Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation

Wang, Ying; Ding, Jun; Yang, Huajun; Yan, Zuoqin; Cao, Wei; Li, Yang-bai

doi:10.1371/journal.pone.0143568

Cited by 6 publications

(5 citation statements)

References 62 publications

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“…Therefore, these genes might play important roles during chicken growth and development. Interestingly, GAPDH gene, one of the most commonly used housekeeping gene [ 33 , 34 ], was identified as a DEG in this study because of its significantly lower expression level at 16 weeks of age than at 4 and 12 weeks of age. And in some other previous studies [ 35 , 36 ], it was shown that the expression of GAPDH were not always stable in different tissues or under different experimental conditions.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic profile of leg muscle during early growth in chicken

Xue

Zhang

et al. 2017

PLoS ONE

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The early growth pattern, especially the age of peak growth, of broilers affects the time to market and slaughter weight, which in turn affect the profitability of the poultry industry. However, the underlying mechanisms regulating chicken growth and development have rarely been studied. This study aimed to identify candidate genes involved in chicken growth and investigated the potential regulatory mechanisms of early growth in chicken. RNA sequencing was applied to compare the transcriptomes of chicken muscle tissues at three developmental stages during early growth. In total, 978 differentially expressed genes (DEGs) (fold change ≥ 2; false discovery rate < 0.05) were detected by pairwise comparison. Functional analysis showed that the DEGs are mainly involved in the processes of cell growth, muscle development, and cellular activities (such as junction, migration, assembly, differentiation, and proliferation). Many of the DEGs are well known to be related to chicken growth, such as MYOD1, GH, IGF2BP2, IGFBP3, SMYD1, CEBPB, FGF2, and IGFBP5. KEGG pathway analysis identified that the DEGs were significantly enriched in five pathways (P < 0.1) related to growth and development: extracellular matrix–receptor interaction, focal adhesion, tight junction, insulin signaling pathway, and regulation of the actin cytoskeleton. A total of 42 DEGs assigned to these pathways are potential candidate genes inducing the difference in growth among the three developmental stages, such as MYH10, FGF2, FGF16, FN1, CFL2, MAPK9, IRS1, PHKA1, PHKB, and PHKG1. Thus, our study identified a series of genes and several pathways that may participate in the regulation of early growth in chicken. These results should serve as an important resource revealing the molecular basis of chicken growth and development.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic profile of leg muscle during early growth in chicken

Xue

Zhang

et al. 2017

PLoS ONE

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“…Target prediction and functional analysis of these genes, including ENSGALT00000099549, ENSGALT00000103341, ENSGALT00000097648, XR_001468386.1, XR_003077640.1, and XR_001464460.2, showed that many lncRNA target mRNAs were associated with steroid hormone biosynthesis, ovarian steroidogenesis, TGF-β signaling pathway, prolactin signaling pathway, MAPK signaling pathway, estrogen signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, MAPK signaling pathway, and cell adhesion molecules. In our previous studies, steroid hormone biosynthesis and the PI3K-Akt signaling pathway were also altered in pigeons under monochromatic light (Wang et al, 2015 , 2019 ). Huang et al ( 1979 ) suggested that progesterone is synthesized by GCs, and Hu et al ( 2017 ) concluded that PI3K and AMPK signaling pathways converge to modulate ERK activity, and thereby regulate GC differentiation.…”

Section: Discussionmentioning

confidence: 84%

Transcriptome Analysis of Long Noncoding RNAs and mRNAs in Granulosa Cells of Jinghai Yellow Chickens Illuminated With Red Light

Wang

Shi²,

Zhang

et al. 2021

Front. Genet.

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Jinghai Yellow chickens are a new indigenous breed with a dual purpose in China, but their egg laying performance is limited. Compared with white light (WL), exposure to red light (RL) can improve the egg laying performance of hens. Herein, to elucidate the molecular mechanism by which RL affects the egg laying performance, RNA sequencing was used to analyze long noncoding RNAs (lncRNAs) and mRNAs from granulosa cells of small yellow follicles from Jinghai Yellow chickens in RL and WL groups. A total of 12,466 lncRNAs were identified among the assembled transcripts, of which 168 lncRNAs were significantly different between the RL and WL groups (101 downregulated and 67 upregulated). Additionally, 1182 differentially expressed mRNAs were identified (958 downregulated and 224 upregulated). Integrated network analysis demonstrated that numerous differential mRNAs were involved in follicular development through steroid hormone synthesis, oocyte meiosis, and the PI3K-Akt signaling pathway. The impact of lncRNAs on cis and trans target mRNAs indicates that some lncRNAs play important roles in follicular development of small yellow follicles. The results provide a starting point for studies aimed at understanding the molecular mechanisms by which monochromatic light affects follicular development and egg production in hens.

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“…After total RNA was reverse-transcribed, quantitative real-time PCR (qRT-PCR) was performed on an ABI 7500 thermocycler (Applied Biosystems). The GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was used as the internal reference gene for normalization of expression data ( Wang Y. et al 2015 ). Primers used in the present study are listed in Supplemental Material, Table S1 .…”

Section: Methodsmentioning

confidence: 99%

“…The development of the RNA-Sequencing (RNA-Seq) technique has opened new opportunities for researchers to obtain huge amounts of information about the transcriptome profile of tissues of interest, which help in the acquisition of knowledge concerning the mechanism of lipid deposition in livestock ( Jeong et al 2013 ; Chen et al 2015 ; Wang Z. et al 2015 ; Miao et al 2015 ). To our best knowledge, there are no data available in the literature regarding the gene expression profiles in the muscle and liver tissues of squabs.…”

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confidence: 99%

Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)

Zhou

Wei

et al. 2016

G3 Genes|Genomes|Genetics

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Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs.

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Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation

Cited by 6 publications

References 62 publications

Transcriptomic profile of leg muscle during early growth in chicken

Transcriptomic profile of leg muscle during early growth in chicken

Transcriptome Analysis of Long Noncoding RNAs and mRNAs in Granulosa Cells of Jinghai Yellow Chickens Illuminated With Red Light

Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)

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