A Single Nucleotide Polymorphism within the Interferon Gamma Receptor 2 Gene Perfectly Coincides with Polledness in Holstein Cattle

Glatzer, S; Merten, Nina Johanna; Dierks, Claudia; Wöhlke, Anne; Philipp, Ute; Distl, O.

doi:10.1371/journal.pone.0067992

Cited by 14 publications

(28 citation statements)

References 18 publications

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“…This conclusion is inconsistent with that of Glatzer et al [5] who reported the existence of a progeny-proven heterozygous polled Holstein-Friesian sire that carried neither the P 80kbID mutation nor a Celtic mutation. Unfortunately, since the identity of this bull was not provided, we could not verify these results.…”

Section: Resultscontrasting

confidence: 82%

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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: Resultscontrasting

confidence: 82%

“…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%

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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“…In recent years, with the significant expansion of the genomic sequence data in many aquaculture species, more and more studies have focus on the identification of SNPs in aquaculture species (Hayes, Laerdahl, Lien, Moen, Berg, Hindar, Davidson, Koop, Adzhubei & Høyheim 2007;Ciobanu, Bastiaansen, Magrin, Rocha, Jiang, Yu, Geiger, Deeb, Rocha, Gong, Kinghorn, Plastow, Van der Steen & Mileham 2010;Li, He, Yang, Shan, Tan & Gao 2010;Van Bers, Crooijmans, Groenen, Dibbits & Komen 2012). However, the association studies between the SNPs and the production traits for most aquaculture species, especially for the Chinese mitten crab, are still limited comparing with that in other domestic animals (Clop, Marcq, Takeda, Pirottin, Tordoir, Bib e, Bouix, Caiment, Elsen, Eychenne, Larzul, Laville, Meish, Milenkovic, Tobin, Charlier & Georges 2006;Daga et al 2013;Glatzer et al 2013;Kim et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Identification of SNPs in the 5′-flanking region and 3′-UTR of theMIHgene and their association with precocity of the Chinese mitten crabEriocheir sinensis

Tang

et al. 2014

Aquac Res

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Moult-inhibiting hormone (MIH), an important regulator of steroidogenesis, inhibits the synthesis of ecdysteroid in Y-organ (YO) and plays a significant role in the regulation of moulting and postembryonic development of crustacean. Because unsuccessful moulting have been widely observed in precocious crabs, we investigated whether genetic variants in the 5 0 -flanking region and 3 0 -untranslated region (3 0 -UTR) of the MIH gene are associated with precocity of the Chinese mitten crab. Thirty individual DNA samples were sequenced to search for SNPs in the 5 0 -flanking region and 3 0 -UTR of the MIH gene. Five SNPs (g.196 T>A, g.230 C>T, g.305 T>C, g.323 C>A and g.372 C>T) in the 5 0 -flanking region and 6 SNPs (g.2677 C>T, g.2759 T>A, g.2807 T>C, g.3042 A>G, g.3088 T>G and g.3295 T>G) in the 3 0 -UTR of the MIH gene were selected for the individual genotyping in a two-stage association study. We found that a SNP g.3088 T>G in the 3 0 -UTR of MIH gene was consistently associated with precocity of the Chinese mitten crab in stage 1 and stage 2, with a per-allele OR (Odds Ratio) of 1.469 (95% CI: 1.169-1.844) after two stages combined (P = 0.001). However, no significant associations were observed between the other 10 SNPs and precocity of the Chinese mitten crab. To our best knowledge, this is the first association study between various SNP genotypes and phenotype attributes in Chinese mitten crab. Our findings suggest that the SNP g.3088 T>G may be a candidate marker for effective marker-assisted selection to decrease the precocity of the Chinese mitten crab in future studies.

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“…PCR direct sequencing with DNA derived from heterozygotes confirmed the SNP (Figure ). The risk allele was a candidate allele of polledness in Holstein (Glatzer et al, ). Polledness in cattle is an autosomal dominant trait; however, all heterozygotes had horns in this study.…”

Section: Resultsmentioning

confidence: 99%

Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle

Sasaki

Muraki

Inoue

et al. 2019

Animal Science Journal

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Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position‐unassigned SNPs, or “buried SNPs” include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.

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A Single Nucleotide Polymorphism within the Interferon Gamma Receptor 2 Gene Perfectly Coincides with Polledness in Holstein Cattle

Cited by 14 publications

References 18 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

Identification of SNPs in the 5′-flanking region and 3′-UTR of theMIHgene and their association with precocity of the Chinese mitten crabEriocheir sinensis

Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle

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