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A nonsense mutation in PLD4 is associated with a zinc deficiency-like syndrome in Fleckvieh cattle.

Jung S, Pausch H, Langenmayer MC, Schwarzenbacher H, Majzoub-Altweck M, Gollnick NS, Fries R - BMC Genomics (2014)

Bottom Line: The deleterious effect of the mutation is manifested in a significantly lower survival rate of descendants from risk matings when compared with the survival rate of descendants from non-risk matings.The deleterious allele has an estimated frequency of 1.1% in the Fleckvieh population.Our results provide strong evidence that a newly identified recessive disorder in the Fleckvieh population is caused by a nonsense mutation in PLD4, most likely resulting in an impaired function of the encoded protein.

View Article: PubMed Central - PubMed

Affiliation: Chair of Animal Breeding, Technische Universitaet Muenchen, 85354 Freising, Germany. ruedi.fries@tum.de.

ABSTRACT

Background: Bovine hereditary zinc deficiency (BHZD) is an autosomal recessive disorder of cattle, first described in Holstein-Friesian animals. Affected calves suffer from severe skin lesions and show a poor general health status. Recently, eight calves with the phenotypic appearance of BHZD have been reported in the Fleckvieh cattle population.

Results: In spite of the similar disease phenotypes, SLC39A4, the gene responsible for BHZD in Holstein-Friesian was excluded as underlying gene for the disorder in the affected Fleckvieh calves. In order to identify the disease-associated region, genotypes of eight affected calves obtained with the Illumina BovineHD BeadChip comprising 777,962 SNPs were contrasted with the genotypes of 1,339 unaffected animals. A strong association signal was observed on chromosome 21 (P = 5.87 × 10(-89)). Autozygosity mapping in the eight affected animals revealed a common segment of extended homozygosity encompassing 1,023 kb (BTA 21: 70,550,045 - 71,573,501). This region contains 17 genes/transcripts, among them two genes encoding gastro-intestinal zinc transporters (CRIP1, CRIP2). However, no mutation that was compatible with recessive inheritance could be detected in these candidate genes. One of the affected calves was re-sequenced together with 42 unaffected Fleckvieh animals. Analysis of the sequencing data revealed a nonsense mutation (p.W215X) in a phospholipase encoding gene (PLD4) as candidate causal polymorphism. To confirm the causality, genotypes of the p.W215X-mutation were obtained from 3,650 animals representing three different breeds. None of the unaffected animals was homozygous for the defect allele, while all eight affected calves were homozygous. The deleterious effect of the mutation is manifested in a significantly lower survival rate of descendants from risk matings when compared with the survival rate of descendants from non-risk matings. The deleterious allele has an estimated frequency of 1.1% in the Fleckvieh population.

Conclusion: Our results provide strong evidence that a newly identified recessive disorder in the Fleckvieh population is caused by a nonsense mutation in PLD4, most likely resulting in an impaired function of the encoded protein. Although the phenotype of affected calves strongly resembles BHZD, a zinc deficiency resulting from malabsorption is unlikely to be responsible for the diseased Fleckvieh calves.

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A nonsense mutation inPLD4is perfectly associated with the disease phenotype. Genomic structure of bovine PLD4(A). Grey boxes represent exons. The red box represents exon 6 including rs378824791, introducing a premature stop codon. Genomic and protein sequence of exon 6 of PLD4(B). The affected codon (p.W215X, TGG → TGA) is highlighted with red colour.
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Fig4: A nonsense mutation inPLD4is perfectly associated with the disease phenotype. Genomic structure of bovine PLD4(A). Grey boxes represent exons. The red box represents exon 6 including rs378824791, introducing a premature stop codon. Genomic and protein sequence of exon 6 of PLD4(B). The affected codon (p.W215X, TGG → TGA) is highlighted with red colour.

Mentions: The compatible InDel-polymorphism (rs381259516) is also segregating among 191 non-Fleckvieh animals (128 Holstein, 15 Jersey, 48 Angus), which have been sequenced in the context of the 1000 bull genomes project [15]. No regulatory or functional consequence was predicted for the compatible SNP (rs385301007) in intron 30 of LOC100299595. Manual re-annotation of INF2 revealed that the presumed missense mutation (rs384306864) is not located within the coding region of the gene (Additional file 3). Therefore, these three variants were excluded as being causal for the described phenotype. Only a point mutation in exon 6 of PLD4, resulting in a premature stop codon (c.G645A, p.W215X, BTA 21:71,001,232 bp, rs378824791) (Figure 4, Additional file 3), was retained as candidate causal mutation. The resulting protein is shortened by 273 amino acids and lacks essential domains for enzymatic activity [16, 17]. The mutation was confirmed by Sanger sequencing (Additional file 4).Figure 4


A nonsense mutation in PLD4 is associated with a zinc deficiency-like syndrome in Fleckvieh cattle.

Jung S, Pausch H, Langenmayer MC, Schwarzenbacher H, Majzoub-Altweck M, Gollnick NS, Fries R - BMC Genomics (2014)

A nonsense mutation inPLD4is perfectly associated with the disease phenotype. Genomic structure of bovine PLD4(A). Grey boxes represent exons. The red box represents exon 6 including rs378824791, introducing a premature stop codon. Genomic and protein sequence of exon 6 of PLD4(B). The affected codon (p.W215X, TGG → TGA) is highlighted with red colour.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4117962&req=5

Fig4: A nonsense mutation inPLD4is perfectly associated with the disease phenotype. Genomic structure of bovine PLD4(A). Grey boxes represent exons. The red box represents exon 6 including rs378824791, introducing a premature stop codon. Genomic and protein sequence of exon 6 of PLD4(B). The affected codon (p.W215X, TGG → TGA) is highlighted with red colour.
Mentions: The compatible InDel-polymorphism (rs381259516) is also segregating among 191 non-Fleckvieh animals (128 Holstein, 15 Jersey, 48 Angus), which have been sequenced in the context of the 1000 bull genomes project [15]. No regulatory or functional consequence was predicted for the compatible SNP (rs385301007) in intron 30 of LOC100299595. Manual re-annotation of INF2 revealed that the presumed missense mutation (rs384306864) is not located within the coding region of the gene (Additional file 3). Therefore, these three variants were excluded as being causal for the described phenotype. Only a point mutation in exon 6 of PLD4, resulting in a premature stop codon (c.G645A, p.W215X, BTA 21:71,001,232 bp, rs378824791) (Figure 4, Additional file 3), was retained as candidate causal mutation. The resulting protein is shortened by 273 amino acids and lacks essential domains for enzymatic activity [16, 17]. The mutation was confirmed by Sanger sequencing (Additional file 4).Figure 4

Bottom Line: The deleterious effect of the mutation is manifested in a significantly lower survival rate of descendants from risk matings when compared with the survival rate of descendants from non-risk matings.The deleterious allele has an estimated frequency of 1.1% in the Fleckvieh population.Our results provide strong evidence that a newly identified recessive disorder in the Fleckvieh population is caused by a nonsense mutation in PLD4, most likely resulting in an impaired function of the encoded protein.

View Article: PubMed Central - PubMed

Affiliation: Chair of Animal Breeding, Technische Universitaet Muenchen, 85354 Freising, Germany. ruedi.fries@tum.de.

ABSTRACT

Background: Bovine hereditary zinc deficiency (BHZD) is an autosomal recessive disorder of cattle, first described in Holstein-Friesian animals. Affected calves suffer from severe skin lesions and show a poor general health status. Recently, eight calves with the phenotypic appearance of BHZD have been reported in the Fleckvieh cattle population.

Results: In spite of the similar disease phenotypes, SLC39A4, the gene responsible for BHZD in Holstein-Friesian was excluded as underlying gene for the disorder in the affected Fleckvieh calves. In order to identify the disease-associated region, genotypes of eight affected calves obtained with the Illumina BovineHD BeadChip comprising 777,962 SNPs were contrasted with the genotypes of 1,339 unaffected animals. A strong association signal was observed on chromosome 21 (P = 5.87 × 10(-89)). Autozygosity mapping in the eight affected animals revealed a common segment of extended homozygosity encompassing 1,023 kb (BTA 21: 70,550,045 - 71,573,501). This region contains 17 genes/transcripts, among them two genes encoding gastro-intestinal zinc transporters (CRIP1, CRIP2). However, no mutation that was compatible with recessive inheritance could be detected in these candidate genes. One of the affected calves was re-sequenced together with 42 unaffected Fleckvieh animals. Analysis of the sequencing data revealed a nonsense mutation (p.W215X) in a phospholipase encoding gene (PLD4) as candidate causal polymorphism. To confirm the causality, genotypes of the p.W215X-mutation were obtained from 3,650 animals representing three different breeds. None of the unaffected animals was homozygous for the defect allele, while all eight affected calves were homozygous. The deleterious effect of the mutation is manifested in a significantly lower survival rate of descendants from risk matings when compared with the survival rate of descendants from non-risk matings. The deleterious allele has an estimated frequency of 1.1% in the Fleckvieh population.

Conclusion: Our results provide strong evidence that a newly identified recessive disorder in the Fleckvieh population is caused by a nonsense mutation in PLD4, most likely resulting in an impaired function of the encoded protein. Although the phenotype of affected calves strongly resembles BHZD, a zinc deficiency resulting from malabsorption is unlikely to be responsible for the diseased Fleckvieh calves.

Show MeSH
Related in: MedlinePlus