Deep RNA-Seq reveals genetics and nutritional regulation of miRNomes in mammary gland of lactating Holstein and Montbéliarde cows

Résumé En

The mammary gland (MG) is a complex secretory organ synthetizing milk, the production and composition of which vary under genetic and nutrition regulations. The mechanisms underlying the variations are not totally understood. MicroRNAs (miRNAs, small non-coding RNAs) regulate the expression of genes involved in many cellular processes, including in MG. The objective was to identify the effects of feed restriction and dairy breed on bovine MG miRNomes. Five Holstein and 6 Montbéliarde multiparous cows in midlactation (165 ± 21 DIM) underwent 6 d of feed restriction (meeting 50% of NEL requirements calculated before the challenge). Milk, fat, protein and lactose yield were measured before and during restriction. MiRNomes were analyzed by RNA-Seq using Illumina HiSeq 4000 from MG biopsies performed 1 d before (control) and on d 6 of feed restriction. Statistical analyses for milk production and composition and for miRNAs were performed using mixed models of SAS and the DESeq2 package of R, respectively. Significance was considered at Padj = 0.05. As expected, milk, fat, protein, and lactose yields were lower in Montbéliarde than in Holstein cows and decreased by feed restriction. RNA-Seq analyses revealed 623 distinctly expressed miRNAs, among which 596 are known and 27 predicted. Breed influenced the expression of 19 miRNAs during the control period. The restriction modified the expression of 33 miRNAs in MG of Holstein cows, but only 2 miRNAs tended (padj = 0.10) to change in MG of Montbéliarde cows. Three miRNAs (miR-25, miR-2898, and miR-500) were commons between those modified by restriction and by breed. MiR-25 presented a high expression in lactating MG (over 4000 counts) and is known to repress triacylglycerol synthesis and lipid accumulation in mammary epithelial cells. The expression of miR-25 was higher whereas milk fat were lower in Montbéliarde and after restriction. In conclusion, we showed genetics and nutrition regulation of MG miRNomes, which suggest a potential role of miRNAs MG function and may be related to milk production and composition.