A gene expression estimator of intramuscular fat percentage for use in both cattle and sheep.

Bing Guo,Brian P Dalrymple,Paul L Greenwood,Guanghong Zhou,Kritaya Kongsuwan,Wangang Zhang

doi:10.1186/2049-1891-5-35

Abstract

BackgroundThe expression of genes encoding proteins involved in triacyglyceride and fatty acid synthesis and storage in cattle muscle are correlated with intramuscular fat (IMF)%. Are the same genes also correlated with IMF% in sheep muscle, and can the same set of genes be used to estimate IMF% in both species?ResultsThe correlation between gene expression (microarray) and IMF% in the longissimus muscle (LM) of twenty sheep was calculated. An integrated analysis of this dataset with an equivalent cattle correlation dataset and a cattle differential expression dataset was undertaken. A total of 30 genes were identified to be strongly correlated with IMF% in both cattle and sheep. The overlap of genes was highly significant, 8 of the 13 genes in the TAG gene set and 8 of the 13 genes in the FA gene set were in the top 100 and 500 genes respectively most correlated with IMF% in sheep, P-value = 0. Of the 30 genes, CIDEA, THRSP, ACSM1, DGAT2 and FABP4 had the highest average rank in both species. Using the data from two small groups of Brahman cattle (control and Hormone growth promotant-treated [known to decrease IMF% in muscle]) and 22 animals in total, the utility of a direct measure and different estimators of IMF% (ultrasound and gene expression) to differentiate between the two groups were examined. Directly measured IMF% and IMF% estimated from ultrasound scanning could not discriminate between the two groups. However, using gene expression to estimate IMF% discriminated between the two groups. Increasing the number of genes used to estimate IMF% from one to five significantly increased the discrimination power; but increasing the number of genes to 15 resulted in little further improvement.ConclusionWe have demonstrated the utility of a comparative approach to identify robust estimators of IMF% in the LM in cattle and sheep. We have also demonstrated a number of approaches (potentially applicable to much smaller groups of animals than conventional methods) to using gene expression to rank animals for IMF% within a single farm/treatment, or to estimate differences in IMF% between two farms/treatments.

Highlights

The expression of genes encoding proteins involved in triacyglyceride and fatty acid synthesis and storage in cattle muscle are correlated with intramuscular fat (IMF)%
Expression of genes in the TAG, FA and PPARG gene sets was correlated with IMF% in sheep The correlation between gene expression and IMF% in sheep longissimus muscle (LM) across the full set of 20 samples was calculated (Table 1)
The 46 genes from the TAG, FA and PPARG gene sets and related genes identified in cattle were ranked in the cattle and sheep datasets by their correlation coefficients, and Differential expression (DE) values in the cattle DE dataset (Table 1). 8 of the 13 genes in the previously defined TAG gene set were in the top 100 genes most correlated with IMF% in sheep, P-value = 0, 8 of the 13 genes in the previously defined FA gene set were in the top 500 genes most correlated with IMF% in sheep, Pvalue = 0, and 6 of the 15 genes in the previously defined PPARG gene set were in the top 1,000 genes most correlated with IMF% in sheep, P-value < 10−10

Summary

Introduction

The expression of genes encoding proteins involved in triacyglyceride and fatty acid synthesis and storage in cattle muscle are correlated with intramuscular fat (IMF)%. Compared to beefrelated research (see [4,5]), few publications have focussed on the molecular mechanism of IMF deposition in sheep. In. In our previous studies in cattle, three gene sets, designated as the “TAG gene set” (triglyceride synthesis and storage), the “FA gene set” (fatty acid synthesis and storage) and the “PPARG gene set” (Peroxisome proliferatoractivated receptor gamma), were identified based on the expression profiles of the genes in the LM across development in two crosses [4]. The expression of genes from these three gene sets, in particular the TAG gene set, was correlated with IMF deposition in cattle

Methods

Results

Conclusion