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

Zhang X, Huang L, Wu T, Feng Y, Ding Y, Ye P, Yin Z - PLoS ONE (2015)

Bottom Line: 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.These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People's Republic of China.

ABSTRACT
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.

No MeSH data available.


Comparative results of gene expression levels and differentially expressed gene distributions between the ovaries of Yorkshire pigs with extremely high (YH) and low (YL) litter size.(A) Venn diagram showing genes only expressed in the YH group (yellow circle), only expressed in the YL group (light red circle), and common to both groups (intersection). (B) Scatter plot of differentially expressed genes (YH vs. YL). Red points represent upregulated genes with log2 (fold change) > 1 and padj < 0.05 (–log10 (padj) ≥ 1.3); Blue points represent downregulated genes with log2 (fold change) < -1 and padj < 0.05 (–log10 (padj) ≥ 1.3). Green points represent genes with no significant difference. Fold change = gene normalized expression of the YH group / gene normalized expression of the YL group.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4591126&req=5

pone.0139514.g001: Comparative results of gene expression levels and differentially expressed gene distributions between the ovaries of Yorkshire pigs with extremely high (YH) and low (YL) litter size.(A) Venn diagram showing genes only expressed in the YH group (yellow circle), only expressed in the YL group (light red circle), and common to both groups (intersection). (B) Scatter plot of differentially expressed genes (YH vs. YL). Red points represent upregulated genes with log2 (fold change) > 1 and padj < 0.05 (–log10 (padj) ≥ 1.3); Blue points represent downregulated genes with log2 (fold change) < -1 and padj < 0.05 (–log10 (padj) ≥ 1.3). Green points represent genes with no significant difference. Fold change = gene normalized expression of the YH group / gene normalized expression of the YL group.

Mentions: After mapping to the pig genome, a total of 17 485 and 19 178 genes were obtained from the YH and YL libraries, respectively. Four hundred and two genes were expressed only in YH, 2 059 genes were expressed only in YL, and 17 083 genes were co-expressed in both libraries (Fig 1A). A total of 1 243 genes were differentially expressed between the two groups, in which 897 genes were upregulated and 346 genes were downregulated in the YH group (Fig 1B and S2 Table). The 10 most differentially expressed genes (log2FoldChange ≥4) from the total of 1 243 DEGs identified between the high and low litter size samples were: homogentisate 1,2 dioxygenase (HGD); phosphoenylpyruvate carboxykinase (PCK1), HSD17B2; early growth response 4 (EGR4), a member of the ras oncogene family (RAB33A); solute carrier protein family 6 (SLC6A20B); zinc finger protein (GLI1); U6 spliceosomal RNA (U6); solute carrier protein family 7 (SLC7A11); and spectrin alpha chain eyrythrocytic 1 (SPTA1), respectively (Table 3).


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

Zhang X, Huang L, Wu T, Feng Y, Ding Y, Ye P, Yin Z - PLoS ONE (2015)

Comparative results of gene expression levels and differentially expressed gene distributions between the ovaries of Yorkshire pigs with extremely high (YH) and low (YL) litter size.(A) Venn diagram showing genes only expressed in the YH group (yellow circle), only expressed in the YL group (light red circle), and common to both groups (intersection). (B) Scatter plot of differentially expressed genes (YH vs. YL). Red points represent upregulated genes with log2 (fold change) > 1 and padj < 0.05 (–log10 (padj) ≥ 1.3); Blue points represent downregulated genes with log2 (fold change) < -1 and padj < 0.05 (–log10 (padj) ≥ 1.3). Green points represent genes with no significant difference. Fold change = gene normalized expression of the YH group / gene normalized expression of the YL group.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591126&req=5

pone.0139514.g001: Comparative results of gene expression levels and differentially expressed gene distributions between the ovaries of Yorkshire pigs with extremely high (YH) and low (YL) litter size.(A) Venn diagram showing genes only expressed in the YH group (yellow circle), only expressed in the YL group (light red circle), and common to both groups (intersection). (B) Scatter plot of differentially expressed genes (YH vs. YL). Red points represent upregulated genes with log2 (fold change) > 1 and padj < 0.05 (–log10 (padj) ≥ 1.3); Blue points represent downregulated genes with log2 (fold change) < -1 and padj < 0.05 (–log10 (padj) ≥ 1.3). Green points represent genes with no significant difference. Fold change = gene normalized expression of the YH group / gene normalized expression of the YL group.
Mentions: After mapping to the pig genome, a total of 17 485 and 19 178 genes were obtained from the YH and YL libraries, respectively. Four hundred and two genes were expressed only in YH, 2 059 genes were expressed only in YL, and 17 083 genes were co-expressed in both libraries (Fig 1A). A total of 1 243 genes were differentially expressed between the two groups, in which 897 genes were upregulated and 346 genes were downregulated in the YH group (Fig 1B and S2 Table). The 10 most differentially expressed genes (log2FoldChange ≥4) from the total of 1 243 DEGs identified between the high and low litter size samples were: homogentisate 1,2 dioxygenase (HGD); phosphoenylpyruvate carboxykinase (PCK1), HSD17B2; early growth response 4 (EGR4), a member of the ras oncogene family (RAB33A); solute carrier protein family 6 (SLC6A20B); zinc finger protein (GLI1); U6 spliceosomal RNA (U6); solute carrier protein family 7 (SLC7A11); and spectrin alpha chain eyrythrocytic 1 (SPTA1), respectively (Table 3).

Bottom Line: 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.These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People's Republic of China.

ABSTRACT
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.

No MeSH data available.