Transcriptomic analysis of Rongchang pig brains and livers

Gan, Ling; Xie, Liwei; Fu-yuan, Zuo; Zhang, Xiang; He, Ningjia

doi:10.1016/j.gene.2015.01.051

Cited by 12 publications

(7 citation statements)

References 48 publications

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“…Genes that are highly expressed in reproductive tissues or cells may also indicate that the gene itself is activated, as shown in previous studies [ 57 – 59 ]. Therefore, we identified the 10 most highly expressed genes in the ovaries of high and low litter size pigs, respectively ( Table 7 ).…”

Section: Discussionmentioning

confidence: 72%

Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Zhang

Huang

et al. 2015

PLoS ONE

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Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

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Section: Discussionmentioning

confidence: 72%

Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Zhang

Huang

et al. 2015

PLoS ONE

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“…Rongchang pig, as a Chinese native fat‐type pig breed, is known for good meat quality and relatively high lean percentage (Gan, Xie, Zuo, Xiang, & He, ). Thus, it would be a useful model for studying muscle development of indigenous pig breed.…”

Section: Introductionmentioning

confidence: 99%

Deciphering the miRNA transcriptome of Rongchang pig longissimus dorsi at weaning and slaughter time points

Chen

Zhao

Dou

et al. 2020

Animal Physiology Nutrition

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MicroRNA (miRNA) is essential for the process of gene posttranscriptional regulation in skeletal muscle of many species, such as mice, cattle and so on. However, a little number of miRNAs have been reported in the muscle development of Chinese native pig breeds. In this study, the longissimus dorsi transcripts of Chinese native Rongchang pig at weaning and slaughter time points were analysed for miRNA‐seq. The results showed that 19 novel and 186 known miRNAs involved in the Rongchang pig skeletal muscle development were identified. Based on these findings, we further confirmed that porcine miR‐127, miR‐299 and miR‐432‐5p were obviously down‐expressed in adult pig (287 days of age), while miR‐7134‐3p and 664‐5p were significantly up‐expressed in weaning pig (35 days of age). In other words, these miRNAs could be the potential molecular markers and play vital roles in the muscle development process. Moreover, we found miR‐127 could inhibit the proliferation and myogenesis of porcine satellite cells in longissimus dorsi muscle. Our findings will provide deep insight into miRNA function for pork quality research with Chinese indigenous pig breeds.

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“…For humans, a transcriptome abundance atlas of 29 paired healthy human tissues was generated from the Human Protein Atlas project; this analysis revealed that strong mRNA differences within and across various tissues exist [ 12 ]. Transcriptome differential studies between different tissues are also widely found in domestic animals, such as transcriptome analysis of brain and liver in the Rongchang pig revealed tissue specificity through the identification of 5575 and 4600 DEGs in brains and livers, respectively [ 13 ]. Furthermore, a multiple tissue transcriptome analysis identified feed efficiency variations in related genes and biological pathways in the growing pig [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling across Five Tissues of Giant Panda

Wang

et al. 2020

BioMed Research International

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Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.

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Transcriptomic analysis of Rongchang pig brains and livers

Cited by 12 publications

References 48 publications

Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Deciphering the miRNA transcriptome of Rongchang pig longissimus dorsi at weaning and slaughter time points

Transcriptome Profiling across Five Tissues of Giant Panda

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