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An across-breed genome wide association analysis of susceptibility to paratuberculosis in dairy cattle.

Abstract Paratuberculosis is a chronic disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). It occurs worldwide and causes a significant loss in the animal production industry. There is no cure for MAP infection and vaccination is problematic. Identification of genetics of susceptibility could be a useful adjunct for programs that focus on management, testing and culling of diseased animals. A case-control, genome-wide association study (GWAS) was conducted using Holstein and Jersey cattle in a combined analysis in order to identify markers and chromosomal regions associated with susceptibility to MAP infection across-breed. A mixed-model method (GRAMMAR-GC) implemented in the GenABEL R package and a Bayes C analysis implemented in GenSel software were used as alternative approaches to conduct GWAS analysis focused on single SNPs and chromosomal segments, respectively. After conducting quality control, 22 406 SNPs from 2157 individuals were available for the GRAMMAR-GC (Bayes C) analysis and 45 640 SNPs from 2199 individuals were available for the Bayes C analysis. One SNP located on BTA27 (8·6 Mb) was identified as moderately associated (P < 5 × 10-5, FDR = 0·44) in the GRAMMAR-GC analysis of the combined breed data. Nine 1 Mb windows located on BTA 2, 3 (3 windows), 6, 8, 25, 27 and 29 each explained ≥1% of the total proportion of genetic variance in the Bayes C analysis. In an analysis ignoring differences in linkage phase, two moderately significantly associated SNPs were identified; ARS-BFGL-NGS-19381 on BTA23 (32 Mb) and Hapmap40994-BTA-46361 on BTA19 (61 Mb). New common genomic regions and candidate genes have been identified from the across-breed analysis that might be involved in the immune response and susceptibility to MAP infection.
PMID
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Authors

Mayor MeshTerms
Keywords

Gene

Johne's disease

cow

Journal Title the journal of dairy research
Publication Year Start




PMID- 28252359
OWN - NLM
STAT- In-Process
DA  - 20170302
LR  - 20170302
IS  - 1469-7629 (Electronic)
IS  - 0022-0299 (Linking)
VI  - 84
IP  - 1
DP  - 2017 Feb
TI  - An across-breed genome wide association analysis of susceptibility to
      paratuberculosis in dairy cattle.
PG  - 61-67
LID - 10.1017/S0022029916000807 [doi]
AB  - Paratuberculosis is a chronic disease of ruminants caused by Mycobacterium avium 
      subspecies paratuberculosis (MAP). It occurs worldwide and causes a significant
      loss in the animal production industry. There is no cure for MAP infection and
      vaccination is problematic. Identification of genetics of susceptibility could be
      a useful adjunct for programs that focus on management, testing and culling of
      diseased animals. A case-control, genome-wide association study (GWAS) was
      conducted using Holstein and Jersey cattle in a combined analysis in order to
      identify markers and chromosomal regions associated with susceptibility to MAP
      infection across-breed. A mixed-model method (GRAMMAR-GC) implemented in the
      GenABEL R package and a Bayes C analysis implemented in GenSel software were used
      as alternative approaches to conduct GWAS analysis focused on single SNPs and
      chromosomal segments, respectively. After conducting quality control, 22 406 SNPs
      from 2157 individuals were available for the GRAMMAR-GC (Bayes C) analysis and 45
      640 SNPs from 2199 individuals were available for the Bayes C analysis. One SNP
      located on BTA27 (8.6 Mb) was identified as moderately associated (P &lt; 5 x 10-5, 
      FDR = 0.44) in the GRAMMAR-GC analysis of the combined breed data. Nine 1 Mb
      windows located on BTA 2, 3 (3 windows), 6, 8, 25, 27 and 29 each explained &gt;/=1%
      of the total proportion of genetic variance in the Bayes C analysis. In an
      analysis ignoring differences in linkage phase, two moderately significantly
      associated SNPs were identified; ARS-BFGL-NGS-19381 on BTA23 (32 Mb) and
      Hapmap40994-BTA-46361 on BTA19 (61 Mb). New common genomic regions and candidate 
      genes have been identified from the across-breed analysis that might be involved 
      in the immune response and susceptibility to MAP infection.
FAU - Sallam, Ahmed M
AU  - Sallam AM
AD  - Department of Animal Sciences,College of Agricultural and Life
      Sciences,University of Wisconsin-Madison,Madison,WI 53706,USA.
FAU - Zare, Yalda
AU  - Zare Y
AD  - Department of Animal Sciences,College of Agricultural and Life
      Sciences,University of Wisconsin-Madison,Madison,WI 53706,USA.
FAU - Alpay, Fazli
AU  - Alpay F
AD  - Department of Animal Sciences,College of Agricultural and Life
      Sciences,University of Wisconsin-Madison,Madison,WI 53706,USA.
FAU - Shook, George E
AU  - Shook GE
AD  - Department of Dairy Science,College of Agricultural and Life Sciences,University 
      of Wisconsin-Madison,Madison,WI 53706,USA.
FAU - Collins, Michael T
AU  - Collins MT
AD  - Department of Pathobiological Science,School of Veterinary Medicine,University of
      Wisconsin-Madison,Madison,WI 53706,USA.
FAU - Alsheikh, Samir
AU  - Alsheikh S
AD  - Animal and Poultry Production Division,Desert Research Center,Al-Mataria
      11753,Cairo,Egypt.
FAU - Sharaby, Mahmoud
AU  - Sharaby M
AD  - Animal and Fish Production Department,Faculty of Agriculture,University of
      Alexandria,El-Shatby,Alexandria,Egypt.
FAU - Kirkpatrick, Brian W
AU  - Kirkpatrick BW
AD  - Department of Animal Sciences,College of Agricultural and Life
      Sciences,University of Wisconsin-Madison,Madison,WI 53706,USA.
LA  - eng
PT  - Journal Article
PL  - England
TA  - J Dairy Res
JT  - The Journal of dairy research
JID - 2985125R
OTO - NOTNLM
OT  - Gene
OT  - Johne's disease
OT  - cow
EDAT- 2017/03/03 06:00
MHDA- 2017/03/03 06:00
CRDT- 2017/03/03 06:00
AID - S0022029916000807 [pii]
AID - 10.1017/S0022029916000807 [doi]
PST - ppublish
SO  - J Dairy Res. 2017 Feb;84(1):61-67. doi: 10.1017/S0022029916000807.

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