, NDVSU, Jabalpur, M.P, 482001, India
| | - Vaishali Khare
- College of Veterinary Science and Animal Husbandry, NDVSU, Jabalpur, M.P, 482001, India
| | - Sita Prasad Tiwari
- College of Veterinary Science and Animal Husbandry, NDVSU, Jabalpur, M.P, 482001, India
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Cosenza G, Martin P, Garro G, Gallo D, Auzino B, Ciampolini R, Pauciullo A. A novel allelic donkey β-lactogobulin I protein isoform generated by a non-AUG translation initiation codon is associated with a nonsynonymous SNP. J Dairy Sci 2023; 106:4158-4170. [PMID: 37080792 DOI: 10.3168/jds.2022-22598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/17/2022] [Indexed: 04/22/2023]
Abstract
β-Lactoglobulin I (β-LG I) is one of the most important whey proteins in donkey milk. However, to our knowledge, there has been no study focusing on the full nucleotide sequences of this gene (BLG I). Current investigation of donkey BLG I gene is very limited with only 2 variants (A and B) characterized so far at the protein level. Recently, a new β-LG I variant, with a significantly higher mass (+1,915 Da) than known variants has been detected. In this study, we report the whole nucleotide sequence of the BLG I gene from 2 donkeys, whose milk samples are characterized by the β-LG I SDS-PAGE band with a normal electrophoretic mobility (18,514.25 Da, β-LG I B1 form) the first, and by the presence of a unique β-LG I band with a higher electrophoretic mobility (20,428.5 Da, β-LG I D form) the latter. A high genetic variability was found all over the 2 sequenced BLG I alleles. In particular, 16 polymorphic sites were found in introns, one in the 5' flanking region, 3 SNPs in the 5' untranslated region and one SNP in the coding region (g.458G > A) located at the 40th nucleotide of exon 2 and responsible for the AA substitutions p.Asp28 > Asn in the mature protein. Two SNPs (g.920-922CAC > TGT and g.1871G/A) were genotyped in 93 donkeys of 2 Italian breeds (60 Ragusana and 33 Amiatina, respectively) and the overall frequencies of g.920-922CAC and g.1871A were 0.3065 and 0.043, respectively. Only the rare allele g.1871A was observed to be associated with the slower migrating β-LG I. Considering this genetic diversity and those found in the database, it was possible to deduce at least 5 different alleles (BLG I A, B, B1, C, D) responsible for 4 potential β-LG I translations. Among these alleles, B1 and D are those characterized in the present research, with the D allele of real novel identification. Haplotype data analysis suggests an evolutionary pathway of donkey BLG I gene and a possible phylogenetic map is proposed. Analyses of mRNA secondary structure showed relevant changes in the structures, as consequence of the g.1871G > A polymorphism, that might be responsible for the recognition of an alternative initiation site providing an additional signal peptide. The extension of 19 AA sequence to the mature protein, corresponding to the canonical signal peptide with an additional alanine residue, is sufficient to provide the observed molecular weight of the slower migrating β-LG I encoded by the BLG I D allele.
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Affiliation(s)
- G Cosenza
- Department of Agricultural Sciences, University of Naples "Federico II," 80055 Portici (Na), Italy.
| | - P Martin
- Université Paris-Saclay, INRAE, MICALIS Institute, PAPPSO, 78350 Jouy-en-Josas, France
| | - G Garro
- Department of Agricultural Sciences, University of Naples "Federico II," 80055 Portici (Na), Italy
| | - D Gallo
- Department of Agricultural Sciences, University of Naples "Federico II," 80055 Portici (Na), Italy
| | - B Auzino
- Department of Veterinary Science, University of Pisa, 56100, Italy
| | - R Ciampolini
- Department of Veterinary Science, University of Pisa, 56100, Italy.
| | - A Pauciullo
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
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Deng TX, Ma XY, Lu XR, Duan AQ, Shokrollahi B, Shang JH. Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes. J Dairy Sci 2021; 105:1327-1337. [PMID: 34955275 DOI: 10.3168/jds.2021-21102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 12/11/2022]
Abstract
Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.
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Affiliation(s)
- T X Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| | - X Y Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X R Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - A Q Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Borhan Shokrollahi
- Department of Animal Science, Faculty of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran 5595-73919
| | - J H Shang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
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6
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Zhu R, Feng X, Wei Y, Guo D, Li J, Liu Q, Jiang J, Shi D, Huang J. lncSAMM50 Enhances Adipogenic Differentiation of Buffalo Adipocytes With No Effect on Its Host Gene. Front Genet 2021; 12:626158. [PMID: 33841496 PMCID: PMC8033173 DOI: 10.3389/fgene.2021.626158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022] Open
Abstract
Fat deposition is one of the most important traits that are mediated by a set of complex regulatory factors in meat animals. Several researches have revealed the significant role of long non-coding RNAs (lncRNAs) in fat deposition while the precise regulatory mechanism is still largely elusive. In this study, we investigated the lncRNA profiles of adipose and muscle tissues in buffalo by using the Illumina HiSeq 3000 platform. In total, 43,809 lncRNAs were finally identified based on the computer algorithm. A comparison analysis revealed 241 lncRNAs that are differentially expressed (DE) in adipose and muscle tissues. We focused on lncSAMM50, a DE lncRNA that has a high expression in adipose tissue. Sequence alignment showed that lncSAMM50 is transcribed from the antisense strand of the upstream region of sorting and assembly machinery component 50 homolog (SAMM50), a gene involved in the function of mitochondrion and is subsequently demonstrated to inhibit the adipogenic differentiation of 3T3-L1 adipocyte cells in this study. lncSAMM50 is highly expressed in adipose tissue and upregulated in the mature adipocytes and mainly exists in the nucleus. Gain-of-function experiments demonstrated that lncSAMM50 promotes the adipogenic differentiation by upregulating adipogenic markers but with no effect on its host gene SAMM50 in buffalo adipocytes. These results indicate that lncSAMM50 enhances fat deposition in buffalo and provide a new factor for the regulatory network of adipogenesis.
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Affiliation(s)
- Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jiaojiao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jianrong Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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Rehman SU, Hassan FU, Luo X, Li Z, Liu Q. Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. Animals (Basel) 2021; 11:904. [PMID: 33809937 PMCID: PMC8004149 DOI: 10.3390/ani11030904] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/17/2022] Open
Abstract
The buffalo was domesticated around 3000-6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.
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Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
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Chemello G, Biasato I, Gai F, Capucchio MT, Colombino E, Schiavone A, Gasco L, Pauciullo A. Effects of Tenebrio molitor larvae meal inclusion in rainbow trout feed: myogenesis-related gene expression and histomorphological features. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1945959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Giulia Chemello
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli studi di Torino, Torino, Italy
| | - Ilaria Biasato
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli studi di Torino, Torino, Italy
| | - Francesco Gai
- Istituto di scienze delle produzioni alimentari, Consiglio Nazionale delle Ricerche, Torino, Italy
| | - Maria Teresa Capucchio
- Istituto di scienze delle produzioni alimentari, Consiglio Nazionale delle Ricerche, Torino, Italy
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Torino, Italy
| | - Elena Colombino
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Torino, Italy
| | - Achille Schiavone
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Torino, Italy
| | - Laura Gasco
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli studi di Torino, Torino, Italy
| | - Alfredo Pauciullo
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli studi di Torino, Torino, Italy
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