veterinary

sciences
Review

Genomic Tools and Animal Health

Ricardo Zanella
School of Agronomy and Veterinary Medicine, College of Veterinary Medicine, University of Passo Fundo,
Passo Fundo RS 99052, Brazil; [email protected]; Tel.: +55-54-3316-8485
Academic Editor: Patrick Butaye
Received: 13 June 2016; Accepted: 9 August 2016; Published: 7 September 2016

Abstract: Animals have been selected to improve their productivity in order to increase the
profitability to the producer. In this scenario, not much attention was given to health traits. As a
consequence of that, selection was made for animals with higher production and a shortened
productive life. In addition to that, the intense production system used in livestock has forced
animals to be exposed to higher pathogen loads, therefore predisposing them to infections. Infectious
diseases are known to be caused by micro-organisms that are able to infect and colonize the host,
affecting their physiological functions and causing problems in their production and on animal
welfare. Even with the best management practices, diseases are still the most important cause of
economic losses in the animal industry. In this review article we have addressed the new tools that
could be used to select animals to better cope with diseases and pathogens.
Keywords: animal health; GWAS; genomic selection; infectious diseases

1. Introduction
Animal selection has historically been based on production traits, and not much attention was
given to selection for health traits. This resulted in modern cows with high milk yields and reduced
fertility, and shortened productive lives, caused by increased susceptibility to postpartum metabolic
disorders. However, even in the selection for animals with higher production, it was possible to observe
individual differences to challenges in the host response to diseases [1]. Selection has been used to
control or manage infectious diseases, such as anthelmintics for parasite control, ascaricides for tick
control and antibiotics to control bacterial diseases, and this have created major resistance problems.
As a consequence of that, breeders and agricultural industries are now facing an intense pressure to
select animals for enhanced disease resistance and tolerance with better welfare conditions [2].
In the last decades, important attention was given to acute infections caused by emerging diseases,
especially those that infect humans from other host species. Those are called zoonotic diseases,
and are caused by different pathogenic agents. The circulation of zoonotic agents between humans,
animals, and the environment is a concern for animal and public health. According to the Institute of
Medicine [3], more than 65% of emerging infectious diseases were caused by zoonotic agents, resulting
in annually indirect economic losses of over $200 billion [4]. In this context it is expected that infectious
disease will cause major economic losses in the livestock sector worldwide.
Many diseases will affect the animals productivity. Generally, it will occur in the early stages of
infection (subclinical), when there is a lack of evidence of infection, which, if untreated, can progress
to severe clinical disorders. The overall consequences of diseases on animal production are great.
Generally, infected animals have lower performance rates, costs associated with animal treatment,
increased mortality rates and possibly reproductive failure [5,6]. Complete knowledge of the disease
mechanism is needed for the decision on the protocol and treatment to be used.
Vaccination and good management practices have been widely used to control and to avoid
pathogens spreading in populations, providing variable levels of protection. However, the mechanism

Vet. Sci. 2016, 3, 21; doi:10.3390/vetsci3030021

www.mdpi.com/journal/vetsci

Vet. Sci. 2016, 3, 21

2 of 8

involving immune protection is not fully understood; therefore, not all the animals respond to the
treatment, leading to the discovery of new approaches to address those failures [7,8]. It is common
to observe in a vaccinated population some differences in the immune response between animals [7].
Also, differences in the severity of infection of animals exposed to similar doses of pathogens were
found, suggesting a possible role of genetics involved with tolerance and resistance to infection [9].
Resistance can be defined as the hosts ability to resist an infection or to control the parasite lifecycle,
and tolerance is the hosts ability to tolerate infection and show little or no effects of disease [9,10].
Up to this moment, the consequences of breeding animals for disease resistance or tolerance in
relation to production traits are not known. It is known that selection for disease traits needs to be
conducted within the herd, as opposed of production traits which can be done individually. This is
because when working with infectious diseases, animals may infect each other directly or indirectly.
Therefore, the health status between animals within the same herd is not independent of the other
animals, since it depends on the host genetic makeup and also on the epidemiology of the disease.
Many factors have been identified to influence animal health; therefore, it is very complicated to
evaluate and to study the host genetics and pathogen interaction. The most difficult concept in the
experimental design is how to define and to establish the correct phenotype. How can we assume
that an animal is resistant to a disease if we do not know the pathogen load that the animals have
been exposed to or if the animal was even exposed? In this context, assumptions need to be made to
evaluate animal exposure to pathogens, and it is expected that animals sharing the same environment
are possibly experiencing the same amount and type of pathogens. The sensitivity and specificity of
the diagnostic tools used are also very important to identify the epidemiologic status of animals in a
herd. Different tests can result in a conflicting phenotypic classification, and therefore it can result in a
broad range of outcomes with spurious results. Therefore, the success of genomic selection for health
traits starts with correct phenotype collection and the accuracy of the diagnostic test. Animals can be
infected without presenting clinical signs, or may be considered a false negative. The accuracy of the
determination of the infectious status of the animal is directly related to the sensitivity and specificity
of the diagnostic test [11], and different results can be obtained when different methodologies are
applied. However, a true confirmation is obtained when the pathogen is isolated and sequenced from
the organ or systems being affected by a specific disease. In addition to that, pathogen colonization
will result in changes in the immune system of the animal, possibly altering the gene expression profile
of tissues being infected or even having a global effect. Those changes in the host will have a direct or
indirect effect on the disease phenotype.
In this review we have addressed and explored some of the challenges related to animal
health, and some of the new tools that could be used to select animals to better cope with diseases
and pathogens.
2. Infection-Disease Transmission
Several risk factors have been identified to influence whether an animal that was exposed to an
agent will become infected or not. In addition to that, they can determine whether the infection will
result in, sooner or later, clinical disease, depending on the host immune response. Some of those risk
factors can be associated with animal and pathogen genetic composition, the nutritional state of the
host at the time of infection, and the environmental conditions. Those factors can also be associated
with the spread of the pathogen among other animals [1]. However, in all the cases of infection, the
necessary condition is circulating levels of a specific pathogen in a population.
The transmission of pathogens from a reservoir may be continuous or sporadic; however, once
the infection is in the host population it may follow different pathways. In a population, the presence
of a reservoir can directly transmit the pathogen to the host (Figure 1, Arrow A) in a sporadic or in a
continuous way [1]. Once the host population becomes infected, it can be their own continuous source
of infection (Figure 1, Arrow C), or result in a cross-contamination to the reservoir (Figure 1, Arrow
B). The selection being imposed on the pathogens in the host may differ from the one being imposed

Vet. Sci.
2016, 3, 21
Vet. Sci. 2016,
3, 21

3 of 8

3 of 8

B). The selection being imposed on the pathogens in the host may differ from the one being imposed
in the reservoir;
therefore,
genetic
makeupin
in the
the pathogens
onon
different
populations
may vary,
in the reservoir;
therefore,
the the
genetic
makeup
pathogens
different
populations
may vary,
resulting in different levels of disease severity and infectivity. The initial step in controlling the spread
resulting in different levels of disease severity and infectivity. The initial step in controlling the spread
of diseases is the identification and control of those risk factors.

of diseases is the identification and control of those risk factors.

Figure 1. Model of disease transmission among or within populations.

Figure 1. Model of disease transmission among or within populations.

3. Selection
for Resistance or Tolerance
3. Selection for Resistance or Tolerance
To control
the spread
of diseases,
we first
need
to to
control
(resistance),
and
second it is
To control
the spread
of diseases,
we first
need
controlthe
theinfection
infection (resistance),
and
second
necessary
tonecessary
reduce the
the disease
The main
to control
the infection
is
it is
to severity
reduce theofseverity
of the(tolerance).
disease (tolerance).
Theobjective
main objective
to control
the
infection
is to reduce
the number
of infected
animals (prevalence)
a herd or population,
to reduce
the number
of infected
animals
(prevalence)
in a herd orinpopulation,
reducingreducing
the infectious
infectious
the existing
population.
two basic
genetic approaches
pressurethe
among
the pressure
existingamong
population.
There
are two There
basicare
genetic
approaches
that can that
be used to
can be used to select animals to fight a pathogenic infection (resistance and tolerance).
select animals to fight a pathogenic infection (resistance and tolerance).
The first method is to select for animals that are resistant or less susceptible to infection;
Thefurthermore,
first method
is to animals
select for
animals
thatas are
resistant
less (Figure
susceptible
to infection;
susceptible
can be
subdivided
tolerant
and lessor
tolerant
2). Resistance
furthermore,
susceptible
animals
can
be subdivided
tolerant
and
lessexposed
tolerant
2). [12].
Resistance
was defined
as the ability
of an
organism
to preventasthe
infection
when
to (Figure
a pathogen
Gondaasand
[13] identified
a QTLthe
(Quantitative
on BTA20
was defined
thecolleagues
ability ofinan2007
organism
to prevent
infection Trait
whenLoci)
exposed
to a affecting
pathogen [12].
susceptibility
to Mycobacterium
paratuberculosis
in US Holstein
cows. Using
a similar
Gonda and
colleagues
in 2007 [13]
identified a(MAP)
QTL infection
(Quantitative
Trait Loci)
on BTA20
affecting
approach for phenotypic classification, Settles and colleagues [14] tested animals for the presence of
susceptibility to Mycobacterium paratuberculosis (MAP) infection in US Holstein cows. Using a similar
MAP with a different diagnostic method with better sensitivity and specificity. Using a genome-wide
approach
for phenotypic classification, Settles and colleagues [14] tested animals for the presence of
association analysis (GWAS), a chromosomal region on BTA3 associated with MAP tissue infection
MAP with
different
diagnostic
with better
sensitivity
and
specificity.
in aagroup
of Holstein
cowsmethod
was identified.
Investigation
of this
region
on BTA3Using
using a42genome-wide
single
association
analysis
(GWAS),
a kb
chromosomal
region
on of
BTA3
associated
with MAP
infection
nucleotides
to explore
a 235
region identified
a region
10.6 kb,
possibly harboring
the tissue
causative
mutation
involved
in
MAP
infection
[15].
Further
investigation
using
a
gene
set
enrichment
analysis
in a group of Holstein cows was identified. Investigation of this region on BTA3 using 42 single
identified
the gene
Endothelin-2
located
near theofSNP
Nucleotide
Polymorphism)
nucleotides
to explore
a 235
kb region(END2)
identified
a region
10.6(Single
kb, possibly
harboring
the causative
previously identified by Settles and colleagues [15] to be involved with MAP infection in cattle [16].
mutation involved in MAP infection [15]. Further investigation using a gene set enrichment analysis
EDN2 encodes a member of the protein family of secretory vasoconstrictive peptides and works as a
identified
thefor
gene
Endothelin-2
(END2)
located
near the SNP
(Single
Nucleotide
ligand
the endothelin
receptors,
initiating
an intracellular
signaling
cascade,
which canPolymorphism)
modulate
previously
by Settles
and colleagues
[15]
to be involved
with candidate
MAP infection
in cattle [16].
MAPidentified
tissue infection
[9]. Therefore,
this is a great
positional
and functional
gene involved
in MAP infection.
EDN2 encodes
a member of the protein family of secretory vasoconstrictive peptides and works as a
ligand for the endothelin receptors, initiating an intracellular signaling cascade, which can modulate
MAP tissue infection [9]. Therefore, this is a great positional and functional candidate gene involved in
MAP infection.
To explore the role of EDN2 and MAP infection, nuclear extracts from freshly harvested ileo-cecal
lymph nodes from Holstein cows were used to characterize differences in the binding affinities of
the sequences harboring the significant SNPs on BTA3. Luciferase reporter assays were performed
to confirm the transcriptional activity of EDN2, demonstrating mobility shifts, indicating that one or
more variants in the promoter of EDN2 may result in susceptibility to MAP tissue infection in Holstein
cattle [17].
The second approach that can be used is to select for animals which are genetically tolerant to the
pathogenic infection. Raberg and colleagues [12] presented empirical evidence for genetic variation
leading to tolerance in animals using a mouse model to study malaria. Their definition of tolerance
was based on individuals who respond to a pathogenic infection in such a way that limits the damage
(fitness) to the host without affecting the pathogen burden. Tolerance is generally described as the
relationship between the levels of infection intensity and fitness. Therefore, in a tolerant animal,
the amount of infection has little or no effect on the fitness of the individual [10,15]. Production

Vet. Sci. 2016, 3, 21

4 of 8

performance tends to be reduced in animals with higher pathogen loads, and this is illustrated in
Vet. Sci. 2016, 3, 21
4 of 8
Figure 3, which shows a representation of the performance and level of infection.

Vet. Sci. 2016, 3, 21

Figure 2. Schematic diagram of host pathogen interaction-disease infection mode.

5 of 8

Figure 2. Schematic diagram of host pathogen interaction-disease infection mode.

To explore the role of EDN2 and MAP infection, nuclear extracts from freshly harvested ileocecal lymph nodes from Holstein cows were used to characterize differences in the binding affinities
of the sequences harboring the significant SNPs on BTA3. Luciferase reporter assays were performed
to confirm the transcriptional activity of EDN2, demonstrating mobility shifts, indicating that one or
more variants in the promoter of EDN2 may result in susceptibility to MAP tissue infection in
Holstein cattle [17].
The second approach that can be used is to select for animals which are genetically tolerant to
the pathogenic infection. Raberg and colleagues [12] presented empirical evidence for genetic
variation leading to tolerance in animals using a mouse model to study malaria. Their definition of
tolerance was based on individuals who respond to a pathogenic infection in such a way that limits
the damage (fitness) to the host without affecting the pathogen burden. Tolerance is generally
described as the relationship between the levels of infection intensity and fitness. Therefore, in a
tolerant animal, the amount of infection has little or no effect on the fitness of the individual [10,15].
Production performance tends to be reduced in animals with higher pathogen loads, and this is
illustrated in Figure 3, which shows a representation of the performance and level of infection.
Figure
3. Susceptible
animals
can
bebetolerant
higher
infection
associated
Figure
3. Susceptible
animals
can
tolerant or
or non-tolerant;
non-tolerant; a ahigher
infection
loadload
associated
with with
lowerlower
losses
in the
performance
highertolerance
tolerance
where
increased
losses
losses
in the
performanceisisananindication
indication of higher
(A)(A)
where
increased
losses
in in
performance
caused
by increased
infectionload
loadis
is an
an indication
indication ofofa aless
tolerant
animal
(B). (B).
performance
caused
by increased
infection
less
tolerant
animal
Genetic tolerance has been evaluated in cattle that were infected with MAP and its genetic

Genetic tolerance has been evaluated in cattle that were infected with MAP and its genetic
association was tested using a GWAS, and a region on BTA15 encoding the gene GNA12 was
association
was For
tested
using
a GWAS,
and a region
on BTA15
the gene
GNA12
was to
associated.
associated.
this,
tolerance
was measured
as the
amountencoding
of MAP fecal
shedding
relative
the
For this,
tolerance
was
measured
as
the
amount
of
MAP
fecal
shedding
relative
to
the
levels
of MAP
levels of MAP tissue infection [10,15]. High levels of fecal shedding on Johnes positive animals are
tissuegenerally
infection
[10,15].
High
levels
of
fecal
shedding
on
Johnes
positive
animals
are
generally
associated with disease severity, since they are negatively correlated with milk production,
fat content
protein
content,
lower
life and
an increased
of days between
associated
with and
disease
severity,
since
theyproductive
are negatively
correlated
withnumber
milk production,
fat content
pregnancies,
as well
as high
disease transmission
to thenumber
herd [13,1820].
of
and protein
content,
lower
productive
life and an rates
increased
of daysTherefore,
between levels
pregnancies,
MAP fecal shedding could be used as an accurate measurement of animal fitness.
Differences in the genetic background between animals also need to be taken into account when
evaluating association with genetic markers, to reduce the possibility of identifying erroneous
markers involved with the phenotype being studied. This test can be conducted using the pair-wise
identical by state test (IBS) computed between all the animals in the study and plotted using a multidimensional scaling plot (MDS for better visualization.

Vet. Sci. 2016, 3, 21

5 of 8

as well as high disease transmission rates to the herd [13,1820]. Therefore, levels of MAP fecal
shedding could be used as an accurate measurement of animal fitness.
Differences in the genetic background between animals also need to be taken into account when
evaluating association with genetic markers, to reduce the possibility of identifying erroneous markers
involved with the phenotype being studied. This test can be conducted using the pair-wise identical by
state test (IBS) computed between all the animals in the study and plotted using a multi-dimensional
scaling plot MDS for better visualization.
4. Selection for Better Immune Response
Another approach that could be used is to select for animals that will have a better response
when challenged with pathogens. Vaccination is considered the most powerful tool used to control
and to diminish the parasite burden, reducing the clinical signs and the transmission of the pathogen
within animals [21]. However, animal response to vaccination can vary within individuals, with some
individuals not responding at all or having different levels of protection [22].
In the livestock sector, most of the economic losses have been associated with infection with
pathogens. To overcome those losses, several strategies have been proposed and implemented with
unsatisfactory results. For example, influenza virus is still considered the most prevalent respiratory
pathogen circulating among animals and humans, causing a major impact to the economy and the
populations health. Therefore, there is a need to develop new methodologies to increase the efficacy
of the current methods.
Here, we present results of an association study of genetic markers with the immune response to
influenza vaccination in a swine herd [7]. Animals were vaccinated with an inactivated H1N1pdm
virus and tested for the association of genetic markers with immune response efficacy to influenza
vaccination (IAV). The animal immune response was measured based on the presence or absence of
Vet. Sci. 2016, 3, 21
6 of 8
antibodies to IAV (qualitative measurement), and also based on the levels of antibodies produced
by
the animals (quantitative).
Using the response to vaccination as a qualitative phenotype, a region on SSC12 was identified
Using the response to vaccination as a qualitative phenotype, a region on SSC12 was identified to
to be associated with the immune response. When we tested the efficacy of the response to the
be associated with the immune response. When we tested the efficacy of the response to the vaccination
vaccination as a quantitative phenotype, four additional associated chromosomes were identified:
as a quantitative phenotype, four additional associated chromosomes were identified: SSC0, SSC1,
SSC0, SSC1, SSC7 and SSC15 [7]. These results suggest the complexity of the immune traits when
SSC7 and SSC15 [7]. These results suggest the complexity of the immune traits when used to test their
used to test their interaction with host genetics.
interaction with host genetics.
However, even in vaccinated animals we can have responders that will become infected, and
However, even in vaccinated animals we can have responders that will become infected, and those
those animals can recover from infection but will present losses in production. Those losses are
animals can recover from infection but will present losses in production. Those losses are generally
generally associated with lower production or even reproductivity failure (Figure 4).
associated with lower production or even reproductivity failure (Figure 4).

Figure 4. Representation of animal response to vaccination.

Figure 4. Representation of animal response to vaccination.

5. New Approaches to Old Problems

The great advantage of high-throughput sequencing is the ability to generate a large amount of
genomic information to address complex problems. In addition to that, the use of genomic
sequencing for the identification of specific pathogens associated with diseases has been facilitated,

Vet. Sci. 2016, 3, 21

6 of 8

5. New Approaches to Old Problems

The great advantage of high-throughput sequencing is the ability to generate a large amount of
genomic information to address complex problems. In addition to that, the use of genomic sequencing
for the identification of specific pathogens associated with diseases has been facilitated, allowing for
the identification of genomic variations associated with the pathogenicity of specific agents and the
sensitivity to specific treatment drugs.
In dairy cows, clinical mastitis is considered a complex health disorder which will impact the
farms profitability and the animal welfare. The heritability associated with this disorder can range
from 0.01 to 0.42, indicating the involvement of genetic components with the appearance of this
disorder [23]. Using whole genomic association studies (GWAS), genetic markers were identified on
chromosomes 2, 14 and 20 as associated with susceptibility to this disorder, indicating a polygenic
effect [23]. Some of the genes located near the associated markers were involved with immune
response activation and mammary gland metabolism. Despite those findings, it was proposed that
susceptibility to clinical mastitis is regulated by different genes related to immune response which are
pathogen-specific; therefore, animal selection for resistance to a specific pathogen might not work for
different pathogens.
Recent studies have applied the RNA sequencing technique to unsolved biological problems,
especially for the identification of genes involved with illness [2426]. This new methodology uses the
whole transcriptome sequencing of a specific tissue at a specific time point. This might be a useful
tool to investigate the genetic mechanisms involved with the host infection and with the host immune
response to an infection. Beside the advantage of using a small number of animals, this methodology
will possibly be able to give the whole picture of what is happening transcriptomically when the
animal is facing a challenge, especially within an infection.
The host-pathogen interaction has been described in a study using the RNA-Seq approach, which
investigated both viral and host gene expression in a mouse model after H1N1 infection. An important
gene involved with viral replication and host defense has been identified in this model. The use of this
methodology could be applied to elucidate the host-pathogen interactions, increasing the knowledge
of genes involved with host susceptibility or survival during infections [27].
As an example, animals with different genotypes (AA, AG, GG) for a specific marker on exon 5 of
EDN2 (the gene involved with resistance to MAP infection) had different levels of its expression in the
lymph nodes. This indicates a possible suppression of the gene expression in animals with a specific
genotype when exposed to specific challenges [28]. However, this study was conducted evaluating
the transcription profile using only one gene in one tissue, without accounting for the effect of other
genes. The use of high-throughput sequencing offers us an opportunity for the identification of global
transcriptomic changes during specific challenges in different tissues at the same time.
6. Conclusions
Genetic selection for animals that are resistant, or tolerant or for animals that have a better immune
response to vaccination can help diminish the impact of diseases in the livestock sector. However,
it is not known what the best strategy is and what the long-term consequences are when selecting for
those traits. However, if selection for those traits can reduce human exposure to infectious pathogens,
it offers a potential to reduce the health risks in a population.
Acknowledgments: The data used in this paper was originated from projects funded by: Washington State
University Center for Reproductive Biology, Berry College, BJT grant 373167/2012-1 and 447470/2014-0 from the
National Council of Scientific and Technological Development (CNPq) and ARD/PPP/FAPERGS/CNPq 08/2014.
No funding was provided for publication fees.
Conflicts of Interest: The author declares no conflict of interest.

Vet. Sci. 2016, 3, 21

7 of 8

References
1.
2.
3.

4.

5.
6.

7.

8.
9.
10.

11.

12.
13.

14.
15.

16.

17.

18.

Bishop, S.C.; Stear, M.J. Genetic and epidemiological relationships between productivity and disease
resistance: Gastrointe stinal parasite infection in growing lambs. Anim. Sci. 1999, 69, 515524. [CrossRef]
Bishop, S. Disease Genetics: From Concepts to Utilisation. In Presented at the Short Course at Iowa State
University, Ames, IA, USA, 26 June 2014.
National Research Council (US) Committee on Achieving Sustainable Global Capacity for Surveillance and
Response to Emerging Diseases of Zoonotic Origin. Sustaining Global Surveillance and Response to Emerging
Zoonotic Diseases; Keusch, G.T., Pappaioanou, M., Gonzalez, M.C., Scott, K.A., Tsai, P., Eds.; National
Academies Press: Washington, DC, USA, 2009.
World Bank. Volume One: Towards A One Health Approach for Controlling Zoonotic Diseases. World
Bank: Washington, DC, USA, 2010. Available online: http://documents.worldbank.org/curated/en/
214701468338937565/Volume-one-towards-a-one-health-approach-for-controlling-zoonotic-diseases
(accessed on 10 August 2016).
Snowder, G.D.; van Vleck, L.D.; Cundiff, L.V.; Bennett, G.L. Bovine respiratory disease in feedlot cattle:
Environmental, genetic, and economic factors. J. Anim. Sci. 2006, 84, 19992008. [CrossRef] [PubMed]
Garcia, M.D.; Thallman, R.M.; Wheeler, T.L.; Shackelford, S.D.; Casas, E. Effect of bovine respiratory disease
and overall pathogenic disease incidence on carcass traits. J. Anim. Sci. 2010, 88, 491496. [CrossRef]
[PubMed]
Zanella, R.; Gava, D.; Peixoto, J.O.; Schaefer, R.; Ciacci-Zanella, J.R.; Biondo, N.; da Silva, M.V.; Cantao, M.E.;
Ledur, M.C. Unravelling the genetic components involved in the immune response of pigs vaccinated against
influenza virus. Virus Res. 2015, 210, 327336. [CrossRef] [PubMed]
Davies, G.; Genini, S.; Bishop, S.C.; Guiffra, E. An assessment of opportunities to dissect host genetic
variation in resistance to infectious diseases in livestock. Animal 2009, 3, 415436. [CrossRef] [PubMed]
McSpadden, K.; Caires, K.; Zanella, R. The effect of mycobacterium avium subspecies paratuberculosis
exposure on animal health. Acta Sci. Vet. 2013, 41, 1095.
Zanella, R.; Settles, M.L.; McKay, S.D.; Schnabel, R.; Taylor, J.; Whitlock, R.H.; Schukken, Y.; Van Kessel, J.S.;
Smith, J.M.; Neibergs, H.L. Identification of loci associated with tolerance to Johnes disease in Holstein
cows. Anim. Genet. 2011, 42, 2838. [CrossRef] [PubMed]
Fulton, R.W.; Confer, A.W. Laboratory test descriptions for bovine respiratory disease diagnosis and their
strengths and weaknesses: Gold standards for diagnosis, do they exist? Can. Vet. J. 2012, 53, 754761.
[PubMed]
Raberg, L.; Sim, D.; Read, A.F. Disentangling genetic variation for resistance and tolerance to infectious
diseases in animals. Science 2007, 318, 812814. [CrossRef] [PubMed]
Gonda, M.G.; Kirkpatrick, B.W.; Shook, G.E.; Collins, M.T. Identification of a QTL on BTA20 affecting
susceptibility to Mycobacterium avium ssp. paratuberculosis infection in U.S. Holsteins. Anim. Genet. 2007,
38, 389396. [CrossRef] [PubMed]
Neibergs, H.L.; Settles, M.L.; Whitlock, R.H.; Taylor, J.F. GSEA-SNP identifies genes associated with Johnes
disease in cattle. Mamm. Genome 2010, 21, 419425. [CrossRef] [PubMed]
Settles, M.; Zanella, R.; McKay, S.D.; Schnabel, R.D.; Taylor, J.F.; Whitlock, R.; Schukken, Y.; Van Kessel, J.S.;
Smith, J.M.; Neibergs, H. A whole genome association analysis identifies loci associated with Mycobacterium
avium subsp. paratuberculosis infection status in U.S. Holstein cattle. Anim. Genet. 2009, 40, 655662.
[CrossRef] [PubMed]
Zanella, R.; Whitlock, R.H.; Neibergs, H.L. Short Communication: Refinement of genetic regions associated
with Mycobacterium avium subspecies paratuberculosis tissue infection and to tolerance to Johnes disease.
J. Dairy Sci. 2011, 94, 42304236. [CrossRef] [PubMed]
Neibergs, H.L.; Wang, Z.; Zanella, R.; Scraggs, E.R.; Van Tassell, C.; White, S.; Sieverkropp, K.D.; Neupane, M.;
Knie, B.; Neibergs, H.M.; et al. Deciphering the role of EDN2 in Mycobacterium avium spp paratuberculosis
tissue infection. In Proceedings of the Plant and Animal Genome XXI Conference, San Diego, CA, USA,
1116 January 2013.
Benedictus, G.; Dijkhuizen, A.A.; Stelwagen, J. Economic losses due to paratuberculosis in dairy cattle.
Vet. Rec. 1987, 121, 142146. [CrossRef] [PubMed]

Vet. Sci. 2016, 3, 21

19.
20.

21.
22.

23.

24.

25.

26.
27.

28.

8 of 8

Mcnab, W.B.; Meek, A.H.; Duncan, J.R.; Brooks, B.W.; Van Dreumel, A.A. An evaluation of selected screening
tests for bovine paratuberculosis. Can. J. Vet. Res. 1991, 55, 252259. [PubMed]
Nordlund, K.V.; Goodger, W.J.; Pelletier, J.; Collins, M.T. Associations between subclinical paratuberculosis
and milk production, milk components, and somatic cell counts in dairy herds. J. Am. Vet. Med. Assoc. 1996,
208, 18721876. [PubMed]
Kimman, T.G.; Vanderbriel, R.J.; Hoebee, B. Genetic variation in the response to vaccination.
Public Health Genom. 2007, 10, 201217. [CrossRef] [PubMed]
Poland, G.A.; Ovsyannikova, I.G.; Kennedy, R.B.; Lambert, N.D.; Kirkland, J.L. A systems biology approach
to the effect of aging, immunosenescence and vaccine response. Curr. Opin. Immunol. 2014, 29, 6268.
[CrossRef] [PubMed]
Tiezzi, F.; Parker-Gaddis, K.L.; Cole, J.B.; Clay, J.S.; Maltecca, C. A Genome-wide association study for clinical
mastitis in first parity U.S. holstein cows using single-step approach and genomic matrix re-weighting
procedure. PLoS ONE 2015, 10, e0114919. [CrossRef] [PubMed]
Wang, E.T.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S.F.; Schroth, G.P.;
Burge, C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456, 470476.
[CrossRef] [PubMed]
Wilhelm, B.T.; Briau, M.; Austin, P.; Faubert, A.; Boucher, G.; Chagnon, P.; Hope, K.; Girard, S.; Mayotte, N.;
Landry, J.R.; et al. RNA-seq analysis of two closely related leukemia clones that differ in their self-renewal
capacity. Blood 2011, 117, e27e38. [CrossRef] [PubMed]
Blekhman, R.; Marioni, J.C.; Zumbo, P.; Stephens, M.; Gilad, Y. Sex-specific and lineage-specific alternative
splicing in primates. Genome Res. 2010, 20, 180189. [CrossRef] [PubMed]
Wilk, E.; Pandey, A.K.; Leist, S.R.; Hatesuer, B.; Preusse, M.; Pommerenke, C. RNAseq expression analysis of
resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus
replication and important for host resistance to infection. BMC Genom. 2015, 16, 655. [CrossRef] [PubMed]
Zanella, R. Identification of Chromosomal Regions Associated with Infectious Diseases in Cattle.
Ph.D. Thesis, Washington State University, Pullman, WA, USA, 2011.
2016 by the author; licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC-BY) license (http://creativecommons.org/licenses/by/4.0/).