Journal Article

Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content

Grosperrin, Philippe, Boichard, Didier, French Ministry of Agriculture, Agro-food, and ForestsFrench Dairy Interbranch Organization (CNIEL)Regional Union of Protected Designation Cheeses of Franche-Comte (URFAC)Regional Council of Bourgogne-Franche-Comte, through the project From'MIR, Charles, Mathieu, Rocha, Dominique, Delacroix-Buchet, Agnes, Hozé, Chris, Génétique Animale et Biologie Intégrative (GABI) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Brochard, Mickaël, Conseil Élevage 25-90, Sanchez, Marie-Pierre, Union Montbéliarde de Testage (UMOTEST), Boussaha, Mekki

2021

Overview

The mineral composition of bovine milk plays an important role in determining its nutritional and cheese-making value. Concentrations of the main minerals predicted from mid-infrared spectra produced during milk recording, combined with cow genotypes, provide a unique opportunity to decipher the genetic determinism of these traits. The present study included 1 million test-day predictions of Ca, Mg, P, K, Na, and citrate content from 126,876 Montbéliarde cows, of which 19,586 had genotype data available. All investigated traits were highly heritable (0.50-0.58), with the exception of Na (0.32). A sequence-based genome-wide association study (GWAS) detected 50 QTL (18 affecting two to five traits) and positional candidate genes and variants, mostly located in non-coding sequences. In silico post-GWAS analyses highlighted 877 variants that could be regulatory SNPs altering transcription factor (TF) binding sites or located in non-coding RNA (mainly lncRNA). Furthermore, we found 47 positional candidate genes and 45 TFs highly expressed in mammary gland compared to 90 other bovine tissues. Among the mammary-specific genes, SLC37A1 and ANKH, encoding proteins involved in ion transport were located in the most significant QTL. This study therefore highlights a comprehensive set of functional candidate genes and variants that affect milk mineral content.

• Publisher: Nature Publishing Group,CCSD,Nature Publishing Group UK,Nature Portfolio
• Subject: 631/208/1348 / 631/208/200 / 631/208/205 / Animal genetics / Binding sites / Citric acid / Cow's milk / Genetics / Genome-wide association studies / Genomes / Genotypes / Humanities and Social Sciences / Ion transport / Life Sciences / Mammary gland / Milk / Mineral composition / Minerals / multidisciplinary / Non-coding RNA / Nucleotide sequence / Protein transport / Quantitative trait loci / Regulatory sequences / Science / Science (multidisciplinary) / Single-nucleotide polymorphism
• ISBN: 0006849311000