QTLs associated with resistance to MAP infection in Holstein-Friesian cattle

Sanjay Mallikarjunappa, Mehdi Sargolzaei, Kieran Meade, Niel A Karrow, Sameer D. Pant

Research output: Other contribution to conferencePoster

5 Downloads (Pure)

Abstract

The objective of this study was to perform genome-wide association (GWA) analysis using high-density (HD) imputed genotype data in order to identify putative Quantitative Trait Loci (QTLs) associated with Mycobacterium avium subsp. paratuberculosis (MAP) infection that causes Johne’s disease in cattle. The study was based on the hypothesis that the use of imputed HD SNP genotypes leads to identification of additional associations especially in the regions with low coverage on 50k panel used in the previous study. Therefore, previously analysed 50k genotypes of 232 Holstein-Friesian cows, comprised of a MAP-positive (n = 90) and MAP-negative cohort (n = 142), were imputed to a 777k SNP chip panel using the software package FImpute. Subsequently, principal component regression analysis was used for GWA of imputed genotypes, which revealed 15 putative QTLs (P = 1.99E-6) associated with the MAP infection phenotype on 8 different chromosomes (BTA 5, 7, 10, 14, 15, 16, 20 and 21) of which the QTLs identified on BTA 15, 16, 20 and 21 constituted the new additional QTLs identified in this study. Post-GWAS bioinformatic analysis identified several novel candidate genes underlying these QTLs including NLRP3, IFi47, TRIM41, TNFRSF18, TNFRSF4. Several of these genes have pro-inflammatory properties, which could be indicative of the role of phagocytic cells in eliciting an anti-MAP response during early stages of Johne’s disease pathogenesis. To our knowledge, this is the first study to carry out Johne’s disease GWA analysis using high density SNP genotypes. Our analysis revealed potential QTLs that were associated with resistance to MAP infection, which will now be functionally investigated. Once validated, associated QTLs could be exploited via marker-assisted selection to breed for Johne’s disease resistance in cattle.
Original languageEnglish
Pages22-23
Number of pages2
Publication statusPublished - 2017
Event36th International Society for Animal Genetics - University College Dublin , Dublin, Ireland
Duration: 16 Jul 201721 Jul 2017
http://www.isag.us/2017/ (Conference website)
https://www.isag.us/2017/docs/ISAG2017_Proceedings.pdf (Conference proceedings)

Conference

Conference36th International Society for Animal Genetics
CountryIreland
CityDublin
Period16/07/1721/07/17
OtherIreland is honoured to host the 36th International Society of Animal Genetics (ISAG) Conference in Dublin from July 16 to 21, 2017. The conference will take place in University College Dublin (UCD).

The 2017 ISAG Conference will provide an open and friendly forum for the sharing of knowledge between scientists and practitioners of animal genetics applied to economically important and domesticated species.

The conference will comprise

A series of plenary sessions with invited presentations from the world's leading scientists.

A series of workshop sessions organised by ISAG's standing committees. ISAG has 21 standing committees whose focus covers the applications of greatest interest to ISAG members.

Poster presentations of latest research results from scientists and students. The posters result from an open call for researchers to present their findings.

A series of social functions with the goal of enabling scientists and practitioners to make new contacts and strengthen existing ones.
Internet address

Fingerprint

Mycobacterium avium subsp. paratuberculosis
quantitative trait loci
Holstein
paratuberculosis
cattle
infection
genotype
phagocytes
bioinformatics
marker-assisted selection
disease resistance
regression analysis
genes
pathogenesis
chromosomes
breeds
phenotype
cows
genome

Cite this

Mallikarjunappa, S., Sargolzaei, M., Meade, K., Karrow, N. A., & Pant, S. D. (2017). QTLs associated with resistance to MAP infection in Holstein-Friesian cattle. 22-23. Poster session presented at 36th International Society for Animal Genetics, Dublin, Ireland.
Mallikarjunappa, Sanjay ; Sargolzaei, Mehdi ; Meade, Kieran ; Karrow, Niel A ; Pant, Sameer D. / QTLs associated with resistance to MAP infection in Holstein-Friesian cattle. Poster session presented at 36th International Society for Animal Genetics, Dublin, Ireland.2 p.
@conference{bda3ff160ef84f5cbfa1f9878c032521,
title = "QTLs associated with resistance to MAP infection in Holstein-Friesian cattle",
abstract = "The objective of this study was to perform genome-wide association (GWA) analysis using high-density (HD) imputed genotype data in order to identify putative Quantitative Trait Loci (QTLs) associated with Mycobacterium avium subsp. paratuberculosis (MAP) infection that causes Johne’s disease in cattle. The study was based on the hypothesis that the use of imputed HD SNP genotypes leads to identification of additional associations especially in the regions with low coverage on 50k panel used in the previous study. Therefore, previously analysed 50k genotypes of 232 Holstein-Friesian cows, comprised of a MAP-positive (n = 90) and MAP-negative cohort (n = 142), were imputed to a 777k SNP chip panel using the software package FImpute. Subsequently, principal component regression analysis was used for GWA of imputed genotypes, which revealed 15 putative QTLs (P = 1.99E-6) associated with the MAP infection phenotype on 8 different chromosomes (BTA 5, 7, 10, 14, 15, 16, 20 and 21) of which the QTLs identified on BTA 15, 16, 20 and 21 constituted the new additional QTLs identified in this study. Post-GWAS bioinformatic analysis identified several novel candidate genes underlying these QTLs including NLRP3, IFi47, TRIM41, TNFRSF18, TNFRSF4. Several of these genes have pro-inflammatory properties, which could be indicative of the role of phagocytic cells in eliciting an anti-MAP response during early stages of Johne’s disease pathogenesis. To our knowledge, this is the first study to carry out Johne’s disease GWA analysis using high density SNP genotypes. Our analysis revealed potential QTLs that were associated with resistance to MAP infection, which will now be functionally investigated. Once validated, associated QTLs could be exploited via marker-assisted selection to breed for Johne’s disease resistance in cattle.",
keywords = "cattle, genome-wide association, imputation, genetic marker, genetic improvement",
author = "Sanjay Mallikarjunappa and Mehdi Sargolzaei and Kieran Meade and Karrow, {Niel A} and Pant, {Sameer D.}",
year = "2017",
language = "English",
pages = "22--23",
note = "36th International Society for Animal Genetics ; Conference date: 16-07-2017 Through 21-07-2017",
url = "http://www.isag.us/2017/, https://www.isag.us/2017/docs/ISAG2017_Proceedings.pdf",

}

Mallikarjunappa, S, Sargolzaei, M, Meade, K, Karrow, NA & Pant, SD 2017, 'QTLs associated with resistance to MAP infection in Holstein-Friesian cattle' 36th International Society for Animal Genetics, Dublin, Ireland, 16/07/17 - 21/07/17, pp. 22-23.

QTLs associated with resistance to MAP infection in Holstein-Friesian cattle. / Mallikarjunappa, Sanjay; Sargolzaei, Mehdi; Meade, Kieran; Karrow, Niel A; Pant, Sameer D.

2017. 22-23 Poster session presented at 36th International Society for Animal Genetics, Dublin, Ireland.

Research output: Other contribution to conferencePoster

TY - CONF

T1 - QTLs associated with resistance to MAP infection in Holstein-Friesian cattle

AU - Mallikarjunappa, Sanjay

AU - Sargolzaei, Mehdi

AU - Meade, Kieran

AU - Karrow, Niel A

AU - Pant, Sameer D.

PY - 2017

Y1 - 2017

N2 - The objective of this study was to perform genome-wide association (GWA) analysis using high-density (HD) imputed genotype data in order to identify putative Quantitative Trait Loci (QTLs) associated with Mycobacterium avium subsp. paratuberculosis (MAP) infection that causes Johne’s disease in cattle. The study was based on the hypothesis that the use of imputed HD SNP genotypes leads to identification of additional associations especially in the regions with low coverage on 50k panel used in the previous study. Therefore, previously analysed 50k genotypes of 232 Holstein-Friesian cows, comprised of a MAP-positive (n = 90) and MAP-negative cohort (n = 142), were imputed to a 777k SNP chip panel using the software package FImpute. Subsequently, principal component regression analysis was used for GWA of imputed genotypes, which revealed 15 putative QTLs (P = 1.99E-6) associated with the MAP infection phenotype on 8 different chromosomes (BTA 5, 7, 10, 14, 15, 16, 20 and 21) of which the QTLs identified on BTA 15, 16, 20 and 21 constituted the new additional QTLs identified in this study. Post-GWAS bioinformatic analysis identified several novel candidate genes underlying these QTLs including NLRP3, IFi47, TRIM41, TNFRSF18, TNFRSF4. Several of these genes have pro-inflammatory properties, which could be indicative of the role of phagocytic cells in eliciting an anti-MAP response during early stages of Johne’s disease pathogenesis. To our knowledge, this is the first study to carry out Johne’s disease GWA analysis using high density SNP genotypes. Our analysis revealed potential QTLs that were associated with resistance to MAP infection, which will now be functionally investigated. Once validated, associated QTLs could be exploited via marker-assisted selection to breed for Johne’s disease resistance in cattle.

AB - The objective of this study was to perform genome-wide association (GWA) analysis using high-density (HD) imputed genotype data in order to identify putative Quantitative Trait Loci (QTLs) associated with Mycobacterium avium subsp. paratuberculosis (MAP) infection that causes Johne’s disease in cattle. The study was based on the hypothesis that the use of imputed HD SNP genotypes leads to identification of additional associations especially in the regions with low coverage on 50k panel used in the previous study. Therefore, previously analysed 50k genotypes of 232 Holstein-Friesian cows, comprised of a MAP-positive (n = 90) and MAP-negative cohort (n = 142), were imputed to a 777k SNP chip panel using the software package FImpute. Subsequently, principal component regression analysis was used for GWA of imputed genotypes, which revealed 15 putative QTLs (P = 1.99E-6) associated with the MAP infection phenotype on 8 different chromosomes (BTA 5, 7, 10, 14, 15, 16, 20 and 21) of which the QTLs identified on BTA 15, 16, 20 and 21 constituted the new additional QTLs identified in this study. Post-GWAS bioinformatic analysis identified several novel candidate genes underlying these QTLs including NLRP3, IFi47, TRIM41, TNFRSF18, TNFRSF4. Several of these genes have pro-inflammatory properties, which could be indicative of the role of phagocytic cells in eliciting an anti-MAP response during early stages of Johne’s disease pathogenesis. To our knowledge, this is the first study to carry out Johne’s disease GWA analysis using high density SNP genotypes. Our analysis revealed potential QTLs that were associated with resistance to MAP infection, which will now be functionally investigated. Once validated, associated QTLs could be exploited via marker-assisted selection to breed for Johne’s disease resistance in cattle.

KW - cattle

KW - genome-wide association

KW - imputation

KW - genetic marker

KW - genetic improvement

UR - https://www.isag.us/2017/docs/ISAG2017_Proceedings.pdf

UR - https://www.isag.us/2017/

M3 - Poster

SP - 22

EP - 23

ER -

Mallikarjunappa S, Sargolzaei M, Meade K, Karrow NA, Pant SD. QTLs associated with resistance to MAP infection in Holstein-Friesian cattle. 2017. Poster session presented at 36th International Society for Animal Genetics, Dublin, Ireland.