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

Abstract 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 deciphe...

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Autores principales:	Marie-Pierre Sanchez, Dominique Rocha, Mathieu Charles, Mekki Boussaha, Chris Hozé, Mickaël Brochard, Agnès Delacroix-Buchet, Philippe Grosperrin, Didier Boichard
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/281f829d1c8642f1b12397a138fae9f1
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spelling	oai:doaj.org-article:281f829d1c8642f1b12397a138fae9f12021-12-02T14:20:34ZSequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content10.1038/s41598-021-87078-12045-2322https://doaj.org/article/281f829d1c8642f1b12397a138fae9f12021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87078-1https://doaj.org/toc/2045-2322Abstract 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.Marie-Pierre SanchezDominique RochaMathieu CharlesMekki BoussahaChris HozéMickaël BrochardAgnès Delacroix-BuchetPhilippe GrosperrinDidier BoichardNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Marie-Pierre Sanchez Dominique Rocha Mathieu Charles Mekki Boussaha Chris Hozé Mickaël Brochard Agnès Delacroix-Buchet Philippe Grosperrin Didier Boichard Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content
description	Abstract 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.
format	article
author	Marie-Pierre Sanchez Dominique Rocha Mathieu Charles Mekki Boussaha Chris Hozé Mickaël Brochard Agnès Delacroix-Buchet Philippe Grosperrin Didier Boichard
author_facet	Marie-Pierre Sanchez Dominique Rocha Mathieu Charles Mekki Boussaha Chris Hozé Mickaël Brochard Agnès Delacroix-Buchet Philippe Grosperrin Didier Boichard
author_sort	Marie-Pierre Sanchez
title	Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content
title_short	Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content
title_full	Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content
title_fullStr	Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content
title_full_unstemmed	Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content
title_sort	sequence-based gwas and post-gwas analyses reveal a key role of slc37a1, ankh, and regulatory regions on bovine milk mineral content
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/281f829d1c8642f1b12397a138fae9f1
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Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content

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