Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Liu, Shenhe; Yue, Taohua; Ahmad, Muhammad Jamil; Hu, Xuehai; Zhang, Xinxin; Deng, Ting; Hu, Yan; He, Chao; Zhou, Yang; Yang, Liguo

doi:10.3390/genes11010068

Cited by 35 publications

(20 citation statements)

References 51 publications

(51 reference statements)

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“…In the study, the N50 length of unigenes was 1825 bp, indicating that the sequence assembly was high in quality and suitable for intensive research. Moreover, the N50 could be compared with those of other species [46][47][48]. The average length of the unigenes was larger (1050 bp) (Table 2), than those in previous studies, such as those of Myrica rubra (531 bp) [49] and Sorbus pohuashanensis (770 bp) [50].…”

Section: Discussionmentioning

confidence: 89%

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

DianYun¹,

Cheng²,

Li³

et al. 2020

Preprint

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Background: Dioscorea opposita is a monocotyledonous plant in the Dioscoreaceae family. The rhizome of D. opposita, known as “dioscoreae rhiaoma” or “Chinese yam”, is not only a well-known traditional Chinese medicine, but also a popular health food.Methods:In this study, the leaf and rhizome tissues of D. opposita were collected. Their transcriptome sequenceand were obtained using an Illumina Hiseq 4000 platform. The data was analyzed by bioinformatics software. Likewise, the consistent expression pattern of DEGs was validated with qRT-PCR analysis.Results: A total of 46,982,031 and 53,689,620 clean reads from leaf and rhizome tissues were acquired, respectively (SRP: PRJNA628588). 50,765 unigenes were obtained with an average length of 1050 base pairs (bp). A total of 13,259 significant differentially expressed genes (DEGs) were obtained from leaf versus rhizome tissues, including 5536 up-regulated and 7723 down-regulated unigenes. In addition, 20,607 simple sequence repeats (SSRs) were identified in this study. Conclusions:This study not only enriched the transcriptomic data of D. opposita, but also laid a foundation for the analysis of terpenoid synthesis pathway.

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Section: Discussionmentioning

confidence: 89%

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

DianYun¹,

Cheng²,

Li³

et al. 2020

Preprint

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“…Srikanth et al reported that genes and signaling pathways for innate immunity were altered in PBMCs in heat-stressed Holstein calves [ 37 ]. In addition, Liu et al conducted transcriptome analysis for whole blood to find potential regulatory genes related to heat tolerance in Holstein cows [ 38 ]. They selected heat-tolerant and non-heat-tolerant Holstein cows based on heat-stress scoring parameters such as rectal temperature, respiration rate, and milk yield change, then compared the gene expressions in blood immune cells between heat-tolerant and non-heat-tolerant cows.…”

Section: Discussionmentioning

confidence: 99%

Common and Differential Dynamics of the Function of Peripheral Blood Mononuclear Cells between Holstein and Jersey Cows in Heat-Stress Environment

Kim

Joo

Kim

et al. 2020

Animals

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Heat stress has been reported to affect the immunity of dairy cows. However, the mechanisms through which this occurs are not fully understood. Two breeds of dairy cow, Holstein and Jersey, have distinct characteristics, including productivity, heat resistance, and disease in high-temperature environments. The objective of this study is to understand the dynamics of the immune response of two breeds of dairy cow to environmental change. Ribonucleic acid sequencing (RNA-seq) results were analyzed to characterize the gene expression change of peripheral blood mononuclear cells (PBMCs) in Holstein and Jersey cows between moderate temperature-humidity index (THI) and high THI environmental conditions. Many of the differentially expressed genes (DEGs) identified are associated with critical immunological functions, particularly phagocytosis, chemokines, and cytokine response. Among the DEGs, CXCL3 and IL1A were the top down-regulated genes in both breeds of dairy cow, and many DEGs were related to antimicrobial immunity. Functional analysis revealed that cytokine and chemokine response-associated pathways in both Holstein and Jersey PBMCs were the most important pathways affected by the THI environmental condition. However, there were also breed-specific genes and pathways that altered according to THI environmental condition. Collectively, there were both common and breed-specific altered genes and pathways in Holstein and Jersey cows. The findings of this study expand our understanding of the dynamics of immunity in different breeds of dairy cow between moderate THI and high THI environmental conditions.

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“…Whole transcriptome analysis was used by many researchers to explore various fields of animal genetics ( 78 ). Liu et al ( 79 ) explored the genes associated with heat tolerance and the molecular mechanisms adopted by Chinese Holstein dairy cows through transcriptomic analysis. They reported nearly 200 differentially expressed genes (DEGs) in heat-stressed cattle when compared to their control.…”

Section: Genomic Applications For Identifying Superior Dairy Cows Bestmentioning

confidence: 99%

Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models

et al. 2021

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The current changing climate trend poses a threat to the productive efficacy and welfare of livestock across the globe. This review is an attempt to synthesize information pertaining to the applications of various genomic tools and statistical models that are available to identify climate-resilient dairy cows. The different functional and economical traits which govern milk production play a significant role in determining the cost of milk production. Thus, identification of these traits may revolutionize the breeding programs to develop climate-resilient dairy cattle. Moreover, the genotype–environment interaction also influences the performance of dairy cattle especially during a challenging situation. The recent advancement in molecular biology has led to the development of a few biotechnological tools and statistical models like next-generation sequencing (NGS), microarray technology, whole transcriptome analysis, and genome-wide association studies (GWAS) which can be used to quantify the molecular mechanisms which govern the climate resilience capacity of dairy cows. Among these, the most preferred option for researchers around the globe was GWAS as this approach jointly takes into account all the genotype, phenotype, and pedigree information of farm animals. Furthermore, selection signatures can also help to demarcate functionally important regions in the genome which can be used to detect potential loci and candidate genes that have undergone positive selection in complex milk production traits of dairy cattle. These identified biomarkers can be incorporated in the existing breeding policies using genomic selection to develop climate-resilient dairy cattle.

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Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Cited by 35 publications

References 51 publications

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

Common and Differential Dynamics of the Function of Peripheral Blood Mononuclear Cells between Holstein and Jersey Cows in Heat-Stress Environment

Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models

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