Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Allais‐Bonnet, Aurélie; Grohs, Cécile; Međugorac, Ivica; Krebs, Stefan; Djari, Anis; Graf, Alexander; Fritz, Sébastien; Seichter, Doris; Baur, Aurélia; Ruß, Ingolf; Bouet, Stéphan; Rothammer, Sophie; Wahlberg, Per; Esquerré, Diane; Hozé, Chris; Boussaha, Mekki; Weiss, Bernard; Thépot, Dominique; Fouilloux, Marie-Noëlle; Rossignol, Marie; Marle-Köster, E. van; Hreiðarsdóttir, Gunnfríður Elín; Barbey, Sarah; Dozias, Dominique; Cobo, Emilie; Reversé, Patrick; Catros, Olivier; Marchand, Jean; Soulas, Pascal; Roy, Pierre Van; Marquant-Leguienne, B.; Bourhis, Daniel Le; Clément, Laetitia; Salas-Cortes, L.; Venot, Eric; Pannetier, Maëlle; Phocas, Florence; Klopp, Christophe; Rocha, Dominique; Fouchet, Michel; Journaux, L.; Bernard-Capel, Carine; Ponsart, Claire; Eggen, Andre A.; Blum, Helmut; Gallard, Yves; Boichard, Didier; Pailhoux, Eric; Capitan, Aurélien

doi:10.1371/journal.pone.0063512

Cited by 85 publications

(162 citation statements)

References 76 publications

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“…Previously, we reported and confirmed this recombination in 20 horned offspring of ELBOY RED [2]. A second horned offspring of LAWN BOY P-RED, the recombinant bull ROSSI, carries a large region of the Friesian haplotype that is associated with the polled trait and that comprises P 5ID , P G1654405A , P C1768587A and P G1855898A (Figure 1A and B).…”

Section: Resultssupporting

confidence: 72%

“…Furthermore, of the two additional Friesian SNPs P G1855898A and P T1764239C reported in Allais-Bonnet et al [2], we included only the candidate causal mutation P G1855898A because preliminary Sanger sequencing results indicated that P T1764239C segregated in horned animals. Thus, the 13 Holstein-Friesian individuals were also genotyped for P G1855898A using PCR-RFLP.…”

Section: Methodsmentioning

confidence: 99%

“…In the past years, the position of the POLLED locus on BTA1 was refined [11,12] and candidate causal mutations were identified [2,4,5]. Recently, Medugorac et al [4] demonstrated the existence of at least two different alleles at the POLLED locus in cattle.…”

Section: Introductionmentioning

confidence: 99%

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The 80-kb DNA duplication on BTA1 is the only remaining candidate mutation for the polled phenotype of Friesian origin

et al. 2014

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BackgroundThe absence of horns, called polled phenotype, is the favored trait in modern cattle husbandry. To date, polled cattle are obtained primarily by dehorning calves. Dehorning is a practice that raises animal welfare issues, which can be addressed by selecting for genetically hornless cattle. In the past 20 years, there have been many studies worldwide to identify unique genetic markers in complete association with the polled trait in cattle and recently, two different alleles at the POLLED locus, both resulting in the absence of horns, were reported: (1) the Celtic allele, which is responsible for the polled phenotype in most breeds and for which a single candidate mutation was detected and (2) the Friesian allele, which is responsible for the polled phenotype predominantly in the Holstein-Friesian breed and in a few other breeds, but for which five candidate mutations were identified in a 260-kb haplotype. Further studies based on genome-wide sequencing and high-density SNP (single nucleotide polymorphism) genotyping confirmed the existence of the Celtic and Friesian variants and narrowed down the causal Friesian haplotype to an interval of 145 kb.ResultsAlmost 6000 animals were genetically tested for the polled trait and we detected a recombinant animal which enabled us to reduce the Friesian POLLED haplotype to a single causal mutation, namely a 80-kb duplication. Moreover, our results clearly disagree with the recently reported perfect co-segregation of the POLLED mutation and a SNP at position 1 390 292 bp on bovine chromosome 1 in the Holstein-Friesian population.ConclusionWe conclude that the 80-kb duplication, as the only remaining variant within the shortened Friesian haplotype, represents the most likely causal mutation for the polled phenotype of Friesian origin.

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Section: Resultssupporting

confidence: 72%

Section: Methodsmentioning

confidence: 99%

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The 80-kb DNA duplication on BTA1 is the only remaining candidate mutation for the polled phenotype of Friesian origin

et al. 2014

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“…The small size of the mapped haplotypes suggests that the polled mutation occurred a long time ago as stated by Allais-Bonnet et al [3]. In contrast to previous studies [3], [15] we mapped the polled mutation in Holstein cattle separately and ended up with a 932 kb polled associated interval. This critical interval includes the mapped interval of 212 kb in polled beef cattle and contains 14 annotated genes and loci.…”

Section: Discussionmentioning

confidence: 85%

“…Thus we were able to improve previous mappings based on illumina's bovineSNP50 BeadChip, where the polled locus had been mapped on a 381 kb interval in a mixed breed approach including Holstein and beef breeds [13], [15] and to a 400 kb interval including four different polled haplotypes from Holstein and Charolais cattle respectively [3]. The small size of the mapped haplotypes suggests that the polled mutation occurred a long time ago as stated by Allais-Bonnet et al [3]. In contrast to previous studies [3], [15] we mapped the polled mutation in Holstein cattle separately and ended up with a 932 kb polled associated interval.…”

Section: Discussionmentioning

confidence: 96%

Independent Polled Mutations Leading to Complex Gene Expression Differences in Cattle

et al. 2014

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The molecular regulation of horn growth in ruminants is still poorly understood. To investigate this process, we collected 1019 hornless (polled) animals from different cattle breeds. High-density SNP genotyping confirmed the presence of two different polled associated haplotypes in Simmental and Holstein cattle co-localized on BTA 1. We refined the critical region of the Simmental polled mutation to 212 kb and identified an overlapping region of 932 kb containing the Holstein polled mutation. Subsequently, whole genome sequencing of polled Simmental and Holstein cows was used to determine polled associated genomic variants. By genotyping larger cohorts of animals with known horn status we found a single perfectly associated insertion/deletion variant in Simmental and other beef cattle confirming the recently published possible Celtic polled mutation. We identified a total of 182 sequence variants as candidate mutations for polledness in Holstein cattle, including an 80 kb genomic duplication and three SNPs reported before. For the first time we showed that hornless cattle with scurs are obligate heterozygous for one of the polled mutations. This is in contrast to published complex inheritance models for the bovine scurs phenotype. Studying differential expression of the annotated genes and loci within the mapped region on BTA 1 revealed a locus (LOC100848215), known in cow and buffalo only, which is higher expressed in fetal tissue of wildtype horn buds compared to tissue of polled fetuses. This implicates that the presence of this long noncoding RNA is a prerequisite for horn bud formation. In addition, both transcripts associated with polledness in goat and sheep (FOXL2 and RXFP2), show an overexpression in horn buds confirming their importance during horn development in cattle.

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LncRNAs in domesticated animals: from dog to livestock species

et al. 2021

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Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

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Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Cited by 85 publications

References 76 publications

The 80-kb DNA duplication on BTA1 is the only remaining candidate mutation for the polled phenotype of Friesian origin

The 80-kb DNA duplication on BTA1 is the only remaining candidate mutation for the polled phenotype of Friesian origin

Independent Polled Mutations Leading to Complex Gene Expression Differences in Cattle

LncRNAs in domesticated animals: from dog to livestock species

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