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Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle
Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, Mekki Boussaha, Fabio Pilla, Baldassare Portolano, Salvatore Mastrangelo To cite this version: Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, et al.. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Frontiers in Genetics, Frontiers, 2021, 10.3389/fgene.2021.675569. hal-03210766 HAL Id: hal-03210766 https://hal.inrae.fr/hal-03210766 Submitted on 28 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License ORIGINAL RESEARCH published: 28 April 2021 doi: 10.3389/fgene.2021.675569 Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa 1, Gabriele Senczuk 2, Elena Ciani 3, Roberta -
Tesi Finale Dottorato
INDICE GENERALE 1. INTRODUZIONE............................................................................................................................3 1.1. La tracciabilità dei prodotti di origine animale: alcuni elementi.........................................3 1.2. Elementi di genetica molecolare..........................................................................................4 1.2.1. I marcatori genetici.......................................................................................................4 1.2.2. Lo stato di avanzamento nello studio del genoma degli animali di interesse zootecnico...............................................................................................................................6 1.3. Tracciabilità dei prodotti di origine animale e genetica molecolare....................................8 1.4. I prodotti “monorazza”.......................................................................................................10 1.5. Genetica e biochimica del colore del mantello: alcuni elementi........................................16 1.6. Genetica molecolare e colore del mantello........................................................................19 1.6.1. Il gene MC1R nella specie bovina.............................................................................21 1.6.2. Il gene MC1R nella specie suina................................................................................26 1.6.3. Il gene KIT nella specie bovina..................................................................................26 -
Meta-Analysis of Mitochondrial DNA Reveals Several Population
Table S1. Haplogroup distributions represented in Figure 1. N: number of sequences; J: banteng, Bali cattle (Bos javanicus ); G: yak (Bos grunniens ). Other haplogroup codes are as defined previously [1,2], but T combines T, T1’2’3’ and T5 [2] while the T1 count does not include T1a1c1 haplotypes. T1 corresponds to T1a defined by [2] (16050T, 16133C), but 16050C–16133C sequences in populations with a high T1 and a low T frequency were scored as T1 with a 16050C back mutation. Frequencies of I are only given if I1 and I2 have not been differentiated. Average haplogroup percentages were based on balanced representations of breeds. Country, Region Percentages per Haplogroup N Reference Breed(s) T T1 T1c1a1 T2 T3 T4 I1 I2 I J G Europe Russia 58 3.4 96.6 [3] Yaroslavl Istoben Kholmogory Pechora type Red Gorbatov Suksun Yurino Ukrain 18 16.7 72.2 11.1 [3] Ukrainian Whiteheaded Ukrainian Grey Estonia, Byelorussia 12 100 [3] Estonian native Byelorussia Red Finland 31 3.2 96.8 [3] Eastern Finncattle Northern Finncattle Western Finncattle Sweden 38 100.0 [3] Bohus Poll Fjall cattle Ringamala Cattle Swedish Mountain Cattle Swedish Red Polled Swedish Red-and-White Vane Cattle Norway 44 2.3 0.0 0.0 0.0 97.7 [1,4] Blacksided Trondheim Norwegian Telemark Westland Fjord Westland Red Polled Table S1. Cont. Country, Region Percentages per Haplogroup N Reference Breed(s) T T1 T1c1a1 T2 T3 T4 I1 I2 I J G Iceland 12 100.0 [1] Icelandic Denmark 32 100.0 [3] Danish Red (old type) Jutland breed Britain 108 4.2 1.2 94.6 [1,5,6] Angus Galloway Highland Kerry Hereford Jersey White Park Lowland Black-Pied 25 12.0 88.0 [1,4] Holstein-Friesian German Black-Pied C Europe 141 3.5 4.3 92.2 [1,4,7] Simmental Evolene Raetian Grey Swiss Brown Valdostana Pezzata Rossa Tarina Bruna Grey Alpine France 98 1.4 6.6 92.0 [1,4,8] Charolais Limousin Blonde d’Aquitaine Gascon 82.57 Northern Spain 25 4 13.4 [8,9] 1 Albera Alistana Asturia Montana Monchina Pirenaica Pallaresa Rubia Gallega Southern Spain 638 0.1 10.9 3.1 1.9 84.0 [5,8–11] Avileña Berrenda colorado Berrenda negro Cardena Andaluzia Table S1. -
1 Genetic and Productive Characterization of The
ISSN 1330-7142 UDK = 636.2:636.082 GENETIC AND PRODUCTIVE CHARACTERIZATION OF THE BURLINA CATTLE BREED Chiara Dalvit, R. Dal Zotto, M. De Marchi, M. Cassandro Original scientific paper SUMMARY The Burlina (BUR) is a local Italian cattle breed, its main feature is to be a small sized animal well adapted to live in difficult environment such as mountain areas. Nowadays only 350 cows are enrolled in the Italian Herd Book due to its substitution by more productive breeds. This study proposes a phenotypic and genetic characterization of the BUR breed in comparison with Holstein Friesian (HFR) and Brown Swiss (BSW). The comparison of productive traits showed lower production than HFR and BSW as well as longer productive life and more favourable reproductive traits in BUR animals. The genetic analyses, performed by microsatellites markers, showed the high level of heterozygosity and the genetic distinctiveness of BUR. These findings approve the feasibility of a conservation scheme and suggest the profitability of breeding BUR, especially in difficult environment where the low production can be compensated by longevity and the economic loss by the added value of its typical dairy production. Key-words: Burlina cattle breed, genetic characterization, conservation. INTRODUCTION The Burlina (BUR) is local dairy cattle breed reared in North-East Italy; it is a small sized animal with black spotted coat, well adapted to live in difficult environment as marginal mountain areas thank to its good grazing characteristics. BUR is mainly found in the mountain area of Veneto region (Del Bo et al., 2001) where it has always been reared and appreciated by local farmers. -
Aurochs Genetics, a Cornerstone of European Biodiversity
Aurochs genetics, a cornerstone of European biodiversity Picture: Manolo Uno (c) Staffan Widstrand Authors: • drs. Ronald Goderie (Taurus Foundation); • dr. Johannes A. Lenstra (Utrecht University, Faculty of Veterinary Medicine); • Maulik Upadhyay (pHD Wageningen University); • dr. Richard Crooijmans (Animal Breeding and Genomics Centre, Wageningen University); • ir. Leo Linnartz (Ark Nature) Summary of: Aurochs Genetics, a cornerstone of biodiversity Preface In 2015 a report is written on Aurochs genetics, made possible by a grant from the Dutch Liberty Wildlife fund. This fund provided the Taurus foundation with a grant of EUR 20.000 to conduct genetic research on aurochs and its relation with nowadays so- called ‘primitive’ breeds. This is the summary of that report. This summary shortly describes the current state of affairs, what we do know early 2015 about the aurochs, about domestic cattle and the relationship of aurochs and the primitive breeds used in the Tauros Programme. Nijmegen, December 2015. page 2 Summary of: Aurochs Genetics, a cornerstone of biodiversity Table of contents Preface 2 Table of contents ......................................................................................................... 3 Summary ..................................................................................................................... 4 1 Introduction .......................................................................................................... 6 2 Aurochs: a short description ................................................................................. -
Local Cattle Breeds in Europe Development of Policies and Strategies for Self-Sustaining Breeds
Local cattle breeds in Europe Development of policies and strategies for self-sustaining breeds edited by: Sipke Joost Hiemstra Yvett e de Haas Asko Mäki-Tanila Gustavo Gandini Local cattle breeds in Europe Local cattle breeds in Europe Development of policies and strategies for self-sustaining breeds edited by: Sipke Joost Hiemstra Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, Lelystad, the Netherlands Yvette de Haas Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, Lelystad, the Netherlands Asko Mäki-Tanila MTT Agrifood Research, Joikonen, Finland Gustavo Gandini Department VSA, Faculty of Veterinary Medicine, University of Milan, Milan, Italy Wageningen Academic P u b l i s h e r s This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned. Nothing ISBN: 978-90-8686-144-6 from this publication may be translated, e-ISBN: 978-90-8686-697-7 reproduced, stored in a computerised DOI: 10.3921/978-90-8686-697-7 system or published in any form or in any manner, including electronic, mechanical, reprographic or photographic, without prior Photos cover: written permission from the publisher: CGN and INIA Wageningen Academic Publishers P.O. Box 220 Photos breedcases: 6700 AE Wageningen Veeteelt The Netherlands Kerry Cattle Society www.WageningenAcademic.com MTT EURECA Consortium Partners The individual contributions in this publication and any liabilities arising from them remain the responsibility of the First published, 2010 authors. The publisher is not responsible for possible © Wageningen Academic Publishers damages, which could be a result of content The Netherlands, 2010 derived from this publication. -
Luca Arzilli Associazione Regionale Allevatori Della Toscana
GREEN WEEK "Nature –our health, our wealth“ Farming for diversity Luca Arzilli 4 June 2015 ‐ Brussels Associazione Regionale Allevatori della Toscana Luca Arzilli Associazione Regionale Allevatori della Toscana Preservation and enhancement of the biodiversity of animal species in Tuscany Luca Arzilli GREEN WEEK "Nature –our health, our wealth“ Farming for diversity Associazione Regionale Allevatori della Toscana 4 June 2015 ‐ Brussels ANIMAL BIODIVERSITY IN TUSCANY –local breeds Tuscany has a wide variety of animal and plant species: we have twenty native breeds of different species, in every province. GREEN WEEK "Nature –our health, our wealth“ Farming for diversity Luca Arzilli 4 June 2015 ‐ Brussels Associazione Regionale Allevatori della Toscana ANIMAL BIODIVERSITY IN TUSCANY –the bio‐territory There is a direct relationship between the native breeds and its territory: the age‐long presence of cattle, sheep, goats, horses, pigs and donkeys has patterned the Tuscan country and it continues to preserve it as we all know. GREEN WEEK "Nature –our health, our wealth“ Farming for diversity Luca Arzilli 4 June 2015 ‐ Brussels Associazione Regionale Allevatori della Toscana ANIMAL BIODIVERSITY IN TUSCANY –the bio‐territory The presence of animals and people guarantees the preservation of the environment, of our landscape, the balance between the cultivated areas and forest, rural roads, watercourses, nature and farmhouses. GREEN WEEK "Nature –our health, our wealth“ Farming for diversity Luca Arzilli 4 June 2015 ‐ Brussels Associazione Regionale Allevatori della Toscana ANIMAL BIODIVERSITY IN TUSCANY –the bio‐territory The preservation and the development of biodiversity imply the presence of farmers on the territory to ensure the maintenance of the environmental conditions and the landscapes that characterize Tuscany and its standard of living. -
Testing Scenarios of European Colonization Using Genome-Wide SNP Da
Senczuk et al. Genet Sel Evol (2021) 53:48 https://doi.org/10.1186/s12711-021-00639-w Genetics Selection Evolution RESEARCH ARTICLE Open Access On the origin and diversifcation of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data Gabriele Senczuk1* , Salvatore Mastrangelo2, Paolo Ajmone‑Marsan3, Zsolt Becskei4, Paolo Colangelo5, Licia Colli3, Luca Ferretti6, Taki Karsli7, Hovirag Lancioni8, Emiliano Lasagna9, Donata Marletta10, Christian Persichilli1, Baldassare Portolano2, Francesca M. Sarti9, Elena Ciani11 and Fabio Pilla1 Abstract Background: During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so‑called Podolian trunk, the history of which is still not well established. Here, we used genome‑wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversifcation of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC‑RF) approach. Results: Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of difusion. -
Le Razze Di Bovini Da Carne in Veneto
a cura del SETTORE STUDI ECONOMICI ottobre 2011 I dati della BANCA NAZIONALE dell’ANAGRAFE ZOOTECNICA del MINISTERO DELLA SALUTE istituita presso l’I.Z.S. ABRUZZO E MOLISE, sede di TERAMO INDICE INTRODUZIONE .......................................................................................................................... 2 PREMESSA ................................................................................................................................... 4 IL PATRIMONIO BOVINO ............................................................................................... 5 I DATI ISTAT ............................................................................................................................... 5 IL PATRIMONIO BOVINO VENETO ......................................................................... 8 I DATI DELL’ANAGRAFE BOVINA ......................................................................................... 8 LE RAZZE DA CARNE ............................................................................................................. 13 L’ANDAMENTO MENSILE DELLA NUMEROSITA’ ........................................................... 16 REDAZIONE .............................................................................................................................. 17 1 INTRODUZIONE Questo report di analisi è centrato principalmente sui dati disponibili presso la banca dati dell’Anagrafe Nazionale Zootecnica del Ministero della Salute, consultabili liberamente e direttamente via internet. La -
Genomic Diversity and Population Structure of the Indigenous Greek and Cypriot Cattle Populations Dimitris Papachristou1, Panagiota Koutsouli1, George P
Papachristou et al. Genet Sel Evol (2020) 52:43 https://doi.org/10.1186/s12711-020-00560-8 Genetics Selection Evolution RESEARCH ARTICLE Open Access Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations Dimitris Papachristou1, Panagiota Koutsouli1, George P. Laliotis1, Elisabeth Kunz2, Maulik Upadhyay2, Doris Seichter3, Ingolf Russ3, Bunevski Gjoko4, Nikolaos Kostaras5, Iosif Bizelis1 and Ivica Medugorac2* Abstract Background: The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commer- cial breeds. This study represents the frst comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results: We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic diferentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defned by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. -
Country Report Italy 2011
European Regional Focal Point for Animal Genetic Resources (ERFP) 21 st April 2011 ERFP Country report 2010 – 2011 COUNTRY: ITALY reported by: Giovanni Bittante Strategic Priority Area 1: Characterization, Inventory and Monitoring of Trends and Associated Risks The inventory of Italian animal genetic resources and the monitoring of trends and associated risks has been undertaken and summarized il the paper "Italian animal genetic resources in the Domestic Animal Diversity Information Systm of FAO" (Giovanni Bittante, 2011, Italian Journal of Animal Science,vol 10:e29, Annex 2). Several research activities on this topic have been carried out by Universities and Research Institutions. Among them see the important activity of ConSDABI (Annex 3). Strategic Priority Area 2: Sustainable Use and Development Beyond the systematic control of animals of Italian populations (herd books, pedigree registries, milk recording, type evaluation, etc.) made by the different associations of breeders, as outlined in Annex 2, several projects dealing with sustainable use, products valorisation and development has been carried out by national and local governments, agencies, breeders associations and consortia. Strategic Priority Area 3: Conservation (please give details for the most relevant institutions for national genebanks / cryopreservation in the table in Annex 1) In situ conservation activities are going on for almost all the Italian AnGR, while the project of a national virtual cryo-bank is not yet fully established, despite the intense work of the -
Refining the Genetic Structure and Relationships of European
www.nature.com/scientificreports OPEN Refning the genetic structure and relationships of European cattle breeds through meta‑analysis of worldwide genomic SNP data, focusing on Italian cattle Salvatore Mastrangelo1*, Marco Tolone1, Slim Ben Jemaa2, Gianluca Sottile3, Rosalia Di Gerlando1, Oscar Cortés4, Gabriele Senczuk5, Baldassare Portolano1, Fabio Pilla5 & Elena Ciani6 The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large‑scale, genome‑wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome‑wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate diferences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were observed among domesticated bovid populations from diferent geographic areas, except for Bali cattle. Our fndings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic diferentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene fow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, refecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived‑breeds, in the past experienced a similar non‑European infuence, with African and indicine introgression.