Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems
The aim of the present study was to detect significant SNP (single-nucleotide polymorphism) effects and to annotate potential candidate genes for novel udder health traits in two different farming systems. We focused on specific mastitis pathogens and differential somatic cell fractions from 2198 ud...
Main Authors: | , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2021-06-01
|
Series: | Animals |
Subjects: | |
Online Access: | https://www.mdpi.com/2076-2615/11/6/1839 |
id |
doaj-9d35f83d05af4196b9ee852a3871000e |
---|---|
record_format |
Article |
spelling |
doaj-9d35f83d05af4196b9ee852a3871000e2021-07-01T00:44:29ZengMDPI AGAnimals2076-26152021-06-01111839183910.3390/ani11061839Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming SystemsPatricia Wagner0Tong Yin1Kerstin Brügemann2Petra Engel3Christina Weimann4Karen Schlez5Sven König6Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Ludwigstr. 21b, 35390 Giessen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Ludwigstr. 21b, 35390 Giessen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Ludwigstr. 21b, 35390 Giessen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Ludwigstr. 21b, 35390 Giessen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Ludwigstr. 21b, 35390 Giessen, GermanyLandesbetrieb Hessisches Landeslabor, Schubertstraße 60, D-35392 Gießen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Ludwigstr. 21b, 35390 Giessen, GermanyThe aim of the present study was to detect significant SNP (single-nucleotide polymorphism) effects and to annotate potential candidate genes for novel udder health traits in two different farming systems. We focused on specific mastitis pathogens and differential somatic cell fractions from 2198 udder quarters of 537 genotyped Holstein Friesian cows. The farming systems comprised compost-bedded pack and conventional cubicle barns. We developed a computer algorithm for genome-wide association studies allowing the estimation of main SNP effects plus consideration of SNPs by farming system interactions. With regard to the main effect, 35 significant SNPs were detected on 14 different chromosomes for the cell fractions and the pathogens. Six SNPs were significant for the interaction effect with the farming system for most of the udder health traits. We inferred two possible candidate genes based on significant SNP interactions. <i>HEMK1</i> plays a role in the development of the immune system, depending on environmental stressors. <i>CHL1</i> is regulated in relation to stress level and influences immune system mechanisms. The significant interactions indicate that gene activity can fluctuate depending on environmental stressors. Phenotypically, the prevalence of mastitis indicators differed between systems, with a notably lower prevalence of minor bacterial indicators in compost systems.https://www.mdpi.com/2076-2615/11/6/1839genome-wide associationsgenotype by environment interactionnew free walk housingdifferential somatic cell fractionsudder health |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Patricia Wagner Tong Yin Kerstin Brügemann Petra Engel Christina Weimann Karen Schlez Sven König |
spellingShingle |
Patricia Wagner Tong Yin Kerstin Brügemann Petra Engel Christina Weimann Karen Schlez Sven König Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems Animals genome-wide associations genotype by environment interaction new free walk housing differential somatic cell fractions udder health |
author_facet |
Patricia Wagner Tong Yin Kerstin Brügemann Petra Engel Christina Weimann Karen Schlez Sven König |
author_sort |
Patricia Wagner |
title |
Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems |
title_short |
Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems |
title_full |
Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems |
title_fullStr |
Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems |
title_full_unstemmed |
Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems |
title_sort |
genome-wide associations for microscopic differential somatic cell count and specific mastitis pathogens in holstein cows in compost-bedded pack and cubicle farming systems |
publisher |
MDPI AG |
series |
Animals |
issn |
2076-2615 |
publishDate |
2021-06-01 |
description |
The aim of the present study was to detect significant SNP (single-nucleotide polymorphism) effects and to annotate potential candidate genes for novel udder health traits in two different farming systems. We focused on specific mastitis pathogens and differential somatic cell fractions from 2198 udder quarters of 537 genotyped Holstein Friesian cows. The farming systems comprised compost-bedded pack and conventional cubicle barns. We developed a computer algorithm for genome-wide association studies allowing the estimation of main SNP effects plus consideration of SNPs by farming system interactions. With regard to the main effect, 35 significant SNPs were detected on 14 different chromosomes for the cell fractions and the pathogens. Six SNPs were significant for the interaction effect with the farming system for most of the udder health traits. We inferred two possible candidate genes based on significant SNP interactions. <i>HEMK1</i> plays a role in the development of the immune system, depending on environmental stressors. <i>CHL1</i> is regulated in relation to stress level and influences immune system mechanisms. The significant interactions indicate that gene activity can fluctuate depending on environmental stressors. Phenotypically, the prevalence of mastitis indicators differed between systems, with a notably lower prevalence of minor bacterial indicators in compost systems. |
topic |
genome-wide associations genotype by environment interaction new free walk housing differential somatic cell fractions udder health |
url |
https://www.mdpi.com/2076-2615/11/6/1839 |
work_keys_str_mv |
AT patriciawagner genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems AT tongyin genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems AT kerstinbrugemann genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems AT petraengel genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems AT christinaweimann genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems AT karenschlez genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems AT svenkonig genomewideassociationsformicroscopicdifferentialsomaticcellcountandspecificmastitispathogensinholsteincowsincompostbeddedpackandcubiclefarmingsystems |
_version_ |
1721347857906139136 |