Animals' Transcriptome Response to Environment Change

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (15 July 2021) | Viewed by 15899

Special Issue Editors

Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, Jeollabuk-do, Korea
Interests: genomic prediction (selection); GWAS, RNA-seq; multi-omics integration; climate change in animals
Special Issues, Collections and Topics in MDPI journals
Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
Interests: NGS; animal genomics; transcriptomics; epigenomics; metagenomics

Special Issue Information

Dear Colleagues,

As we know, animals are exposed to diverse environmental (non-genetic) conditions in different geographical locations, different feeding and rearing systems. So, animals are able to adapt with the help of their dynamically changing genomic architecture. Transcriptome analysis has emerged as a powerful tool to explore the physiological response to the environment and identify the genes with large effect on adaptive response to the diverse environment.

In this Special Issue, we invite manuscripts that reports of the genes and pathways that respond to multiple environmental factors such as temperature, humidity, altitude, longitude, feeding composition, supplements, rearing facility etc. in livestock animals. This Special Issue also aims to bring together the latest advances in the subject of multi-omics in livestock animals under different environmental conditions.

Dr. Jong-Eun Park
Dr. Himansu Kumar
Guest Editors

Manuscript Submission Information

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Keywords

  • Transcriptomics
  • RNA-Seq.
  • Genetic response
  • Environmental factors
  • Livestock animal

Published Papers (5 papers)

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Research

15 pages, 3290 KiB  
Article
Transcriptomic Response under Heat Stress in Chickens Revealed the Regulation of Genes and Alteration of Metabolism to Maintain Homeostasis
by Hana Kim, Hyeran Kim, Pilnam Seong, Devender Arora, Donghyun Shin, Woncheoul Park and Jong-Eun Park
Animals 2021, 11(8), 2241; https://0-doi-org.brum.beds.ac.uk/10.3390/ani11082241 - 30 Jul 2021
Cited by 12 | Viewed by 4224
Abstract
Chicken is important livestock that serves as a vital food source which remain largely affected by heat stress. Therefore, we performed the transcriptome analysis to help understand the mechanisms of heat stress response in chickens. In the animal experiments, we grouped them into [...] Read more.
Chicken is important livestock that serves as a vital food source which remain largely affected by heat stress. Therefore, we performed the transcriptome analysis to help understand the mechanisms of heat stress response in chickens. In the animal experiments, we grouped them into a normal and severe at 21 and 33 °C, with identified physiologic parameters for 2-weeks. Subsequently, RNA-seq analysis was performed to identify DEGs with a false discovery rate < 0.05 and a fold change ≥ 1.5. In the physiological parameters, we observed average daily gain was declined, rectal temperature and respiration rate was increased in severe group. Among total 245 DEGs, 230 and 15 genes were upregulated and downregulated, respectively. In upregulated DEGs, HSPs, MYLK2, and BDKRB1 genes were identified as key genes in heat stress. The KEGG pathway analysis showed involvement in the ATP metabolic process, MAPK signaling pathway and calcium signaling pathway with related protein processing and synthesis. In conclusion, with induced heat stress, such changes in physiologic parameters alter the neuroendocrine system, and we observed that the heat stress environment regulates such Heat shock protein genes to protect the cells and proteins from an altered metabolism. These findings provide a more comprehensive understanding of the heat stress response in poultry. Full article
(This article belongs to the Special Issue Animals' Transcriptome Response to Environment Change)
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14 pages, 2958 KiB  
Article
Transcriptome Profiling Reveals a Divergent Adaptive Response to Hyper- and Hypo-Salinity in the Yellow Drum, Nibea albiflora
by Xiang Zhao, Zhicheng Sun, Tianxiang Gao and Na Song
Animals 2021, 11(8), 2201; https://0-doi-org.brum.beds.ac.uk/10.3390/ani11082201 - 25 Jul 2021
Cited by 6 | Viewed by 3110
Abstract
The yellow drum (Nibea albiflora) is an important marine economic fish that is widely distributed in the coastal waters of the Northwest Pacific. In order to understand the molecular regulatory mechanism of the yellow drum under salinity stress, in the present [...] Read more.
The yellow drum (Nibea albiflora) is an important marine economic fish that is widely distributed in the coastal waters of the Northwest Pacific. In order to understand the molecular regulatory mechanism of the yellow drum under salinity stress, in the present study, transcriptome analysis was performed under gradients with six salinities (10, 15, 20, 25, 30, and 35 psu). Compared to 25 psu, 907, 1109, 1309, 18, and 243 differentially expressed genes (DEGs) were obtained under 10, 15, 20, 30, and 35 psu salinities, respectively. The differential gene expression was further validated by quantitative real-time PCR (qPCR). The results of the tendency analysis showed that all DEGs of the yellow drum under salinity fluctuation were mainly divided into three expression trends. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the PI3K-Akt signaling pathway, Jak-STAT signaling pathway as well as the glutathione metabolism and steroid biosynthesis pathways may be the key pathways for the salinity adaptive regulation mechanism of the yellow drum. G protein-coupled receptors (GPCRs), the solute carrier family (SLC), the transient receptor potential cation channel subfamily V member 6 (TRPV6), isocitrate dehydrogenase (IDH1), and fructose-bisphosphate aldolase C-B (ALDOCB) may be the key genes in the response of the yellow drum to salinity stress. This study explored the transcriptional patterns of the yellow drum under salinity stress and provided fundamental information for the study of salinity adaptability in this species. Full article
(This article belongs to the Special Issue Animals' Transcriptome Response to Environment Change)
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16 pages, 2331 KiB  
Article
Endocrine Signals Altered by Heat Stress Impact Dairy Cow Mammary Cellular Processes at Different Stages of the Dry Period
by Véronique Ouellet, João Negrao, Amy L. Skibiel, Valerie A. Lantigua, Thiago F. Fabris, Marcela G. Marrero, Bethany Dado-Senn, Jimena Laporta and Geoffrey E. Dahl
Animals 2021, 11(2), 563; https://0-doi-org.brum.beds.ac.uk/10.3390/ani11020563 - 21 Feb 2021
Cited by 6 | Viewed by 2211
Abstract
Hormonal alterations occurring under late gestation heat stress may disturb mammary gland remodelling, resulting in a reduced milk yield during the subsequent lactation. We investigated the effects of an altered endocrine environment on mammary gene expression at different stages of the dry period. [...] Read more.
Hormonal alterations occurring under late gestation heat stress may disturb mammary gland remodelling, resulting in a reduced milk yield during the subsequent lactation. We investigated the effects of an altered endocrine environment on mammary gene expression at different stages of the dry period. Mammary gland biopsies from in vivo-cooled (CL) or heat-stressed (HT) cows were collected at d 3 and 35 relative to dry-off and divided into explants. Explants were incubated in vitro for 24 h in one of three media: Basal: no prolactin or estrogen; CL-mimic: Basal + low prolactin + high 17β-estradiol, or HT-mimic: Basal + high prolactin + low 17β-estradiol. Real time qPCR was used to quantify gene expression. We established that late-gestation heat stress changes the expression of prolactin and oestrogen receptors, downregulates genes involved in apoptosis, autophagy and proliferation at d 3 and upregulates genes related to those cellular processes at d 35. Moreover, compared with in vivo treatments, we showed that the expression of fewer genes was impacted by in vitro treatments which aimed to mimic the hormonal response of cows exposed to a different environment. Further research will continue to uncover the mechanisms behind the production impairments caused by late-gestation heat stress. Full article
(This article belongs to the Special Issue Animals' Transcriptome Response to Environment Change)
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14 pages, 1778 KiB  
Article
Cardiac Transcriptomics Reveals That MAPK Pathway Plays an Important Role in Hypoxia Tolerance in Bighead Carp (Hypophthalmichthys nobilis)
by Ying Zhou, Weiwei Luo, Xiaomu Yu, Junru Wang, Yizhao Feng and Jingou Tong
Animals 2020, 10(9), 1483; https://0-doi-org.brum.beds.ac.uk/10.3390/ani10091483 - 24 Aug 2020
Cited by 14 | Viewed by 2304
Abstract
As aquatic animals, fishes often encounter various situations of low oxygen, and they have evolved the ability to respond to hypoxia stress. Studies of physiological and molecular responses to hypoxia stress are essential to clarify genetic mechanisms underlying hypoxia tolerance in fish. In [...] Read more.
As aquatic animals, fishes often encounter various situations of low oxygen, and they have evolved the ability to respond to hypoxia stress. Studies of physiological and molecular responses to hypoxia stress are essential to clarify genetic mechanisms underlying hypoxia tolerance in fish. In this study, we performed acute hypoxia treatment in juvenile bighead carp (Hypophthalmicthys nobilis) by decreasing water O2 from 6.5 mg/L to 0.5 mg/L in three hours. This hypoxia stress resulted in a significant increase in blood lactate and serum glucose. Comparisons of heart transcriptome among hypoxia tolerant (HT), hypoxia sensitive (HS), and normoxia control (NC) groups showed that 820, 273, and 301 differentially expressed genes (DEGs) were identified in HS vs. HT, NC vs. HS, and NC vs. HT (false discovery rate (FDR) < 0.01, Fold Change> 2), respectively. KEGG pathway enrichment showed that DEGs between HS and HT groups were mainly involved in mitogen-activated protein kinase (MAPK) signaling, insulin signaling, apoptosis, tight junction and adrenergic signaling in cardiomyocytes pathways, and DEGs in MAPK signaling pathway played a key role in cardiac tolerance to hypoxia. Combined with the results of our previous cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis of hypoxia stress in this species, such genes as stbp2, ttn, mapk, kcnh, and tnfrsf were identified in both studies, representing the significance of these DEGs in hypoxia tolerance in bighead carp. These results provide insights into the understanding of genetic modulations for fish heart coping with hypoxia stress and generate basic resources for future breeding studies of hypoxia resistance in bighead carp. Full article
(This article belongs to the Special Issue Animals' Transcriptome Response to Environment Change)
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18 pages, 2238 KiB  
Article
Comparative Transcriptomic Analysis of the Pituitary Gland between Cattle Breeds Differing in Growth: Yunling Cattle and Leiqiong Cattle
by Xubin Lu, Abdelaziz Adam Idriss Arbab, Zhipeng Zhang, Yongliang Fan, Ziyin Han, Qisong Gao, Yujia Sun and Zhangping Yang
Animals 2020, 10(8), 1271; https://0-doi-org.brum.beds.ac.uk/10.3390/ani10081271 - 25 Jul 2020
Cited by 11 | Viewed by 2780
Abstract
The hypothalamic–pituitary–thyroid (HPT) axis hormones regulate the growth and development of ruminants, and the pituitary gland plays a decisive role in this process. In order to identify pivotal genes in the pituitary gland that could affect the growth of cattle by regulating the [...] Read more.
The hypothalamic–pituitary–thyroid (HPT) axis hormones regulate the growth and development of ruminants, and the pituitary gland plays a decisive role in this process. In order to identify pivotal genes in the pituitary gland that could affect the growth of cattle by regulating the secretion of hormones, we detected the content of six HPT hormones related to growth in the plasma of two cattle breeds (Yunling and Leiqiong cattle, both also known as the zebu cattle) with great differences in growth and compared the transcriptome data of their pituitary glands. Our study found that the contents of GH, IGF, TSH, thyroxine, triiodothyronine, and insulin were significantly different between the two breeds, which was the main cause of the difference in growth; 175 genes were identified as differentially expressed genes (DEGs). Functional association analyses revealed that DEGs were mainly involved in the process of transcription and signal transduction. Combining the enrichment analysis and protein interaction analysis, eight DEGs were predicted to control the growth of cattle by affecting the expression of growth-related hormones in the pituitary gland. In summary, our results suggested that SLC38A1, SLC38A3, DGKH, GNB4, GNAQ, ESR1, NPY, and GAL are candidates in the pituitary gland for regulating the growth of Yunling and Leiqiong cattle by regulating the secretion of growth-related hormones. This study may help researchers further understand the growth mechanisms and improve the artificial selection of zebu cattle. Full article
(This article belongs to the Special Issue Animals' Transcriptome Response to Environment Change)
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