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Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature

Nature Genetics volume 43, pages 405–413 (2011)Cite this article

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Abstract

We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a ∼780-kb interval using a Hidden Markov Model–based approach that simultaneously exploits linkage and linkage disequilibrium. We re-sequenced the interval in six sires with known QTL genotype and identified 13 clustered candidate quantitative trait nucleotides (QTNs) out of >9,572 discovered variants. We eliminated five candidate QTNs by studying the phenotypic effect of a recombinant haplotype identified in a breed diversity panel. We show that the QTL influences fetal expression of seven of the nine genes mapping to the ∼780-kb interval. We further show that two of the eight candidate QTNs, mapping to the PLAG1-CHCHD7 intergenic region, influence bidirectional promoter strength and affect binding of nuclear factors. By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene.

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Figure 1: Linkage mapping of a body size QTL in an HF × J F2 cross.
Figure 2: Linkage and LD fine-mapping of the body size QTL.
Figure 3: Annotated genes and markers within the re-sequenced ∼780-kb QTL interval.
Figure 4: Effect of QTN genotype on the expression level of nine positional candidate genes in fetal liver, bone, muscle and brain.
Figure 5: Effects of ss319607405 and ss319607406 on bidirectional promoter strength using a luciferase reporter assay.
Figure 6: Effect of QTL genotype on binding of trans-acting nuclear factors.
Figure 7: Exploiting a naturally occurring null allele to exclude the causality of the CHCHD7 gene.

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Acknowledgements

This work was funded by Livestock Improvement Corporation (LIC; Hamilton, New Zealand) and by grants from the Unit of Animal Genomics, the University of Liège, the Communauté Française de Belgique (ARC Biomod) and the Belgian Science Policy Organisation (SSTC Genefunc PAI). T.D. is Research Associate of the Fond National de Recherche Scientifique. We are grateful for the support of the GIGA-R sequencing core facility.

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Author notes

  1. Latifa Karim, Haruko Takeda, Li Lin and Tom Druet: These authors contributed equally to this work.

Authors and Affiliations

  1. Unit of Animal Genomics, Interdisciplinary Institute of Applied Genomics (GIGA-R) and Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium

    Latifa Karim, Haruko Takeda, Li Lin, Tom Druet, Denis Baurain, Nadine Cambisano, Frédéric Farnir, Bernard Grisart, Michel Georges & Wouter Coppieters

  2. Livestock Improvement Corporation (LIC), Hamilton, New Zealand

    Juan A C Arias, Bevin L Harris, Mike D Keehan & Richard J Spelman

  3. ViaLactia BioSciences, Auckland, New Zealand

    Stephen R Davis

  4. DairyNZ, Hamilton, New Zealand

    Mathew D Littlejohn

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Contributions

J.A.C.A., B.L.H., M.D.K. and R.J.S. designed and performed line-cross QTL mapping in the F2 population. L.K., L.L., N.C., B.G. and W.C. developed additional BTA14 markers, genotyped the F2 population and performed half-sibling QTL mapping. T.D., F.F. and W.C. performed combined linkage and LD QTL fine mapping. L.K. and W.C. performed high throughput resequencing and analysis of the 780-kb confidence interval. L.L. performed sequence finishing of the 780-kb interval. L.K., N.C. and W.C. performed haplotype analysis in the breed diversity panel. S.R.D. collected fetal samples. L.K., H.T. and L.L. checked the integrity of the open reading frames. H.T., L.L., M.D.L. and M.G. performed quantitative RT-PCR experiments. H.T. performed the allelic imbalance tests. H.T. performed the reporter assays. L.K. and H.T. performed the EMSA. S.R.D., M.D.K. and R.J.S. generated and performed initial analysis of the transcriptome data. T.D., D.B. and W.C. performed eQTL analyses. L.L. analyzed the effect of the CHCHD7 splice site variant. W.C. and T.D. performed the QCA. M.G. designed experiments, analyzed data and wrote the manuscript.

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Correspondence to Michel Georges.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–12, Supplementary Tables 1–3 and Supplementary Note. (PDF 6262 kb)

Supplementary Table 4

Expression data for eQTL analysis (XLS 190 kb)

Supplementary Table 5

Pedigree file for eQTL analysis (XLS 247 kb)

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Karim, L., Takeda, H., Lin, L. et al. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat Genet 43, 405–413 (2011). https://doi.org/10.1038/ng.814

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