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Expertise scientifique collective, synthèse du rapport, INRA (France). Biodiversité des espaces agricoles et services écologiques rendus par cette biodiversité. . double histoire: celle du concept de biodiversité, et celle des évolutions de une logique agronomique qui cherche à limiter l'érosion de la diversité génétique.
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Fetuses produced with the semen of heterozygous or mosaic bulls were genotyped as previously described  ,  to confirm their genotype. Markers with call rates lower than 0. Quality control also included parentage checking in the small paternal half-sib design and elimination of remaining Mendelian inconsistencies. A total of 1, markers located within the first three megabases of BTA01 were included in the study.
All together, BTA01 haplotypes were composed of 2, and 2, markers along this chromosome in Charolais and Holstein, respectively. Because sires and maternal grand-sires of all animals are genotyped, these phases are highly reliable. As an additional security, only animals belonging to half-sib families with a minimum of ten progeny per sire were kept i.
Finally, only recombining haplotypes with a minimum of two carriers with accurate and concordant phenotypes were considered for the mapping of the Polled locus. The bp reads were mapped on the UMD3. Only reads with a unique mapping and a minimal quality of 30 were kept. PCR duplicates were filtered and a pileup of the mapped reads was created for each animal using SAMtools . Finally, detection of Copy Number Variation was performed according to Medugorac et al. The average sequence depth of non-repetitive sequences within the polled intervals ranged from 5. Genome assembly gaps and regions with null coverage mapping to the restrained Polled intervals were PCR amplified and sequenced using the Sanger method, as described in the following section.
To refine the localization of the recombination point in recombining Friesian haplotypes, eight polymorphisms among the candidates were genotyped based on a dichotomous approach. The seven SNP g.chipguan-qa.zencode.guru/33975.php
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The list of all the primers used in this study is available in Table S4. The resulting amplicons were purified and bidirectionally sequenced by Eurofins MWG Germany using conventional Sanger sequencing. Polymorphisms were detected with NovoSNP software . The kb duplication was genotyped by PCR-Electrophoresis. This diagnostic test does not make it possible to distinguish the homozygous from the heterozygous carriers of the kb duplication.
However, this was not a problem since only heterozygous carriers of recombining haplotypes were analyzed at this step. For the latter diagnostic test, the wt and mutated alleles correspond to bp and bp fragments, respectively. Finally, two different strategies were implemented to genotype the large panel of 2, animals for the Celtic mutation, the Friesian kb duplication and the three other candidate mutations for the Friesian allele SNP g.
A total of animals were genotyped in France for these five mutations, as mentioned above. In the rare cases where animals were homozygous for the three candidate SNP alleles associated with the Friesian allele, another SNP g. The other 2, animals were genotyped for the Celtic mutation, the Friesian kb duplication, SNP g. Genotypes for candidate SNP g.
Of note, in both datasets, no recombination was observed within the Friesian haplotype between the Friesian candidate mutations or mutations showing strong linkage disequilibrium with them. The gene content of the Celtic and Friesian Polled intervals was assessed based on the gene annotation available for the UMD3. Region encompassing the Celtic mutation was PCR amplified from genomic DNA of American bison Bison bison , water buffalo Bubalus Bubalis , Nilgai Boselaphus tragocamelus , blackbuck antelope Antilope cervicapra , Siberian ibex Capra sibirica , Wild goat Capra aegagrus , Siberian bighorn sheep Ovis nivicola , and fallow deer Dama dama , and bidirectionally sequenced using the Sanger method, as previously described.
Multispecies alignment was generated with ClustalW software, version 2. Digital images were obtained with the NanoZoomer 2. Primer efficiency and specificity were evaluated on bovine genomic DNA. Details of the abnormal prepuce withdrawal phenotype displayed by some polled bulls. The unique candidate causative mutation for the polled Celtic allele and the five candidate causative mutations for the polled Friesian allele according to Medugorac et al.
Distribution of the Celtic and Friesian alleles in a large panel of polled and horned animals. Details of animals and designs used in the different experiments.
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Information on sequences replacing the UMD3. Multispecies alignment of genomic sequences encompassing the Celtic mutation in Bovidae and non- Bovidae ruminant species. The duplicated and deleted segments in the Celtic mutation are underlined and highlighted in yellow, respectively.
The authors would like to thank the numerous cattle breeders, breeding companies, insemination centers and research groups for generously providing samples, phenotypic information and occasional assistance in this research. In particular, we thank B. Boiret, the Humeau family and T.
Baudouin Charolais breeders , B.
Theil Limousin breeder , X. Milon, G. Michel, B. Raimbaud, P. Doradoux J. Thomin, T. Philippe Evolution, Rennes, France , A. Blanchon and S. Boichon and L. Champagne and J. Amigues, L. Genestout, G. Chantry-Darmon and A. Moazami-Goudarzi, S. Chaffaux and S. Charlier and K. Eriksson and S. Wahlberg samples from Sweden , P. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
National Center for Biotechnology Information , U. PLoS One. Published online May Doris Seichter 7 Tierzuchtforschung e. Ingolf Russ 7 Tierzuchtforschung e. Junming Yue, Editor. Author information Article notes Copyright and License information Disclaimer. There are no patents, products in development or marketed products to declare. Received Jan 18; Accepted Apr 2. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
This article has been cited by other articles in PMC. Associated Data Supplementary Materials Figure S1: Details of the abnormal prepuce withdrawal phenotype displayed by some polled bulls. Table S2: Distribution of the Celtic and Friesian alleles in a large panel of polled and horned animals. Table S3: Details of animals and designs used in the different experiments. Table S4: Details on primers used in this study. Document S2: Multispecies alignment of genomic sequences encompassing the Celtic mutation in Bovidae and non- Bovidae ruminant species.
Abstract Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. Introduction What is more natural for cattle than to have horns? Open in a separate window. Figure 1.
Frequency of the most frequent haplotypes across 17 Western European breeds for sliding windows of 79 markers at the beginning of BTA Accurate Mapping of the Polled Locus in Holstein and Charolais, Based on Observed Recombination Events To avoid any bias in mapping the Polled locus, we decided to investigate the French genomic selection dataset for recombination events. Figure 2. Accurate mapping of the Polled locus and identification of candidate causative mutations.
Whole Genome Sequencing Data Confirm Allelic Heterogeneity of the Polled Phenotype To exhaustively identify candidate causative mutations, we then sequenced the complete genome of two animals that were homozygous for the most frequent polled haplotype in their respective breeds i.
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Different Genotyping Strategies Reduce the Number of Candidate Mutations for the Friesian and Celtic Allele to Four and One Polymorphisms, Respectively, Located in Non-Coding Regions To further eliminate candidate mutations for the Friesian allele and refine the localization of the recombination points, we genotyped eight of the 47 candidate polymorphisms in animals carrying recombinant Hol-PH1 haplotypes, using a dichotomous approach.
Different Evidence Suggests That the Polled Mutations Do Not Affect the Expression of a Bovidae-Specific Gene To ascertain that the Celtic and Friesian polled alleles only affect horn development, we surveyed more than French breeders, agricultural engineers and agricultural technicians for putative observation of additional phenotypes associated with polledness. Figure 3. Details of the eyelash and eyelid phenotypes associated with polledness. Figure 4. Histological analyses of horn buds and forehead skin from wild-type fetuses and fetuses affected by different horn-defect syndromes. Figure 5.
EMT No Longer Plays a Role in Horn Ontogenesis at 90 dpc Meanwhile, we investigated the role of other functional candidate genes in the same dataset to obtain better insights into the mechanism involved in normal and pathological horn bud differentiation. Figure 6. Conclusions In conclusion, using exhaustive approaches, we confirmed the allelic heterogeneity of the bovine Polled locus and identified one and four candidate mutations for the Celtic and Friesian alleles, respectively. Animals, Phenotyping and Sampling All animals studied in this project are presented in Table S3 according to their breed or species affiliations and their purpose in the experimental design.
Genotyping of the Candidate Causative Mutations To refine the localization of the recombination point in recombining Friesian haplotypes, eight polymorphisms among the candidates were genotyped based on a dichotomous approach. Analysis of Sequence Conservation around the Celtic Mutation using Multispecies Alignment Region encompassing the Celtic mutation was PCR amplified from genomic DNA of American bison Bison bison , water buffalo Bubalus Bubalis , Nilgai Boselaphus tragocamelus , blackbuck antelope Antilope cervicapra , Siberian ibex Capra sibirica , Wild goat Capra aegagrus , Siberian bighorn sheep Ovis nivicola , and fallow deer Dama dama , and bidirectionally sequenced using the Sanger method, as previously described.
Supporting Information Figure S1 Details of the abnormal prepuce withdrawal phenotype displayed by some polled bulls. TIF Click here for additional data file. DOC Click here for additional data file. Table S2 Distribution of the Celtic and Friesian alleles in a large panel of polled and horned animals.
Table S3 Details of animals and designs used in the different experiments. Table S4 Details on primers used in this study. Document S2 Multispecies alignment of genomic sequences encompassing the Celtic mutation in Bovidae and non- Bovidae ruminant species. Acknowledgments The authors would like to thank the numerous cattle breeders, breeding companies, insemination centers and research groups for generously providing samples, phenotypic information and occasional assistance in this research. References 1. Can Vet J 48 : — Prayaga KC Genetic options to replace dehorning in beef cattle-a review.
Aust J Agric Res 58 : 1—8. Graf B, Senn M Behavioural and physiological responses of calves to dehorning by heat cauterization with or without local anaesthesia. Applied Animal Behaviour Science 62 : — Iowa Agric Exp Sta, Ames 30 : 67—a. Cole LJ The Wisconsin experiment in cross-breeding cattle. J Genet 32 : 33— J Hered 69 : — Nat Genet 4 : — Mamm Genome 6 : — J Hered 87 : — Mamm Genome 8 : — Comp Funct Genomics 6 : — Mamm Genome 16 : — Pretoria: University of Pretoria.
BMC Res Notes 8 : PLoS One 7 : e Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle. BMC Genomics 11 : Anim Genet doi: PLoS One 6 : e Nat Genet 29 : — Genomics 85 : — Mol Ecol 20 : — Genome Biology 10 : R Science : — Tacitus circa 90 AD The Germany. The Oxford translation revised with notes, section 5. Accessed December Translated by G. Macaulay , section A comparative study of prepuces from bulls which evert and those which do not.
Vet Rec 86 : — Am J Hum Genet 67 : — In: Pagon RA, editor.
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