Fat-tail allele-specific expression genes may affect fat deposition in tail of sheep

Abstract

Different sheep breeds show distinct phenotypic plasticity in fat deposition in the tails. The genetic background underlying fat deposition in the tail of sheep is complex, multifactorial, and may involve allele-specific expression (ASE) mechanism to modulate allelic expression. ASE is a common phenomenon in mammals and refers to allelic imbalanced expression modified by cis-regulatory genetic variants that can be observed at heterozygous loci. Therefore, regulatory processes behind the fat-tail formation in sheep may be to some extent explained by cis- regulatory variants, through ASE mechanism, which was investigated in the present study. An RNA-Seq-based variant calling was applied to perform genome-wide survey of ASE genes using 45 samples from seven independent studies comparing the transcriptome of fat-tail tissue between fat- and thin-tailed sheep breeds. Using a rigorous computational pipeline, 115 differential ASE genes were identified, which were narrowed down to four genes (LPL, SOD3, TCP1 and LRPAP1) for being detected in at least two studies. Functional analysis revealed that the ASE genes were mainly involved in fat metabolism. Of these, LPL was of greater importance, as 1) observed in five studies, 2) reported as ASE gene in the previous studies and 3) with a known role in fat deposition. Our findings implied that complex physiological traits, like fat-tail formation, can be better explained by considering various genetic mechanisms, which can be more finely mapped through ASE analyses. The insights gained in this study indicate that biallelic expression may not be a common mechanism in sheep fat-tail development. Hence, allelic imbalance of the fat deposition-related genes can be considered a novel layer of information for future research on genetic improvement and increased efficiency in sheep breeding programs.

Fig 1. A schematic representation of the used bioinformatics pipeline to perform ASE analysis using RNA-Seq data.

Datasets of the seven studies were obtained from GEO database.

Fig 2. The distribution of all identified heterozygous SNPs across the chromosomes of the reference sheep genome.

Fig 3. UpSet plot of the common genes that were subjected to ASE analysis among the different studies.

The bar plots indicate the number of genes shared by specific studies. The horizontal bar chart at the bottom left represents the total number of genes found in each study. The box plots indicate the distribution of allelic ratio values for each breed. Study_2 is excluded as it did not have enough genes to be displayed.

Fig 4. Circos plot displaying the genome-wide distribution of the ASE analysis results.

The outermost ring shows chromosome numbers. The analyzed genes were divided into two groups based on their allelic ratio: the genes with an average allelic ratio above 0.5 in the thin-tail breeds are shown in the first inner ring (purple points). While the genes with an average allelic ratio above 0.5 in fat-tail sheep breeds are presented in the second inner ring (pink points). The heatmaps are accompanied by histograms that show the average allelic ratio of each gene in both tail fat groups. The green and red colors of heatmap indicate the higher allelic ratio in thin- and fat-tailed sheep breeds, respectively.

Fig 5. Allelic ratio of the significant differentially ASE genes in fat- and thin-tailed sheep breeds.

A) Heatmap representation of the allelic ratio for the four significant ASE genes in the used studies. The color scale indicates the intensity of higher expression of the reference allele. B) Box plot related to average allelic ratio of LPL gene in the fat-tail and thin-tailed breeds (FDR = 0.0048).

Fig 6. Sankey plot related to the results of functional enrichment analysis.

The plot shows the connections between the selected significant genes (left) and the enriched biological terms (right).