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Gene networks for total number born in pigs across divergent environments

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Abstract

For reproductive traits such as total number born (TNB), variance due to different environments is highly relevant in animal breeding. In this study, we aimed to perform a gene-network analysis for TNB in pigs across different environments using genomic reaction norm models. Thus, based on relevant single-nucleotide polymorphisms and linkage disequilibrium blocks across environments obtained from GWAS, different sets of candidate genes having biological roles linked to TNB were identified. Network analysis across environment levels resulted in gene interactions consistent with known mammal’s fertility biology, captured relevant transcription factors for TNB biology and pointing out different sets of candidate genes for TNB in different environments. These findings may have important implication for animal production, as optimal breeding may vary depending on later environments. Based on these results, genomic diversity was identified and inferred across environments highlighting differential genetic control in each scenario.

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Acknowledgements

This study was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG), National Institute of Science and Technology–Animal Science, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/NUFFIC, CAPES/DGU, and CAPES/PDSE), and Wageningen University and Topigs Norsvin Research Center.

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Authors and Affiliations

  1. Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570000, Brazil

    Lucas L. Verardo, Fabyano F. Silva, Paulo S. Lopes & Simone E. F. Guimarães

  2. Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands

    Ole Madsen & Martien A. M. Groenen

  3. Topigs Norsvin Research Center, 6641 SZ, Beuningen, The Netherlands

    Marcos S. Lopes, Pramod Mathur & Egbert F. Knol

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  1. Lucas L. Verardo
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  9. Simone E. F. Guimarães
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Correspondence to Lucas L. Verardo.

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Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1—Number of records (y axis) across the number of sires (x axis) used in this study. (PDF 50 KB)

Supplementary material 2 (PDF 45 KB)

Supplementary material 3 (XLSX 56 KB)

335_2017_9696_MOESM4_ESM.pdf

Supplementary Fig. 2—Manhattan plots for the Low, Mean and High environments groups. It was build based on the average SNP variance (y axis) of the levels from each group over chromosome regions (x axis). (PDF 529 KB)

Supplementary material 5 (XLSX 115 KB)

335_2017_9696_MOESM6_ESM.xlsx

Supplementary Table 4—Biological process identified for the three sets of Transcription factors (TF) identified for total number born in each HYM group (Low, Mean and High). The table presents the gene ontology identification (GO-ID), p-values, biological process description and TFs in the test set (XLSX 67 KB)

335_2017_9696_MOESM7_ESM.pdf

Supplementary Fig. 3—Gene-Transcription Factor (TF) network for the Low group. Genes overlapping with relevant SNPs and/or LD blocks for TNB in the Low group (blue nodes), and in common to all groups (pink nodes). Green nodes with blue border are genes in common to Mean group. Associated with these genes, we have TFs (yellow nodes). The node size corresponds to the network analyses (Cytoscape) score where bigger nodes represent higher edges density associated with the number of TF binding sites. (PDF 339 KB)

335_2017_9696_MOESM8_ESM.pdf

Supplementary Fig. 4—Gene-Transcription Factor (TF) network for the Mean group. Genes overlapping with relevant SNPs and/or LD blocks for TNB in the Mean group (green nodes), and in common to all groups (pink nodes). Green nodes with blue and red borders are genes in common to Low and High group, respectively. Associated with these genes, we have TFs (yellow nodes). The node size corresponds to the network analyses (Cytoscape) score where bigger nodes represent higher edges density associated with the number of TF binding sites. (PDF 361 KB)

335_2017_9696_MOESM9_ESM.pdf

Supplementary Fig. 5—Gene-Transcription Factor (TF) network for the High group. Genes overlapping with relevant SNPs and/or LD blocks for TNB in the High group (red nodes), and in common to all groups (pink nodes). Green nodes with red borders are genes in common to Mean group. Associated with these genes, we have TFs (yellow nodes). The node size corresponds to the network analyses (Cytoscape) score where bigger nodes represent higher edges density associated with the number of TF binding sites. (PDF 368 KB)

335_2017_9696_MOESM10_ESM.pdf

Supplementary Fig. 6—Venn diagram showcasing the number of genes and TF in common between the networks from each group: Low, Mean and High. (PDF 24 KB)

335_2017_9696_MOESM11_ESM.pdf

Supplementary Fig. 7—Graph containing the 95% Confidence Interval (based on standard error for solutions of mixed models) for the random slopes (y axis) of the reaction norms for the total number born among 340 sires (horizontal line). (PDF 54 KB)

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Verardo, L.L., Lopes, M.S., Mathur, P. et al. Gene networks for total number born in pigs across divergent environments. Mamm Genome 28, 426–435 (2017). https://doi.org/10.1007/s00335-017-9696-5

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