Genome-wide association study to identify genomic regions associated with Johne's disease in Iranian Holstein cattle

Document Type : Research Paper

Authors

1 Department of Animal Sciences, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

2 Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran

3 College of Agriculture &Natural Resources, University of Tehran, Ares International Campus, jolfa, Iran

4 College of Agriculture &Natural Resources, University of Tehran, Karaj, Iran

Abstract

Paratuberculosis  known as Johne's disease, is a contagious, chronic, intestinal disease in ruminants, which is caused by Mycobacterium avium paratuberculosis subspecies (MAP) and causes a huge economic damage to the livestock industry. There is no effective treatment nor vaccine for MAP infection. Thus, investigating the genetic regions associated with susceptibility to MAP infection can provide a better understanding of paratuberculosis mechanisms and contribute to the genetic improvement of animals. The aim of this study was to identify genomic regions and candidate genes associated with susceptibility to MAP infection in Holstein dairy cattle using a genome-wide association study (GWAS). For this purpose, blood samples of 150 cows were collected, and DNA and serum of them were extracted.The prepared DNA samples were genotyped using bovine SNPchip30k (Illumina). Quality control of genotypes was performed based on the minor allele frequency (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1) 10-6) using PLINK software. The association was performed using a mixed linear model in PLINK software. After quality control, 28749 markers on 142 cows (99 cases and 43 controls) were remained for the further analysis. Associations analysis showed that 16 markers located in chromosomes 30 and 6, were associated with  Johne's disease. Positional candidate genes for Johne's disease were identified. The most important identified genes were LMX1A, THSD7A, ELMOD2, ATP6AP2, RNF150, SLIT3, SDE2, PARP1, PBX1, TFB2M, SMYD3 and PYCR2. Gene ontology analysis showed that most of the identified genes are involved in the nervous system, cytoskeleton system, regulation of cytokines, Golgi apparatus, catalytic activity, calcium ion transport, and resistance to diseases. Whole genome-wide association study (GWAS) and ontology analysis (GO) can help to identify candidate genes and regions related to sensitivity to MAP in dairy cows, which can play an important role in the treatment and prevention of Johne's disease.

Keywords

Main Subjects

Extended Abstract

Introduction and Objective

   Paratuberculosis is a contagious, chronic, intestinal disease in ruminants, which is caused by Mycobacterium avium paratuberculosis subspecies (MAP) infection and causes great economic damage to the livestock industry worldwide. This disease is one of the most important from the economic point of view and one of the most widespread diseases in terms of prevalence, which causes a decrease in fat and protein and an increase in milk somatic cells in dairy cows. There is no effective treatment for MAP infection or vaccine for this disease so far. Thus investigating the genetic regions related to susceptibility to MAP infection can provide a better understanding of paratuberculosis mechanisms and contribute to the genetic improvement of animals. The aim of this study was to identify genomic regions and candidate genes associated with susceptibility to MAP infection in Iranian Holstein dairy cattle using the whole genome-wide association study (GWAS).

 

Material and Methods

   For this purpose, blood samples of 150 cows in an industrial farm were collected, and DNA and serum of them were extracted. The prepared DNA samples were genotyped using k30 microarrays (SNPchip30k) (by Illumina). Quality control of genotypes based on rare allele frequency components (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1) 10-6) and significance test were performed by PLINK software. Analysis of the ontology of genes was done by the online database https://www.Uniprot.org and finally, the ontology diagram of genes was drawn and analyzed by the online database PANTHER.

 

Results

   After quality control, 142 cows (99 cases and 43 controls) and 28749 markers were left for further analysis. Finally, 16 markers were considered higher than the significant threshold, and the most significant markers were located in chromosomes 30 and 6 respectively. Genes associated with selected markers were identified by ensemble and genecards sites. The most important identified genes related to these disease  were LMX1A, THSD7A, ELMOD2, ATP6AP2, RNF150, SLIT3, SDE2, PARP1, PBX1, TFB2M, SMYD3 and PYCR2. Ontology analysis showed that most of these genes are involved in  coding  proteins , cytoplasmic and membrane activities, the nervous system, cytoskeleton system, disease resistance, cytokine regulator, organ Golgi, catalytic activity, calcium ion transport. Also, some of these genes were related to other activities such as reproduction and fertility, mastitis, antiviral response, clinical ketosis, and immune response in dairy cows, as well as muscle growth and meat traits in beef cows.

 

Conclusion

     Whole genome-wide association study (GWAS) and ontology analysis (GO) can help to identify candidate genes and regions related to sensitivity to MAP in dairy cows, which can play an important role in the treatment and prevention of Johne's disease. The most important identified genes related to these disease  were LMX1A, THSD7A, ELMOD2, ATP6AP2, RNF150, SLIT3, SDE2, PARP1, PBX1, TFB2M, SMYD3 and PYCR2.

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Iranian Journal of animal Science
Volume 55, Issue 1
March 2024
Pages 31-45

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History

  • Receive Date: 05 February 2023
  • Revise Date: 22 May 2023
  • Accept Date: 25 May 2023

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