Harmful Mutational Load in the Mitogenomes of Cattle Breeds
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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 -
Revisiting AFLP Fingerprinting for an Unbiased Assessment of Genetic
Utsunomiya et al. BMC Genetics 2014, 15:47 http://www.biomedcentral.com/1471-2156/15/47 RESEARCH ARTICLE Open Access Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle Yuri Tani Utsunomiya1†, Lorenzo Bomba2†, Giordana Lucente2, Licia Colli2,3, Riccardo Negrini2, Johannes Arjen Lenstra4, Georg Erhardt5, José Fernando Garcia1,6, Paolo Ajmone-Marsan2,3* and European Cattle Genetic Diversity Consortium Abstract Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas. Results: We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. -
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. -
The Enigmatic Origin of Bovine Mtdna Haplogroup R: Sporadic Interbreeding Or an Independent Event of Bos Primigenius Domestication in Italy?
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy? Silvia Bonfiglio1, Alessandro Achilli1,2, Anna Olivieri1, Riccardo Negrini3, Licia Colli3, Luigi Liotta4, Paolo Ajmone-Marsan3, Antonio Torroni1, Luca Ferretti1* 1 Dipartimento di Genetica e Microbiologia, Universita` di Pavia, Pavia, Italy, 2 Dipartimento di Biologia Cellulare e Ambientale, Universita` di Perugia, Perugia, Italy, 3 Istituto di Zootecnica, Universita` Cattolica del Sacro Cuore, Piacenza, Italy, 4 Dipartimento di Morfologia, Biochimica, Fisiologia e Produzioni Animali, Universita` di Messina, Messina, Italy Abstract Background: When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. Methodology: The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. -
Relazione Attività Anno 2019
Assemblea Generale dei Soci Cuneo, 30 settembre 2020 RELAZIONE TECNICA ANNO 2019 ASSOCIAZIONE REGIONALE ALLEVATORI DEL PIEMONTE Via Torre Roa, 13 12100 Madonna dell’Olmo - CUNEO www.arapiemonte.it 2 CARICHE SOCIALI Comitato Direttivo Chialva Roberto Presidente ARAP Presidente STA Cuneo Serra Franco Vice presidente Presidente STA Asti Odetti Paolo Vice presidente Presidente STA Torino Bongianino Roberto consigliere Presidente STA Vercelli e Biella Fortunato Mario consigliere Presidente STA Liguria Panizza Sergio consigliere Presidente STA Alessandria Parmigiani Simone consigliere Presidente STA Novara e VCO Dalmasso Elia consigliere Fassino Antonino consigliere Fiandino Davide consigliere Gianoglio Mario consigliere Fina Claudio consigliere Magliana Andrea consigliere Sanmartino Luca consigliere Viarengo Domenico consigliere Collegio Sindacale Morgese Vittorio Presidente Morabito Domenico sindaco effettivo Gallo Elena sindaco effettivo Probiviri Brondelli di Brondello Guido probiviro Salvini Elisabetta probiviro Bovetti Bartolomeo probiviro Direttore Valperga Tiziano 3 ASSOCIAZIONE ITALIANA ALLEVATORI Via XXIV Maggio n. 44/45, 00187 Roma SISTEMA ALLEVATORI DEL PIEMONTE ASSOCIAZIONE REGIONALE ALLEVATORI DEL PIEMONTE e STA* di CUNEO Via Torre Roa, 13, Madonna dell’Olmo – 12100 Cuneo – Tel. 0171/410.800 Fax 0171/ 413.863 e-mail: [email protected] Via dell’Artigianato, 1 – 12030 Monasterolo di Savigliano (CN) Tel. 0172/713972 Fax 0172/726348 e-mail: [email protected] STA di ALESSANDRIA Fraz. Gerlotti, via Casale 113 – 15122 Alessandria - Tel. 0131/1750290 Fax 0131/1750291 e-mail: [email protected] STA di ASTI Via Guttuari, 23 - 14100 Asti - Tel. 0141/530690 Fax 0141/530690 e-mail: [email protected] STA di NOVARA V.C.O. Corso Vercelli, 120 - 28100 Novara - Tel. 0321/453140 Fax 0321/453373 e-mail: [email protected] Regione Nosere - c/o Compl. -
Charakterisierung Von Ernährungsphysiologischen Und Technologischen Eigenschaften Der Milch Und Wirtschaftliche Analyse Von Rinderrassen Im Berggebiet
Aus dem Institut für Tierzucht und Haustiergenetik Professur für Tierzüchtung der Justus-Liebig-Universität Gießen Charakterisierung von ernährungsphysiologischen und technologischen Eigenschaften der Milch und wirtschaftliche Analyse von Rinderrassen im Berggebiet INAUGURAL – DISSERTATION zur Erlangung des Doktorgrades (Dr. agr.) im Fachbereich Agrarwissenschaften, Ökotrophologie und Umweltmanagement der Justus-Liebig-Universität Gießen vorgelegt von Dipl. Ing. agr. Thomas Zanon aus Bozen, Südtirol Gießen, 2020 Mit Genehmigung des Fachbereiches Agrarwissenschaften, Ökotrophologie und Umweltmanagement der Justus-Liebig-Universität Gießen Dekan: Prof. Dr. Klaus Eder Prüfungskommission: 1. Gutachter: Prof. Dr. Sven König 2. Gutachter: Prof. Dr. Dr. Matthias Gauly Prüfer: Prof. Dr. Klaus Eder Prüfer: Prof. Dr. Georg Erhardt Vorsitzende: Prof. Dr. Gesine Lühken Tag der Disputation: 18.09.2020 2 Diese Arbeit wurde im Rahmen des Forschungsprojektes „EIFEAL - European Region Tyrol- South Tyrol-Trentino as Land of Solutions” durchgeführt (CUP-Kodex: I56C18002030002). Es gibt mehr als eine bunte Kuh. Es lebe die Vielfalt der Natur. (Deutsches Sprichwort) For a farm to achieve sustainability, it must be able to take advantage of current opportunities, while managing the conditions that expand future possibilities. (Darnhofer et al. 2010) 3 INHALTSVERZEICHNIS TABELLENVERZEICHNIS ..................................................................................................................... 6 ABBILDUNGSVERZEICHNIS ................................................................................................................ -
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. -
Caratterizzazione Genetica Di Diverse Razze Bovine Tramite Un Set Di 128 Snps DNA Fingerprinting of Different Cattle Breeds Using a Set of 128 Snps
Caratterizzazione genetica di diverse razze bovine tramite un set di 128 SNPs DNA fingerprinting of different cattle breeds using a set of 128 SNPs A. Pozzi1, S. Arabi1, C. Previtali1, R. Capoferri1, A. Galli2, M. Montedoro1 e G. Bongioni1 1 Istituto Sperimentale Italiano “L. Spallanzani” Rivolta d’Adda (Cremona), IT [email protected] 2 CREA Centro di ricerca Zootecnia e Acquacoltura (Lodi, IT) L’Italia grazie alla sua storia, alle sue tradizioni ed alla tipologia del territorio è un Paese particolarmente ricco di biodiversità: si contano oltre 200 razze zootecniche adattatesi nei secoli a produrre in ambienti diversificati per clima e vegetazione. La conservazione della biodiversità delle specie zootecniche è universalmente riconosciuta come una priorità importante, sia per aspetti ecologici, sociali e culturali, sia per il mantenimento del territorio, delle comunità rurali e delle tradizioni. La ricerca in ambito genetico-molecolare e le innovazioni tecnologiche possono essere un valido strumento a tutela della biodiversità. Oggetto di questo studio è stata la caratterizzazione di 20 razze bovine presenti in Italia, al fine di valutarne la diversità genetica tramite approccio molecolare, con l’utilizzo di un chip a 128 SNPs su piattaforma Open Array: 88 SNPs sono stati individuati nel pannello proposto per ISAG Bovine Comparison Test 2011 e, i restanti 40, nel database dbSNP dell’NCBI. Complessivamente sono stati analizzati 513 soggetti appartenenti alle 20 razze (25 campioni per razza) di seguito elencate: Bruna Alpina, Frisona, Valdostana Pezzata Rossa, Pezzata Rossa Italiana, Piemontese, Reggiana, Rendena, Grigia, Pinzgauer, Jersey, Valdostana Pezzata Nera, Charolaise, Marchigiana, Chianina, Limousine, Romagnola, Castana, Blue Belga, Montbeillarde, Blonde d’Aquitaine. -
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 -
Cornella Bianca Rer A008
REGIONE EMILIA-ROMAGNA Atti amministrativi GIUNTA REGIONALE Atto del Dirigente a firma DETERMINAZIONE n° 1721 del 18/02/2015 unica: Proposta: DPG/2015/82 del 08/01/2015 Struttura proponente: SERVIZIO RICERCA, INNOVAZIONE E PROMOZIONE DEL SISTEMA AGROALIMENTARE DIREZIONE GENERALE AGRICOLTURA, ECONOMIA ITTICA, ATTIVITA' FAUNISTICO-VENATORIE Oggetto: L.R. 1/2008. APPROVAZIONE DELLA REVISIONE DELLE SCHEDE DI RAZZE ANIMALI GIA' ISCRITTE AL REPERTORIO VOLONTARIO REGIONALE DI RISORSE GENETICHE INDIGENE AGRARIE, SECONDO LE "LINEE GUIDA PER LA CONSERVAZIONE E LA CARATTERIZZAZIONE DELLA BIODIVERSITA' VEGETALE, ANIMALE E MICROBICA DI INTERESSE PER L'AGRICOLTURA" DI CUI AL DECRETO DEL MIPAAF N. 171/2012. Autorità emanante: IL RESPONSABILE - SERVIZIO RICERCA, INNOVAZIONE E PROMOZIONE DEL SISTEMA AGROALIMENTARE Firmatario: GIANCARLO CARGIOLI in qualità di Responsabile di servizio Luogo di adozione: BOLOGNA data: 18/02/2015 pagina 1 di 58 Testo dell'atto SERVIZIO RICERCA, INNOVAZIONE E PROMOZIONE DEL SISTEMA AGROALIMENTARE IL RESPONSABILE Vista la L.R. 29 gennaio 2008, n. 1, “Tutela del patrimonio di razze e varietà locali di interesse agrario del territorio emiliano-romagnolo”; Richiamati in particolare i sottocitati articoli della predetta legge: - l’articolo 5, che istituisce il Repertorio Volontario Regionale delle risorse genetiche agrarie, di seguito denominato Repertorio; - l’articolo 6, che stabilisce le modalità per l’iscrizione al Repertorio; Richiamata, inoltre, la deliberazione della Giunta regionale n. 1469, in data 15 settembre 2008, recante