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.


Venn diagram for identification of key genes influencing porcine litter size.T10DEGs represents the top 10 most DEGs between the high and low litter size samples; T10YH represents the top 10 most expressed genes in the high litter size samples; T10YL represents the top 10 most expressed genes in the low litter size samples; E21OS represents the 21 genes enriched in the steroid metabolic process and ovarian steroidogenesis. Six, in the light green overlapping set surrounded by the red triangle, represents the CO1, GPX3, MSMB, COX3, TIMP1, and CYTB genes; two, in the brown overlapping set surrounded by the red triangle, represents the STAR and HSD3B genes; two, in the light brown overlapping set surrounded by the red triangle, represents the CYP11A1 and SCARB1 genes; and one, in the violet overlapping set surrounded by the red triangle, represents the HSD17B2 gene. Therefore, 11 genes (CO1, GPX3, MSMB, COX3, TIMP1, CYTB, STAR, HSD3B, CYP11A1, SCARB1, and HSD17B2) were present in two or more assemblies.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139514.g003: Venn diagram for identification of key genes influencing porcine litter size.T10DEGs represents the top 10 most DEGs between the high and low litter size samples; T10YH represents the top 10 most expressed genes in the high litter size samples; T10YL represents the top 10 most expressed genes in the low litter size samples; E21OS represents the 21 genes enriched in the steroid metabolic process and ovarian steroidogenesis. Six, in the light green overlapping set surrounded by the red triangle, represents the CO1, GPX3, MSMB, COX3, TIMP1, and CYTB genes; two, in the brown overlapping set surrounded by the red triangle, represents the STAR and HSD3B genes; two, in the light brown overlapping set surrounded by the red triangle, represents the CYP11A1 and SCARB1 genes; and one, in the violet overlapping set surrounded by the red triangle, represents the HSD17B2 gene. Therefore, 11 genes (CO1, GPX3, MSMB, COX3, TIMP1, CYTB, STAR, HSD3B, CYP11A1, SCARB1, and HSD17B2) were present in two or more assemblies.

Mentions: To accurately identify the key genes that may influence porcine litter size, we created a Venn diagram of the 10 most DEGs between high and low litter size samples (Table 3), the 10 most expressed genes in the ovaries of pigs with high litter size (Table 7), the 10 most expressed genes in the ovaries of pigs with low litter size (Table 7), and the 21 genes enriched in the steroid metabolic process and ovarian steroidogenesis of the above-mentioned (S5 Table). The results showed that 11 genes appeared in the two or more sets, including the CO1, glutathione peroxidase 3 (GPX3), beta-microseminoprotein (MSMB), COX3, tissue inhibitor of metalloproteinase 1 (TIMP1), cytochrome b (CYTB), STAR, 3-beta hydroxysteroid dehydrogenase (HSD3B), CYP11A1, SCARB1, and hydroxysteroid (17-beta) dehydrogenase 2 (HSD17B2) (Fig 3). These 11 genes may be candidates for porcine fecundity and litter size.


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)

Venn diagram for identification of key genes influencing porcine litter size.T10DEGs represents the top 10 most DEGs between the high and low litter size samples; T10YH represents the top 10 most expressed genes in the high litter size samples; T10YL represents the top 10 most expressed genes in the low litter size samples; E21OS represents the 21 genes enriched in the steroid metabolic process and ovarian steroidogenesis. Six, in the light green overlapping set surrounded by the red triangle, represents the CO1, GPX3, MSMB, COX3, TIMP1, and CYTB genes; two, in the brown overlapping set surrounded by the red triangle, represents the STAR and HSD3B genes; two, in the light brown overlapping set surrounded by the red triangle, represents the CYP11A1 and SCARB1 genes; and one, in the violet overlapping set surrounded by the red triangle, represents the HSD17B2 gene. Therefore, 11 genes (CO1, GPX3, MSMB, COX3, TIMP1, CYTB, STAR, HSD3B, CYP11A1, SCARB1, and HSD17B2) were present in two or more assemblies.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139514.g003: Venn diagram for identification of key genes influencing porcine litter size.T10DEGs represents the top 10 most DEGs between the high and low litter size samples; T10YH represents the top 10 most expressed genes in the high litter size samples; T10YL represents the top 10 most expressed genes in the low litter size samples; E21OS represents the 21 genes enriched in the steroid metabolic process and ovarian steroidogenesis. Six, in the light green overlapping set surrounded by the red triangle, represents the CO1, GPX3, MSMB, COX3, TIMP1, and CYTB genes; two, in the brown overlapping set surrounded by the red triangle, represents the STAR and HSD3B genes; two, in the light brown overlapping set surrounded by the red triangle, represents the CYP11A1 and SCARB1 genes; and one, in the violet overlapping set surrounded by the red triangle, represents the HSD17B2 gene. Therefore, 11 genes (CO1, GPX3, MSMB, COX3, TIMP1, CYTB, STAR, HSD3B, CYP11A1, SCARB1, and HSD17B2) were present in two or more assemblies.
Mentions: To accurately identify the key genes that may influence porcine litter size, we created a Venn diagram of the 10 most DEGs between high and low litter size samples (Table 3), the 10 most expressed genes in the ovaries of pigs with high litter size (Table 7), the 10 most expressed genes in the ovaries of pigs with low litter size (Table 7), and the 21 genes enriched in the steroid metabolic process and ovarian steroidogenesis of the above-mentioned (S5 Table). The results showed that 11 genes appeared in the two or more sets, including the CO1, glutathione peroxidase 3 (GPX3), beta-microseminoprotein (MSMB), COX3, tissue inhibitor of metalloproteinase 1 (TIMP1), cytochrome b (CYTB), STAR, 3-beta hydroxysteroid dehydrogenase (HSD3B), CYP11A1, SCARB1, and hydroxysteroid (17-beta) dehydrogenase 2 (HSD17B2) (Fig 3). These 11 genes may be candidates for porcine fecundity and litter size.

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.