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Rennet-induced milk coagulation is an important trait for cheese production. Recent studies have reported an alarming frequency of cows producing poorly coagulating milk unsuitable for cheese production. Several genetic factors are known to affect milk coagulation, including variation in the major milk proteins; however, recent association studies indicate genetic effects from other genomic regions as well. The aim of this study was to detect genetic variation affecting milk coagulation properties, measured as curd-firming rate (CFR) and milk pH. This was achieved by examining allele frequency differences between pooled whole-genome sequences of phenotypically extreme samples (pool-seq).. Curd-firming rate and raw milk pH were measured for 415 Danish Holstein cows, and each animal was sequenced at low coverage. Pools were created containing whole genome sequence reads from samples with "extreme" values (high or low) for both phenotypic traits. A total of 6,992,186 and 5,295,501 SNP were assessed in relation to CFR and milk pH, respectively. Allele frequency differences were calculated between pools and 32 significantly different SNP were detected, 1 for milk pH and 31 for CFR, of which 19 are located on chromosome 6. A total of 9 significant SNP, which were selected based on the possible function of proximal candidate genes, were genotyped in the entire sample set ( = 415) to test for an association. The most significant SNP was located proximal to , explaining 33% of the phenotypic variance. , coding for κ-casein, is the most studied in relation to milk coagulation due to its position on the surface of the casein micelles and the direct involvement in milk coagulation. Three additional SNP located on chromosome 6 showed significant associations explaining 7, 3.6, and 1.3% of the phenotypic variance of CFR. The significant SNP on chromosome 6 were shown to be in linkage disequilibrium with the SNP peaking proximal to ; however, after accounting for the genotype of the peak SNP within this QTL, significant effects (-value < 0.1) could still be detected for 2 of the SNP accounting for 2 and 1% of the phenotypic variance. These 2 interesting SNP were located within introns or proximal to the candidate genes-solute carrier family 4 (sodium bicarbonate cotransporter), member 4 () and LIM and calponin homology domains 1 (), respectively-making them interesting targets for further analysis.

Made available in DSpace on 2014-12-03T13:07:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-04-17Bitstream added on 2014-12-03T13:24:33Z : No. of bitstreams: 1 WOS000335177200001.pdf: 750548 bytes, checksum: 075b52b143f984a79a48dec1b9a68ce6 (MD5) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 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. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.Conclusions: The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources. Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, SP, Brazil Univ Cattol Sacro Cuore, Inst Zootech, Piacenza, Italy Univ Cattol Sacro Cuore, BioDNA Biodivers & Ancient DNA Res Ctr, Piacenza, Italy Univ Utrecht, Fac Vet Med, Utrecht, Netherlands Univ Giessen, Inst Anim Breeding & Genet, D-35390 Giessen, Germany Univ Estadual Paulista, Fac Med Vet Aracatuba, BR-16050680 Aracatuba, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, SP, Brazil Univ Estadual Paulista, Fac Med Vet Aracatuba, BR-16050680 Aracatuba, SP, Brazil FAPESP: 11/16643-2 FAPESP: 13/12829-0

This article documents the addition of 83 microsatellite marker loci and 96 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bembidion lampros, Inimicus japonicus, Lymnaea stagnalis, Panopea abbreviata, Pentadesma butyracea, Sycoscapter hirticola and Thanatephorus cucumeris (anamorph: Rhizoctonia solani). These loci were cross-tested on the following species: Pentadesma grandifolia and Pentadesma reyndersii. This article also documents the addition of 96 sequencing primer pairs and 88 allele-specific primers or probes for Plutella xylostella. Fil: Molecular Ecology Resources Primer Development Consortium. Molecular Ecology Resources Editorial Office; Canadá Fil: Ahanchede, Adam. Universite d’Abomey-Calavi. Faculty of Agronomic Sciences; Benín Fil: Fernandez Alfaya, Jose Elias. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Andersen, L. W.. University Aarhus; Dinamarca Fil: Azam, Didier. Institut Nationale de Recherches Agronomiques. Unite Experimentale d’Ecologie et Ecotoxicologie Aquatique; Francia Fil: Bautista, Ma. Anita M.. The Ohio State University. College Of Biological Sciences. Departament Of Entomology; Estados Unidos Fil: Besnard, Anne Laure. Institut National de la Recherche Agronomique; Francia Fil: Bigatti, Gregorio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Bouetard, Anthony. Institut National de la Recherche Agronomique; Francia Fil: Coutellec, Marie Agnes. Institut National de la Recherche Agronomique; Francia Fil: Ewedjè, Eben Ezer B. K.. Universite Libre de Bruxelles; Bélgica. Universite d’Abomey-Calavi; Benín Fil: Fuseyo, Reiko. National Research Institute of Fisheries Engineering. Fisheries Research Agency; Japón Fil: García Jimenez, Ricardo. Consejo Superior de Investigaciones Cientificas. Museo Nacional de Cs. Naturales; España Fil: Haratian, M.. Tarbiat Modares University. College of Agriculture; Irán Fil: Hardy, Olivier J.. Universite Libre de Bruxelles; Bélgica Fil: Holm, L. E.. Department of Molecular Biology and Genetics; Dinamarca Fil: Hoy, Casei W.. Ohio State University; Estados Unidos Fil: Koshimizu, Eriko. Tokyo University of Marine Science and Technology; Japón Fil: Loeschcke, V.. Aharhus University; Dinamarca Fil: López Marquez, Violeta. Consejo Superior de Investigaciones Cientificas. Museo Nacional de Cs. Naturales; España Fil: Machado, Carlos. University of Maryland; Estados Unidos Fil: Machordom, Annie. Consejo Superior de Investigaciones Cientificas. Museo Nacional de Cs. Naturales; España Fil: Marchi, C.. Aarhus University; Dinamarca Fil: Michel, Andrew P.. Ohio State University; Estados Unidos Fil: Micheneau, Claire. Universite Libre de Bruxelles; Bélgica. James Cook University; Australia Fil: Mittapalli, Omprakash. Ohio State University; Estados Unidos Fil: Nagai, Takahiro. Hiroshima Prefectural Technology Research Institute; Japón Fil: Okamoto, Nobuaki. Tokyo University of Marine Science and Technology; Japón Fil: Pan, Ying. Guangxi University; China Fil: Panitz, F.. Department of Molecular Biology and Genetics; Dinamarca Fil: Safaie, N.. Tarbiat Modares University,; Irán Fil: Sakamoto, Takashi. Tokyo University of Marine Science and Technology; Japón Fil: Sharifnabi, B.. Isfahan University of Technology; Irán Fil: Tian, En Wei. Chinese Academy of Sciences. South China Botanical Garden; China Fil: Yu, Hui. Chinese Academy of Sciences. South China Botanical Garden; China

Molecular Ecology Resources Primer Development Consortium [et al.], Isolation and characterisation of microsatellite loci for the 1 southern geoduck Panopea abbreviata (Valenciennes, 1839) through 454 pyrosequencing. This article documents the addition of 83 microsatellite marker loci and 96 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bembidion lampros, Inimicus japonicus, Lymnaea stagnalis, Panopea abbreviata, Pentadesma butyracea, Sycoscapter hirticola and Thanatephorus cucumeris (anamorph: Rhizoctonia solani). These loci were cross-tested on the following species: Pentadesma grandifolia and Pentadesma reyndersii. This article also documents the addition of 96 sequencing primer pairs and 88 allele-specific primers or probes for Plutella xylostella.

454-sequencing of the genome was used to isolate and characterize nuclear 22 microsatellite sequences from the ground beetle Bembidion lampros (Carabidae). A 23 total of 4502 contigs containing di- to penta-nucleotide microsatellite repeats were 24 found (4211 perfect and 289 non-perfect repeats). Primers were developed and tested 25 for 34 microsatellite sequences. Of these 15 were tested on 1140 individual samples 26 amplifying on average 89% of samples and they did not deviate significantly from 27 Hardy-Weinberg and linkage equilibrium. These microsatellite sequences will be useful 28 in studying the effect of agricultural management techniques and various environmental 29 factors on a beneficial agricultural species.

Chantier qualité GA Liste des auteurs de l'European Cattle Genetic Consortium, classés par pays : Austria: R. Baumung, S. Manatrinon, BOKU University, Vienna; Belgium: G. Mommens, University of Ghent, Merelbeke; Denmark: L.-E. Holm, Aarhus University, Tjele; K.B. Withen, B.V. Pedersen, P. Gravlund, University of Copenhagen, Copenhagen; Estonia: H. Viinalass, Estonian University of Life Sciences, Tartu; Finland: J. Kantanen, I. Tapio, M.H. Li, MTT, Jokioinen; France: K. Moazami-Goudarzi, M. Gautier, Denis Laloë, INRA, Jouy-en-Josas; A. Oulmouden, H. Levéziel, INRA, Limoges; P. Taberlet, Université Joseph Fourier et CNRS, Grenoble; Germany: B. Harlizius, School of Veterinary Medicine, Hannover; H. Simianer, H. Täubert, Georg-August-Universität, Göttingen; G. Erhardt, O. Jann, C. Weimann, E.-M. Prinzenberg, Justus-Liebig Universität, Giessen; I. Medugorac, A. Medugorac, M. Förster, Ludwig-Maximilians Universität, Munich; H.M. Mix, Naturschutz International, Grünheide; C. Looft, E. Kalm, Christian-Albrechts-Universität, Kiel; Ireland: D.G. Bradley, C.J. Edwards, D.E. MacHugh, A.R. Freeman, Trinity College, Dublin; Italy: P. Ajmone Marsan, R. Negrini, Università Cattolica del S. Cuore, Piacenza; M. Longeri, G. Ceriotti, M. Zanotti, Università degli Studi di Milano; D. Marletta, A. Criscione, Universita degli Studi di Catania, Catania; A. Valentini, C. Marchitelli, L. Pariset, M.C. Savarese, Università della Tuscia, Viterbo; F. Pilla, Università del Molise, Campobasso; Latvia: Z. Grislis, Latvia University of Agriculture, Jelgava; Lithuania: I. Miceikienė, Lithuanian Veterinary Academy, Kaunas; Netherlands: I.J. Nijman, Utrecht University; W. van Haeringen, L. van de Goor, Van Haeringen Laboratory, Wageningen; Norway: I. Olsaker, Norwegian School of Veterinary Science, Oslo; Portugal: C. Ginja, L.T.Gama, Instituto Nacional de Recursos Biológicos—INIA, Lisbon University, Lisboa; L.T. Gama, Instituto Nacional de Recursos Biológicos-INIA, I.P., Vale de Santarem; J.C. Mateus, Universidade de Trás-os-Montes e Alto Douro, Vila Real; A. Beja-Pereira, N. Ferrand, Oporto University; Russia: Z. Ivanova, R. Popov, I. Ammosov, Yakutian Research Institute of Agricultural Sciences, Yakutsk, Sakha; T. Kiselyova, All-Russian Research Institute for Farm Animals and Breeding, St. Petersburgh-Pushkin; N. Marzanov, All-Russian Research Institute of Animal Husbandry, Dubrovitsy; Serbia: S. Stojanovic, Ministry of Agriculture and Water Management, Belgrade; Slovenia: M. Simčič, P. Dovč, D.Kompan, University of Ljubljana, Domzale; Spain: S. Dunner, Universidad Complutense de Madrid; C. Rodellar, I. Martín-Burriel, Veterinary Faculty, Zaragoza; A. Sánchez, J. Piedrafita, Universitat Autònoma de Barcelona; P.J. Azor, J.V. Delgado, A. Martínez-Martínez, A. Molina, E. Rodero, University of Córdoba; Switzerland: G. Dolf, University of Berne; UK: J.L. Williams, P. Wiener, Roslin Institute; M.W. Bruford, T.C. Bray, Cardiff University, Cardiff; L. Alderson, Countrywide Livestock Ltd, Shrewsbury; USA: M.C.T. Penedo. University of California, Davis, CA; International audience; Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic diversity of cattle.

Population contribution to genetic diversity can be estimated using neutral variation. However, population expansion or hybridization of diverged ancestries may weaken correlation between neutral and non-neutral variation. Microsatellite variation was studied at 25 loci in 20 native and 12 modern or imported northern European sheep breeds. Breed contributions to total gene diversity, allelic richness and mean allele-sharing distance between individuals were measured. Indications of changes in population size and admixtures of divergent ancestries were investigated and the extent of inbreeding was estimated. The northern European sheep demonstrated signs of reduction in effective population size. Many old, small populations made a substantial positive contribution to total molecular variation, but populations with several divergent major ancestries did not contribute substantially to molecular variation, with the exception of the Norwegian Rygja sheep. However, several diverged major ancestries may cause it to contribute less to non-neutral variation than expected from the microsatellite data. Breed uniqueness and within-breed variability generally had opposite effects on breed contributions to molecular diversity. The degree of inbreeding did not reflect the breed contribution to total gene diversity or allelic richness, but inbred populations increased the mean allele-sharing distance between individuals. Our study indicates breed conservation to be especially important in maintaining allelic variation in northern European sheep and supports the evolutionary importance of peripheral populations.

International audience