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Differential gene expression in ovaries of Qira black sheep and Hetian sheep using RNA-Seq technique.

Chen HY, Shen H, Jia B, Zhang YS, Wang XH, Zeng XC - PLoS ONE (2015)

Bottom Line: After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively.A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep.This study provides a basic data for future research of the sheep reproduction.

View Article: PubMed Central - PubMed

Affiliation: School of Pharmacy, Shihezi University, Shihezi, Xinjiang, China.

ABSTRACT
The Qira black sheep and the Hetian sheep are two local breeds in the Northwest of China, which are characterized by high-fecundity and low-fecundity breed respectively. The elucidation of mRNA expression profiles in the ovaries among different sheep breeds representing fecundity extremes will helpful for identification and utilization of major prolificacy genes in sheep. In the present study, we performed RNA-seq technology to compare the difference in ovarian mRNA expression profiles between Qira black sheep and Hetian sheep. From the Qira black sheep and the Hetian sheep libraries, we obtained a total of 11,747,582 and 11,879,968 sequencing reads, respectively. After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively. A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep. Eight differentially expressed genes were randomly selected for validation by real-time RT-PCR. This study provides a basic data for future research of the sheep reproduction.

No MeSH data available.


Comparison of gene expression levels between the two libraries.The expression levels are estimated by RPKM value.
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pone.0120170.g003: Comparison of gene expression levels between the two libraries.The expression levels are estimated by RPKM value.

Mentions: To judge the significance of differences in expressed genes, FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 were used as the threshold. A total of 1,252 significantly differentially expressed genes were identified between the two libraries, with 859 genes upregulated and 393 genes downregulated at Hetian sheep compared with Qira black sheep (S2 Table and Fig. 3). Among these genes, 9 genes 13 genes were found only expressed in the Qira black sheep library and Hetian sheep library respectively. The breakdown of fold-change among the DEGs was showed in Table 3. Interestingly, the number of genes having greater than four-fold difference and two-fold difference accounted for 7.03% and 29.79% of the total DEGs respectively.


Differential gene expression in ovaries of Qira black sheep and Hetian sheep using RNA-Seq technique.

Chen HY, Shen H, Jia B, Zhang YS, Wang XH, Zeng XC - PLoS ONE (2015)

Comparison of gene expression levels between the two libraries.The expression levels are estimated by RPKM value.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366253&req=5

pone.0120170.g003: Comparison of gene expression levels between the two libraries.The expression levels are estimated by RPKM value.
Mentions: To judge the significance of differences in expressed genes, FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 were used as the threshold. A total of 1,252 significantly differentially expressed genes were identified between the two libraries, with 859 genes upregulated and 393 genes downregulated at Hetian sheep compared with Qira black sheep (S2 Table and Fig. 3). Among these genes, 9 genes 13 genes were found only expressed in the Qira black sheep library and Hetian sheep library respectively. The breakdown of fold-change among the DEGs was showed in Table 3. Interestingly, the number of genes having greater than four-fold difference and two-fold difference accounted for 7.03% and 29.79% of the total DEGs respectively.

Bottom Line: After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively.A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep.This study provides a basic data for future research of the sheep reproduction.

View Article: PubMed Central - PubMed

Affiliation: School of Pharmacy, Shihezi University, Shihezi, Xinjiang, China.

ABSTRACT
The Qira black sheep and the Hetian sheep are two local breeds in the Northwest of China, which are characterized by high-fecundity and low-fecundity breed respectively. The elucidation of mRNA expression profiles in the ovaries among different sheep breeds representing fecundity extremes will helpful for identification and utilization of major prolificacy genes in sheep. In the present study, we performed RNA-seq technology to compare the difference in ovarian mRNA expression profiles between Qira black sheep and Hetian sheep. From the Qira black sheep and the Hetian sheep libraries, we obtained a total of 11,747,582 and 11,879,968 sequencing reads, respectively. After aligning to the reference sequences, the two libraries included 16,763 and 16,814 genes respectively. A total of 1,252 genes were significantly differentially expressed at Hetian sheep compared with Qira black sheep. Eight differentially expressed genes were randomly selected for validation by real-time RT-PCR. This study provides a basic data for future research of the sheep reproduction.

No MeSH data available.