Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of Liangshan pig muscle development at the growth curve inflection point and asymptotic stages using digital gene expression profiling

ABSTRACT: 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. 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.

ORGANISM(S): Sus scrofa

SUBMITTER: Linyuan Shen

PROVIDER: E-GEOD-69113 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:There are clear phenotypic differences between Korean native pig (KNP) and Yorkshire (YS) breeds because of different interests for selection. YS has been artificially selected by industrial interests such as a growth rate and a lean meat production, however, KNP has been maintained as a regional breed by local interests such as a fat content in or between muscle and a disease resistance. A comparison of gene expression profile from a major tissue liver can reflect the overall effects of the artificial selection between the two pig breeds through long history. KNP (n=4) and YS (n=4) pigs were raised under the identical conditions. Global gene expression levels were measured in liver samples from these pigs using Affymetrix porcine genome array containing 23,937 probe sets. The clustering analysis based on the individual transcriptome data showed a clear separation between two breeds in the liver tissue. We collected hepato-transcriptome data including 11,993 genes fully detected from four independent samples either in KNP or in YS. Based on both minimum positive false discovery rate (less than 15%) and fold change (|FC| > 1.5), 160 differentially expressed genes (DEGs) were collected from the liver between the two breeds. The functional analysis of these DEGs indicated clear distinctions in intra- and extra-cellular structure, cell proliferation, membrane trafficking, glycolytic pathway, mitochondrial function, protein metabolism, and immune response. The functional characteristics based on the DEGs were useful indicators to explain the differences between these two breeds developed for the specific purposes each other. The hepatic DGEs indicate that the YS has been lost expressivity of genes not required for the fast growth but maintained expressivity of genes for lean muscle production. The tissue-wise gene expression profiles indicate that the liver could be a major place to make the economic distinction between these two pig breeds. Comparing gene expression profiles to discover differentially expressed genes from liver tissue of two different pig breeds: KNP (n=4) vs. YS (n=4).

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Transcriptome analysis of Liangshan pig muscle development at the growth curve inflection point and asymptotic stages using digital gene expression profiling

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