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| Status |
Public on May 25, 2015 |
| Title |
Transcriptome analysis of Liangshan pig muscle development at the growth curve inflection point and asymptotic stages using digital gene expression profiling |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds.
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| Overall design |
The aim of our study is to identify different expression genes that are linked to phenotypic differentiation (eg: grow rate, meat quality) between inflection point and asymptote stages.
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| Contributor(s) |
Shen L, Luo J, Du J, Liu C, Wu X, Pu Q, Fu Y, Tang Q, Liu Y, Yang R, Li X, Tang G, Jiang Y, Li M, Zhang S, Zhu L |
| Citation(s) |
26292092, 26697358 |
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| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Linyuan Shen |
| E-mail(s) |
shenlinyuan0815@163.com
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| Phone |
+86 15181216032
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| Organization name |
Sichuan Agricultural University
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| Department |
College of Animal Science and Technology
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| Street address |
211# Huiming Road
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platforms (1) |
| GPL11429 |
Illumina HiSeq 2000 (Sus scrofa) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA284587 |
| SRA |
SRP058576 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE69113_AIPVUIP_differential_expression.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE69113_BIPVUIP_differential_expression.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE69113_gene_expression_rpkm.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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