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Transcriptome analysis and identification of significantly differentially expressed genes in Holstein calves subjected to severe thermal stress

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Abstract

RNA-Seq analysis was used to characterize transcriptome response of Holstein calves to thermal stress. A total of eight animals aged between 2 and 3 months were randomly selected and subjected to thermal stress corresponding to a temperature humidity index of 95 in an environmentally controlled house for 12 h consecutively for 3 days. A set of 15,787 unigenes were found to be expressed and after a threshold of threefold change, and a Q value <0.05; 502, 394, and 376 genes were found to be differentially expressed on days 1, 2, and 3 out of which 343, 261 and 256 genes were upregulated and 159, 133, and 120 genes were downregulated. Only 356 genes out of these were expressed on all 3 days, and only they were considered as significantly differentially expressed. KEGG pathway analysis revealed that ten pathways were significantly enriched; the top two among them were protein processing in endoplasmic reticulum and MAPK signaling pathways. These results suggest that thermal stress triggered a complex response in Holstein calves and the animals adjusted their physiological and metabolic processes to survive. Many of the genes identified in this study have not been previously reported to be involved in thermal stress response. The results of this study extend our understanding of the animal’s response to thermal stress and some of the identified genes may prove useful in the efforts to breed Holstein cattle with superior thermotolerance, which might help in minimizing production loss due to thermal stress.

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Acknowledgments

This work contributes to the internal project “Cooperative Research Program for Agriculture Science and Technology Development (ID PJ01005002)” and was supported by the National Institute of Animal Science in Rural Development Administration of Korea. Krishnamoorthy Srikanth was supported by 2016 Postdoctoral Fellowship Program of the National Institute of Animal Science, Rural Development Administration, Republic of Korea.

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  1. Animal Genomics and Bioinformatics Division, National Institute of Animal Science, 1500, K & P road, Iseo, Wanju, JB, 55365, South Korea

    Krishnamoorthy Srikanth, Eunjin Lee, Anam Kwan, Youngjo Lim, Gulwon Jang & Hoyoung Chung

  2. Environmental Science Division, National Institute of Animal Science, 1500, K & P road, Iseo, Wanju, JB, 55365, South Korea

    Junyep Lee

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Supplementary File 1

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Supplementary File 2

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Supplemental Fig. 1

Rectal temperature measurement of Holstein calves during the experimental period (PNG 238 kb)

Supplemental Fig. 2

Head temperature measurement of Holstein calves during the experimental period (PNG 185 kb)

Supplemental Fig. 3

Body temperature measurement of Holstein calves during the experimental period (PNG 168 kb)

Supplemental Fig. 4

a Scatter plots of all the genes transcribed on days 1, 2, and 3. Red indicates positive expression and blue indicates negative expression. b A Venn diagram of differentially expressed genes (3 FC and FDR <0.05) on days 1, 2, and 3 (PNG 256 kb)

Supplemental Fig. 5

Hierarchical clustering of all the DEGs that responded to thermal stress. Red corresponds to upregulation and yellow corresponds to downregulation (PNG 43 kb)

Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Table 4

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Srikanth, K., Lee, E., Kwan, A. et al. Transcriptome analysis and identification of significantly differentially expressed genes in Holstein calves subjected to severe thermal stress. Int J Biometeorol 61, 1993–2008 (2017). https://doi.org/10.1007/s00484-017-1392-3

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