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Somenzi E, Partel E, Barbato M, Chero Osorio AM, Colli L, Franceschi N, Mantovani R, Pilla F, Komjanc M, Achilli A, Hauffe HC, Ajmone Marsan P. Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics. Genet Sel Evol 2024; 56:32. [PMID: 38698323 PMCID: PMC11064358 DOI: 10.1186/s12711-024-00900-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. RESULTS Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. CONCLUSIONS The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.
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Affiliation(s)
- Elisa Somenzi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Erika Partel
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Mario Barbato
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Veterinary Science, Università degli Studi di Messina, Messina, Italy
| | - Ana María Chero Osorio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Sulla Biodiversità e sul DNA Antico, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Niccolò Franceschi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Fabio Pilla
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Matteo Komjanc
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Paolo Ajmone Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
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Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
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Moriconi M, Pagliasso G, Fusi F, Vitale N, Guardone L, Vevey M, Dondo A, Razzuoli E, Bergagna S. Is the Introduction into a New Environment Stressful for Young Bulls? Vet Sci 2023; 10:545. [PMID: 37756067 PMCID: PMC10535078 DOI: 10.3390/vetsci10090545] [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: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Several events in an animal's life are considered stressful. Among them, the most studied and significant are transportation, weaning, and adaptation to climate change. Moreover, other events, such as the separation from the dam, moving from the original farm to another, management practices, such as regrouping with other animals, and new hierarchical conditions, represent routine conditions in the bovine's life, which can influence the animal's homeostasis. The purpose of this study is to evaluate the changes in blood parameters of 45 calves introduced into a new environment from their original farms. Blood samples were collected upon arrival at a genetic center (T1), 7 (T2), 30 (T3), and 120 (T4) days after arrival. Blood count, protein electrophoresis, clinical chemistry, and innate immunity parameters were performed on the samples. Significant alterations in some clinical chemistry parameters were related to liver function in the serum protein and the values of IL-6 and TNF-α; the main cytokines mediating the stress response emerged from the results. The evidence indicates the mild response to adaptation stress by calves raised in close association with people after their introduction into a new environment.
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Affiliation(s)
- Martina Moriconi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
| | - Giulia Pagliasso
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
- Azienda Sanitaria Locale di Ciriè, Chivasso, e Ivrea, Via Cavour 29, 10073 Ciriè, Italy
| | - Francesca Fusi
- Italian National Reference Centre for Animal Welfare (CReNBA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy
| | - Nicoletta Vitale
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
| | - Lisa Guardone
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
| | - Mario Vevey
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy
| | - Alessandro Dondo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
| | - Elisabetta Razzuoli
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
| | - Stefania Bergagna
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna148, 10154 Torino, Italy (L.G.)
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Pagliasso G, Moriconi M, Fusi F, Vitale N, Vevey M, Dondo A, Razzuoli E, Bergagna S. Evaluation of the Immune Response to Transport Stress in the Aosta Valley Breed. Vet Sci 2023; 10:vetsci10050351. [PMID: 37235434 DOI: 10.3390/vetsci10050351] [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: 03/08/2023] [Revised: 04/12/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Transportation is a recurring event in a farm animal's life, and it is considered one of the main stressors with possible negative repercussions for both the health and welfare of farm animals. The objective of the present study was to examine the effect of transportation on some blood variables of 45 young bulls moved from their original farms to a livestock collection centre. Transportation took no more than 8 h and was carried out between January and March 2021. Blood samples were taken before transportation (T0), upon arrival at the collection centre (T1), and 7 days after arrival (T2). Samples were processed for blood cell count, clinical chemistry analyses, serum protein electrophoresis, and the evaluation of innate immunity parameters. The results showed a typical stress leukogram with neutrophilia and changes in the neutrophil:lymphocyte ratio. No significant alterations were observed in either serum proteins or pro-inflammatory cytokines. Significant, albeit transient, alterations were observed in some clinical chemistry parameters after transportation, which could be accounted for by stressful conditions such as the transportation itself and handling and mixing with other animals. Our results indicated that the adopted transportation conditions only slightly affected the blood variables under study with no significant impact on animal welfare.
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Affiliation(s)
- Giulia Pagliasso
- Instituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy
- Azienda Sanitaria Locale di Ciriè, Chivasso e Ivrea, Via Cavour 29, 10073 Ciriè, Italy
| | - Martina Moriconi
- Instituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy
| | - Francesca Fusi
- Italian National Reference Centre for Animal Welfare (CReNBA), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy
| | - Nicoletta Vitale
- Instituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy
| | - Mario Vevey
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy
| | - Alessandro Dondo
- Instituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy
| | - Elisabetta Razzuoli
- Instituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy
| | - Stefania Bergagna
- Instituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy
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Romanzin A, Florit E, Degano L, Spanghero M. Feeding efficiency and behaviour of growing bulls from the main Italian dual-purpose breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2146006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Alberto Romanzin
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Eleonora Florit
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Lorenzo Degano
- National Association of Italian Simmental breeders, Udine, Italy
| | - Mauro Spanghero
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, University of Udine, Udine, Italy
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Genetic Differentiation among Livestock Breeds—Values for Fst. Animals (Basel) 2022; 12:ani12091115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The degree of relationship among livestock breeds can be quantified by the Fst statistic, which measures the extent of genetic differentiation between them. An Fst value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, Fst values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that Fst > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of Fst data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds. Abstract (1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Hauser M, Signer-Hasler H, Küttel L, Capitan A, Guldbrandtsen B, Hinrichs D, Flury C, Seefried FR, Drögemüller C. Identification of two new recessive MC1R alleles in red-coloured Evolèner cattle and other breeds. Anim Genet 2022; 53:427-435. [PMID: 35451516 PMCID: PMC9373916 DOI: 10.1111/age.13206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 11/27/2022]
Abstract
Sequence variations in the melanocortin-1 receptor (MC1R) gene are associated with melanism in different animal species. Six functionally relevant alleles have been described in cattle to date. In a hypothesis-free approach we performed a genome-wide allelic association study with black, red and wild-coloured cattle of three Alpine cattle breeds (Eringer, Evolèner and Valdostana), revealing a single significant association signal close to the MC1R gene. We searched for candidate causative variants by sequencing the entire coding sequence and identified two novel protein-changing variants. We propose designating the mutant alleles at MC1R:c.424C>T as ev1 and at MC1R:c.263G>A as ev2 . Both affect conserved amino acid residues in functionally important transmembrane domains (p.Arg142Cys and p.Ser88Asn). Both alleles segregate predominantly in the Swiss Evolèner breed. They occur in other European cattle breeds such as Abondance and Rotes Höhenvieh as well. We observed almost perfect association between the MC1R genotypes and the coat colour phenotype in a cohort of 513 black, red and wild-coloured cattle. Animals carrying two copies of MC1R loss-of-function alleles or that were compound heterozygous for e, ev1 , or ev2 have a red to dark red (chestnut-like red) coat colour. These findings expand the spectrum of causal MC1R variants causing recessive red in cattle.
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Affiliation(s)
- Miriam Hauser
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Luzia Küttel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Aurélien Capitan
- ALLICE, Paris, France.,INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dirk Hinrichs
- Department of Animal Breeding, Faculty of Organic Agricultural Sciences, University of Kassel, Witzenhausen, Germany
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Overlapping haplotype blocks indicate shared genomic regions between a composite beef cattle breed and its founder breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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