Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach

Abstract

Background: Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional value. During the dry season, ruminants, particularly those raised in extensive production systems, lose around 30% of their body weight. Seasonal weight loss has important consequences on animal productive performance and health. In this study, RNA sequencing was used to characterize feed restriction effects in dairy goat of 2 breeds with different SWL tolerance: Majorera (tolerant) and Palmera (susceptible). Nine Majorera and ten Palmera goats were randomly distributed in a control and a restricted group: Majorera Control (adequately fed; MC; n = 4), Palmera Control (adequately fed; PC; n = 6), Majorera Restricted (feed restricted; ME; n = 5) and Palmera Restricted (feed restricted; PE; n = 4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis.

Results: From these samples, 24,260 unique transcripts were identified. From those, 82 transcripts were differentially expressed between MC and ME, 99 between PC and PE, twelve between both control groups and twenty-nine between both restricted groups.

Conclusions: Feed restriction affected several biochemical pathways in both breeds such as: carbohydrate and lipid transport; intracellular trafficking, RNA processing and signal transduction. This research also highlights the importance or involvement of the genes in tolerance (ENPP1, S-LZ, MT2A and GPNB) and susceptibility (GPD1, CTPS1, ELOVL6 and NR4A1) to SWL with respectively higher expression in the Majorera restriced group and the Palmera restricted group in comparison to the control groups. In addition, results from the study may be extrapolated to other dairy ruminant species.

Keywords: Goat; Mammary gland; RNA-sequencing; Seasonal weight loss; Transcriptomics.

Fig. 1

Differential gene expression results. a - The number of differentially (up and down-regulated) expressed genes (DEGs) in each comparison established for the study. b - Venn diagram analysis of DEGs in each comparison established for the study. The overlapping regions show common genes among the main comparisons established. MC – Majorera Control ME - Majorera Restricted; PC - Palmera Control and PE - Palmera Restricted. Parameters used: P-value and FDR < 0.05, Log2FC > 1.5 or < − 1.5, and raw number counts> 100 in at least one sample

Fig. 2

Graphic representation of the percentage of genes within each orthologous group obtained via Blast2GO, Cluster of orthologs e-Value 1e-3 for the four studied comparisons. MC – Majorera Control, PC – Palmera Control; ME – Majorera Restricted and PE – Palmera Restricted. For all comparisons: p-value and FDR < 0.05, log2FC > 1.5 or < − 1.5, and raw number counts> 100 in at least one sample

Fig. 3

Heatmaps and hierarchical clustering of the differentially expressed genes in the Palmera (a panel) and the Majorera (b panel) animals. MC – Majorera Control; PC – Palmera Control; ME – Majorera Restricted and PE – Palmera Restricted. Gene symbols are displayed in rows. Dark blue indicates high expression whereas light blue indicates low expression

Fig. 4

Heatmaps and hierarchical clustering of differential abundance transcripts in Control (a panel) and Restricted (b panel) animals. MC – Majorera Control; PC – Palmera Control; ME – Majorera Restricted and PE – Palmera Restricted. Gene symbols are displayed in rows. Dark blue indicates high expression whereas light blue indicates low expression

Fig. 5

Principal Component Analysis (PCA) scatterplot of the four experimental groups using all  differentially expressed genes. Values of FPKM were Log₂ transformed before computation. MC – Majorera Control; PC – Palmera Control; ME – Majorera Restricted and PE – Palmera Restricted

Fig. 6

Expression profiles of the six genes (DPP4; ELOVL6; GK; LIPG; RNASE1 and LOC102182683) used in the qPCR validation. Bars represent the average of FPKM (Fragments per kilo base per million mapped reads) of biological triplicates for each group obtained using RNA-Seq. Orange lines represent the average of relative gene expression of biological triplicates in each group obtained using RT-qPCR. Y-axis: gene expression values; X-axis: Experimental groups. MC – Majorera Control; PC – Palmera Control; ME – Majorera Restricted and PE – Palmera Restricted

Fig. 7

Scatter plot with the Log₂ fold change observed in RNA-Seq and qPCR for the RNASE1, GK, ELOVL6, LIPG, DPP4 and LOC102182683 at the comparisons where the genes where considered DE in the RNA-Seq data