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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.


Verification of the RNA-Seq results using the qPCR method.Fold change values greater than 2 and P < 0.05 indicate overexpression in the YH group, and fold change values less than 0.5 and P < 0.05 indicate overexpression in the YL group. Genes with asterisk differ significantly (P < 0.05).
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pone.0139514.g002: Verification of the RNA-Seq results using the qPCR method.Fold change values greater than 2 and P < 0.05 indicate overexpression in the YH group, and fold change values less than 0.5 and P < 0.05 indicate overexpression in the YL group. Genes with asterisk differ significantly (P < 0.05).

Mentions: Twelve genes were used for qPCR analysis from the ovaries of the YH and YL groups to validate the expression profiles obtained by RNA-Seq. Consistent with the RNA-Seq findings, we verified that hydroxysteroid (17-beta) dehydrogenase 2 (HSD17B2), cytochrome P450 E class group 1 (CYP11A1), steroidogenic acute regulatory protein (STAR), low density lipoprotein receptor (LDLR), scavenger receptor class B member 1 (SCARB1), cytochrome c oxidase, subunit I domain (CO1), and cytochrome c oxidase subunit III domain (COX3) genes were all upregulated, while luteinizing hormone/choriogonadotopin receptor (LHCGR), and insulin-like growth factor 1 (IGF-1) genes were downregulated in high litter size samples. Matrix metallopeptidase 13 (MMP13) gene was not significant difference between the two groups. However, branched-chain amino acid aminotransferase II (BCAT2) and dopachrome tautomerase (DCT) genes were validated as different expression with P > 0.05 in YH versus YL groups (Table 6 and Fig 2). Therefore, results obtained from RNA-Seq were statistically confirmed for 83.3% of the tested genes by qPCR. In all cases, the relative fold change of gene expression was in the same direction between the RNA-Seq and qPCR data.


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)

Verification of the RNA-Seq results using the qPCR method.Fold change values greater than 2 and P < 0.05 indicate overexpression in the YH group, and fold change values less than 0.5 and P < 0.05 indicate overexpression in the YL group. Genes with asterisk differ significantly (P < 0.05).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139514.g002: Verification of the RNA-Seq results using the qPCR method.Fold change values greater than 2 and P < 0.05 indicate overexpression in the YH group, and fold change values less than 0.5 and P < 0.05 indicate overexpression in the YL group. Genes with asterisk differ significantly (P < 0.05).
Mentions: Twelve genes were used for qPCR analysis from the ovaries of the YH and YL groups to validate the expression profiles obtained by RNA-Seq. Consistent with the RNA-Seq findings, we verified that hydroxysteroid (17-beta) dehydrogenase 2 (HSD17B2), cytochrome P450 E class group 1 (CYP11A1), steroidogenic acute regulatory protein (STAR), low density lipoprotein receptor (LDLR), scavenger receptor class B member 1 (SCARB1), cytochrome c oxidase, subunit I domain (CO1), and cytochrome c oxidase subunit III domain (COX3) genes were all upregulated, while luteinizing hormone/choriogonadotopin receptor (LHCGR), and insulin-like growth factor 1 (IGF-1) genes were downregulated in high litter size samples. Matrix metallopeptidase 13 (MMP13) gene was not significant difference between the two groups. However, branched-chain amino acid aminotransferase II (BCAT2) and dopachrome tautomerase (DCT) genes were validated as different expression with P > 0.05 in YH versus YL groups (Table 6 and Fig 2). Therefore, results obtained from RNA-Seq were statistically confirmed for 83.3% of the tested genes by qPCR. In all cases, the relative fold change of gene expression was in the same direction between the RNA-Seq and qPCR data.

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.