In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets

Céline Bourdon,Thierry Tribout,Marie-Pierre Sanchez,Mekki Boussaha,Philippe Bardou,Gwenola Tosser-Klopp,Rachel Rupp,Hélène Larroque,Sandrine Le Guillou,Didier Boichard,Fabienne Le Provost

doi:10.1038/s41598-021-98639-9

Abstract

MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis. Some polymorphisms have been studied in various livestock species from the perspective of pathology or production traits. To target variants that could be the causal variants of dairy traits, genetic variants of microRNAs expressed in the mammary gland or present in milk and localized in dairy quantitative trait loci (QTLs) were investigated in bovine, caprine, and ovine species. In this study, a total of 59,124 (out of 28 millions), 13,427 (out of 87 millions), and 4761 (out of 38 millions) genetic variants in microRNAs expressed in the mammary gland or present in milk were identified in bovine, caprine, and ovine species, respectively. A total of 4679 of these detected bovine genetic variants are located in dairy QTLs. In caprine species, 127 genetic variants are localized in dairy QTLs. In ovine species, no genetic variant was identified in dairy QTLs. This study leads to the detection of microRNA genetic variants of interest in the context of dairy production, taking advantage of whole genome data to identify microRNA genetic variants expressed in the mammary gland and localized in dairy QTLs.

Highlights

MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis
To target microRNA variants that could potentially be the causal variants for these traits, only genetic variants of microRNAs expressed in the mammary gland or present in milk and localized in dairy QTLs were investigated
We developed a pipeline to filter microRNA genetic variants from whole-genome variants in bovine, caprine and ovine species

Summary

Introduction

MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis. A total of 4679 of these detected bovine genetic variants are located in dairy QTLs. In caprine species, 127 genetic variants are localized in dairy QTLs. In ovine species, no genetic variant was identified in dairy QTLs. This study leads to the detection of microRNA genetic variants of interest in the context of dairy production, taking advantage of whole genome data to identify microRNA genetic variants expressed in the mammary gland and localized in dairy QTLs. MicroRNAs are small noncoding RNAs of approximately 22 nucleotides in length that are highly conserved between species[1]. Few data on miRNA role on milk-producing traits have been described: for example microRNAs like miR-21 or miR-143 are abundantly expressed in bovine mammary g land[6]; the miR-24, miR-145, miR-103, miR-152, miR-224 are involved in milk fat traits in bovine or caprine species[7,8,9,10] Both small genetic variations (SNPs and InDels) and structural variations (SVs) may alter microRNAs via their biogenesis or their role on mRNA expression regulation. Differences in mRNA levels affect the density of muscular fibers and muscle and meat quality t raits[21]

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