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A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes.

Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin CJ, Ashwell C, Gourichon D, Tixier-Boichard M, Hallböök F, Andersson L - PLoS Genet. (2015)

Bottom Line: Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES).In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos.We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event.

View Article: PubMed Central - PubMed

Affiliation: Science for Life Laboratory, Dept. of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Dept. of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

ABSTRACT
Duplex-comb (D) is one of three major loci affecting comb morphology in the domestic chicken. Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES). EOMES is a T-box transcription factor that is involved in mesoderm specification during gastrulation. In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos. The confinement of the ectopic expression of EOMES to the ectoderm is in stark contrast to the causal mechanisms underlying the two other major comb loci in the chicken (Rose-comb and Pea-comb) in which the transcription factors MNR2 and SOX5 are ectopically expressed strictly in the mesenchyme. Interestingly, the causal mutations of all three major comb loci in the chicken are now known to be composed of large-scale structural genomic variants that each result in ectopic expression of transcription factors. The Duplex-comb locus also illustrates the evolution of alleles in domestic animals, which means that alleles evolve by the accumulation of two or more consecutive mutations affecting the phenotype. We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event.

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Characterization of the Duplex-comb locus by genetic mapping and whole genome sequencing.(A) The genomic region to which the Duplex-comb locus was mapped to; adapted from the UCSC Genome Browser. Black bars represent regions identified from the backcross mapping population, IBD data from the 60K SNP chip, IBD data from whole genome sequencing and the 20 Kb duplication. SNPs identified from whole genome sequencing are shown in Green, Black and Red corresponding to homozygous reference allele, heterozygous, and homozygous variant allele, respectively. Although not currently annotated in the galGal3 genome build four genes are predicted in this region: EOMES (XM_426003.4), CMC1 (XM_418758.4), AZI2 (XM_418759.4) and RBMS3 (XM_004939420.1). The 20 Kb duplicated region is located ∼200 Kb upstream of EOMES. (B) Several regions within the 20 Kb duplication show elevated conservation and Genomic Evolutionary Rate Profiling (GERP) scores for 19 amniota (blue) and 3 neognath (red) species.
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pgen.1004947.g002: Characterization of the Duplex-comb locus by genetic mapping and whole genome sequencing.(A) The genomic region to which the Duplex-comb locus was mapped to; adapted from the UCSC Genome Browser. Black bars represent regions identified from the backcross mapping population, IBD data from the 60K SNP chip, IBD data from whole genome sequencing and the 20 Kb duplication. SNPs identified from whole genome sequencing are shown in Green, Black and Red corresponding to homozygous reference allele, heterozygous, and homozygous variant allele, respectively. Although not currently annotated in the galGal3 genome build four genes are predicted in this region: EOMES (XM_426003.4), CMC1 (XM_418758.4), AZI2 (XM_418759.4) and RBMS3 (XM_004939420.1). The 20 Kb duplicated region is located ∼200 Kb upstream of EOMES. (B) Several regions within the 20 Kb duplication show elevated conservation and Genomic Evolutionary Rate Profiling (GERP) scores for 19 amniota (blue) and 3 neognath (red) species.

Mentions: The largest region for which D*C and D*V individuals were IBD was 89 Kb in size (38,738,016–38,827,468 bp) which includes the entire 20 Kb duplicated region (Fig. 2A, IBD_reseq track). We identified 6 and 17 paired-end reads that spanned the duplication junctions in D*V and D*C individuals, again confirming the exact duplication breakpoints. We then used the sequencing data to explore if there were any other sequence variants that showed a perfect concordance with D*V and D*C like the 20 Kb duplication. Stringent SNP calling revealed only one high-quality SNP, at position 38,797,948 bp, within the IBD region that showed this pattern and that were not found in other chicken populations with the single comb phenotype [13]. This SNP did not occur at an evolutionary conserved site.


A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes.

Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin CJ, Ashwell C, Gourichon D, Tixier-Boichard M, Hallböök F, Andersson L - PLoS Genet. (2015)

Characterization of the Duplex-comb locus by genetic mapping and whole genome sequencing.(A) The genomic region to which the Duplex-comb locus was mapped to; adapted from the UCSC Genome Browser. Black bars represent regions identified from the backcross mapping population, IBD data from the 60K SNP chip, IBD data from whole genome sequencing and the 20 Kb duplication. SNPs identified from whole genome sequencing are shown in Green, Black and Red corresponding to homozygous reference allele, heterozygous, and homozygous variant allele, respectively. Although not currently annotated in the galGal3 genome build four genes are predicted in this region: EOMES (XM_426003.4), CMC1 (XM_418758.4), AZI2 (XM_418759.4) and RBMS3 (XM_004939420.1). The 20 Kb duplicated region is located ∼200 Kb upstream of EOMES. (B) Several regions within the 20 Kb duplication show elevated conservation and Genomic Evolutionary Rate Profiling (GERP) scores for 19 amniota (blue) and 3 neognath (red) species.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4366209&req=5

pgen.1004947.g002: Characterization of the Duplex-comb locus by genetic mapping and whole genome sequencing.(A) The genomic region to which the Duplex-comb locus was mapped to; adapted from the UCSC Genome Browser. Black bars represent regions identified from the backcross mapping population, IBD data from the 60K SNP chip, IBD data from whole genome sequencing and the 20 Kb duplication. SNPs identified from whole genome sequencing are shown in Green, Black and Red corresponding to homozygous reference allele, heterozygous, and homozygous variant allele, respectively. Although not currently annotated in the galGal3 genome build four genes are predicted in this region: EOMES (XM_426003.4), CMC1 (XM_418758.4), AZI2 (XM_418759.4) and RBMS3 (XM_004939420.1). The 20 Kb duplicated region is located ∼200 Kb upstream of EOMES. (B) Several regions within the 20 Kb duplication show elevated conservation and Genomic Evolutionary Rate Profiling (GERP) scores for 19 amniota (blue) and 3 neognath (red) species.
Mentions: The largest region for which D*C and D*V individuals were IBD was 89 Kb in size (38,738,016–38,827,468 bp) which includes the entire 20 Kb duplicated region (Fig. 2A, IBD_reseq track). We identified 6 and 17 paired-end reads that spanned the duplication junctions in D*V and D*C individuals, again confirming the exact duplication breakpoints. We then used the sequencing data to explore if there were any other sequence variants that showed a perfect concordance with D*V and D*C like the 20 Kb duplication. Stringent SNP calling revealed only one high-quality SNP, at position 38,797,948 bp, within the IBD region that showed this pattern and that were not found in other chicken populations with the single comb phenotype [13]. This SNP did not occur at an evolutionary conserved site.

Bottom Line: Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES).In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos.We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event.

View Article: PubMed Central - PubMed

Affiliation: Science for Life Laboratory, Dept. of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Dept. of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

ABSTRACT
Duplex-comb (D) is one of three major loci affecting comb morphology in the domestic chicken. Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES). EOMES is a T-box transcription factor that is involved in mesoderm specification during gastrulation. In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos. The confinement of the ectopic expression of EOMES to the ectoderm is in stark contrast to the causal mechanisms underlying the two other major comb loci in the chicken (Rose-comb and Pea-comb) in which the transcription factors MNR2 and SOX5 are ectopically expressed strictly in the mesenchyme. Interestingly, the causal mutations of all three major comb loci in the chicken are now known to be composed of large-scale structural genomic variants that each result in ectopic expression of transcription factors. The Duplex-comb locus also illustrates the evolution of alleles in domestic animals, which means that alleles evolve by the accumulation of two or more consecutive mutations affecting the phenotype. We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event.

Show MeSH
Related in: MedlinePlus