Physiological response and microRNA expression profiles in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to acute cold stress

Qiang, Jun; Cui, Yan T.; Tao, Fan; Bao, Wen J.; He, Jie; Li, Xia H.; Xu, Pao; Sun, Libo

doi:10.1038/s41598-017-18512-6

Cited by 24 publications

(12 citation statements)

References 59 publications

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“…A number of studies have used high-throughput next-generation sequencing technology to examine Atlantic salmon [ 14 ], channel catfish ( Ictalurus punctatus ) [ 20 ], zebrafish ( Danio rerio ) [ 21 , 23 , 48 ], Nile tilapia ( Oreochromis niloticus ) [ 24 , 49 , 50 , 51 ], Blue Tilapia ( Oreochromis aureus ) [ 9 ], Japanese flounder ( Paralichthys olivaceus ) [ 52 ], carp ( Cyprinus carpio haematopterus ) [ 22 ], milkfish ( Chanos chanos ) [ 53 ], rainbow trout [ 54 ], and other tropical and temperate aquaculture models of fish for low-temperature domestication-related regulatory mechanism research [ 48 , 55 ]. However, apart from systematically comparing gene expression patterns of specific tissue transcripts of the same fish species possessing different low-temperature tolerance genetic mutations, there is limited information regarding functional genes that can allow for molecular marker-assisted breeding.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, previous genetic studies have used microsatellite markers to facilitate genetic linkage map quantitative trait loci (QTL) mapping [ 17 ] and cold-tolerance marker development [ 7 , 18 , 19 ]. Several studies have attempted to further explore the genetic model and the genetic basis of cold-tolerance in fish [ 20 , 21 , 22 , 23 , 24 ]. However, the mechanisms and pathways underlying the observed variations in cold-tolerance among tilapia fish species remain unknown.…”

Section: Introductionmentioning

confidence: 99%

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Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Chu

Hsu

et al. 2021

Animals

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Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Chu

Hsu

et al. 2021

Animals

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“…The teleost kidney contains two sections: the head kidney, which comprises the anterior portion, and the trunk kidney which extends along the dorsal wall of the body cavity [14]. The head kidney is an important endocrine and hematopoietic-lymphoid organ [15], which plays a key role in initiation of the immune response [16]. The lung showed a large number of specific transcripts largely related to transmembrane ion transport, which aligns with the function of this organ.…”

Section: Discussionmentioning

confidence: 99%

Characterization and analysis of the transcriptome inArapaima gigasusing multi-tissue RNA-sequencing

Martins

Campos

Ribeiro-dos-Santos

et al. 2020

Preprint

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Arapaima gigas is a giant bony tongue air-breathing fish, and a promising species for aquaculture due to its particular features. However, there is still a lack of information on its biology and few transcriptome studies are available. Our aim was to characterize the transcriptome of arapaima in order to shed light on molecular networks contributing to its unique traits. Through RNA-sequencing, we generated a transcriptome from eight tissues (brain, pituitary, heart, muscle, kidney, lung, ovary, and testis) collected from arapaima adults specimens. Using a genome-guided strategy associated with homologous protein evidence, 57,706 transcripts were assembled, which aligned to 23,353 high confidence protein-coding genes. The analysis revealed a global view of expression patterns, as well as it allowed us to identify tissue-specific gene clusters, transcription factors within the clusters, and to compare expression patterns between male and female. These analyses has generated tissue-specific and sex-biased transcriptome profiles, which will be helpful to understand its molecular biology, evolution, and also guide future functional studies of the arapaima.

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“…Thus, AhpC and flavodoxin might also contribute to the survival of fish-adapted GBS strains in fish cells during the infection process. Notably, in Nile tilapia, the respiratory burst activity and phagocytic activity of macrophages decreases with both reduction in temperature and exposure time to the aquatic environment (Qiang et al, 2018 ). In this manner, a higher macrophage activity at high temperature could decrease the sensitivity of fish to pathogens.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Proteome of Fish-Pathogenic Streptococcus agalactiae Are Modulated by Temperature

et al. 2018

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Streptococcus agalactiae is one of the most important pathogens associated with streptococcosis outbreaks in Nile tilapia farms worldwide. High water temperature (above 27°C) has been described as a predisposing factor for the disease in fish. At low temperatures (below 25°C), fish mortalities are not usually observed in farms. Temperature variation can modulate the expression of genes and proteins involved in metabolism, adaptation, and bacterial pathogenicity, thus increasing or decreasing the ability to infect the host. This study aimed to evaluate the transcriptome and proteome of a fish-pathogenic S. agalactiae strain SA53 subjected to in vitro growth at different temperatures using a microarray and label-free shotgun LC-HDMSE approach. Biological triplicates of isolates were cultured in BHIT broth at 22 or 32°C for RNA and protein isolation and submitted for transcriptomic and proteomic analyses. In total, 1,730 transcripts were identified in SA53, with 107 genes being differentially expressed between the temperatures evaluated. A higher number of genes related to metabolism, mainly from the phosphotransferase system (PTS) and ATP-binding cassette (ABC) transport system, were upregulated at 32°C. In the proteome analysis, 1,046 proteins were identified in SA53, of which 81 were differentially regulated between 22 and 32°C. Proteins involved in defense mechanisms, lipid transport and metabolism, and nucleotide transport and metabolism were upregulated at 32°C. A higher number of interactions were observed in proteins involved in nucleotide transport and metabolism. We observed a low correlation between the transcriptome and proteome datasets. Our study indicates that the transcriptome and proteome of a fish-adapted S. agalactiae strain are modulated by temperature, particularly showing differential expression of genes/proteins involved in metabolism, virulence factors, and adaptation.

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Physiological response and microRNA expression profiles in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to acute cold stress

Cited by 24 publications

References 59 publications

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Characterization and analysis of the transcriptome inArapaima gigasusing multi-tissue RNA-sequencing

Transcriptome and Proteome of Fish-Pathogenic Streptococcus agalactiae Are Modulated by Temperature

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