Unraveling inbreeding patterns and selection signals in Alpine Grey cattle
animal,
Год журнала:
2024,
Номер
18(5), С. 101159 - 101159
Опубликована: Апрель 16, 2024
Inbreeding
plays
a
crucial
role
in
livestock
breeding,
influencing
genetic
diversity
and
phenotypic
traits.
Genomic
data
have
helped
address
limitations
posed
by
incomplete
pedigrees,
providing
deeper
insights
into
breed
diversity.
This
study
assesses
inbreeding
levels
via
pedigree
genomic
approaches
analyzes
old
recent
using
runs
of
homozygosity
(ROH),
selection
signals
Alpine
Grey
cattle.
Pedigree
from
165
575
individuals,
analyzed
with
INBUPGF90
software,
computed
coefficients.
Genomic-based
coefficients
derived
PLINK
v1.9.
or
DetectRUNS
R
package
analyses
1
180
individuals'
genotypes.
Common
SNPs
within
ROH
pinpointed
regions,
aggregating
"ROH
islands"
indicative
pressure.
Overlaps
USCS
Genome
Browser
unveiled
gene
presence.
Moderate
correlations
(0.20-0.54)
existed
between
coefficients,
most
estimators
having
higher
(>0.8)
correlation
values.
averaged
0.04
<8
Mb
segments,
0.03
>16
segments;
>90%
ROHs
were
Mb,
indicating
ancient
prevalence.
Recent
proved
less
detrimental
than
cosmopolitan
breeds.
Two
major
islands
on
chromosomes
6
7
harbored
genes
linked
to
immune
response,
disease
resistance
(PYURF,
HERC3),
fertility
(EIF4EBP3,
SRA1).
underscores
the
need
for
detailed
understand
characteristics
historical
changes
local
breeds
like
insights,
especially
ROH,
facilitated
overcoming
limitations,
illuminating
Our
findings
reveal
inbreeding's
enduring
impact
potential
selective
sweeps,
elucidating
traits
Язык: Английский
Development and Application of a 40 K Liquid Capture Chip for Beef Cattle
Animals,
Год журнала:
2025,
Номер
15(9), С. 1346 - 1346
Опубликована: Май 7, 2025
The
availability
of
genome
sequences
and
single-nucleotide
polymorphism
(SNP)
chips
allows
us
to
investigate
the
various
genomic
characteristics
species
by
exploring
genetic
diversity
aid
selection.
SNP
chip
is
a
cost-effective
genotyping
platform
essential
for
molecular
breeding
livestock.
In
this
study,
we
developed
liquid
capture
suitable
five
Hubei
(China)
indigenous
beef
cattle
breeds
based
on
whole-genome
sequencing
datasets.
panel
consisted
42,686
SNPs
(~40
K).
These
were
evenly
distributed
each
bovine
chromosome,
with
majority
having
minor
allele
frequencies
>0.05
located
within
intergenic
regions.
performance
evaluation
was
proceeded
200
individuals,
revealing
that
has
high
call
rate
99.48%.
further
used
examine
population
structure
205
individuals
demonstrated
ability
differentiate
between
foreign
breeds.
also
determine
runs
homozygosity
(ROH)
local
195
individuals.
We
identified
2547
ROH
several
genes
associated
economically
important
traits
in
study
population.
Our
findings
demonstrate
not
only
contributes
understanding
but
provides
valuable
information
future
programs,
thereby
improving
their
production
efficiency
economic
value.
Язык: Английский
Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle
Genes,
Год журнала:
2024,
Номер
15(8), С. 1051 - 1051
Опубликована: Авг. 9, 2024
An
increasing
trend
in
ancestral
and
classical
inbreeding
coefficients
as
well
depression
for
longevity
were
found
the
German
Brown
population.
In
addition,
proportion
of
US
Swiss
genes
is
steadily
Browns.
Therefore,
aim
present
study
was
to
analyze
presence
genomic
localization
runs
homozygosity
(ROH)
order
evaluate
their
associations
with
survival
rates
cows
higher
lactations.
Genotype
data
sampled
2364
Browns
from
258
herds.
The
final
set
included
49,693
autosomal
SNPs.
We
identified
on
average
35.996
±
7.498
ROH
per
individual
a
mean
length
8.323
1.181
Mb.
coefficient
FROH
0.122
0.032
it
decreased
0.074,
0.031
0.006,
when
homozygous
segments
>
8
Mb
(FROH>8),
>16
(FROH>16)
>32
(FROH>32)
considered.
New
showed
highest
correlation
FROH>32,
whereas
had
lowest
correlations
FROH>32.
between
0.572.
significantly
lower
FROH,
FROH>4,
FROH>8
FIS
proportions
<60%
compared
>80%.
Cows
surviving
2nd,
4th,
6th,
8th,
10th
lactation
up
which
due
number
shorter
ROH.
strongest
island
consensus
shared
by
50%
animals
BTA
6
at
85–88
located
this
region
associated
(NPFFR2
ADAMTS3),
udder
health
morphology
(SLC4A4,
NPFFR2,
GC
RASSF6),
milk
production,
protein
percentage,
coagulation
properties
milking
speed
(CSN3).
On
2,
detected
only
genes.
Genes
within
are
predominantly
important
dual-purpose
cattle
breeds
including
Original
For
reaching
more
than
9
lactations,
an
exclusive
7
assumed
be
longevity.
analysis
indicated
that
regions
still
also
containing
affecting
may
have
been
identified.
breeding
should
prevent
any
further
increase
run
program
balanced
weights
robustness
Язык: Английский
Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
Genetics Selection Evolution,
Год журнала:
2024,
Номер
56(1)
Опубликована: Май 2, 2024
Abstract
Background
Rendena
is
a
dual-purpose
cattle
breed,
which
primarily
found
in
the
Italian
Alps
and
eastern
areas
of
Po
valley,
recognized
for
its
longevity,
fertility,
disease
resistance
adaptability
to
steep
Alpine
pastures.
It
categorized
as
'vulnerable
extinction'
with
only
6057
registered
animals
2022,
yet
no
comprehensive
analyses
molecular
diversity
have
been
performed
date.
The
aim
this
study
was
analyse
origin,
genetic
diversity,
genomic
signatures
selection
using
data
from
samples
collected
2000
2018,
shed
light
on
breed's
evolution
conservation
needs.
Results
Genetic
analysis
revealed
that
breed
shares
components
various
valley
breeds,
marked
proximity
Original
Braunvieh
reflecting
historical
restocking
efforts
across
region.
shows
related
both
milk
meat
production,
environmental
adaptation
immune
response,
latter
being
possibly
result
multiple
rinderpest
epidemics
swept
eighteenth
century.
An
population
spanning
18
years
showed
an
increase
mean
level
inbreeding
over
time,
confirmed
by
number
runs
homozygosity
per
individual,
larger
2018
sample.
Conclusions
while
sharing
common
origin
Brown
Swiss,
has
developed
distinct
traits
enable
it
thrive
environment
make
highly
valued
local
farmers.
Preserving
these
adaptive
features
essential,
not
maintaining
enhancing
ability
traditional
animal
husbandry
adapt
changing
environments,
but
also
guaranteeing
resilience
sustainability
livestock
system
livelihoods
within
valley.
Язык: Английский
Genome Wide Association Studies for milk production traits in two autochthonous Aosta cattle breeds
animal,
Год журнала:
2024,
Номер
18(10), С. 101322 - 101322
Опубликована: Сен. 12, 2024
Язык: Английский
Assessing major genes allele frequencies and the genetic diversity of the native Aosta cattle female population
Italian Journal of Animal Science,
Год журнала:
2023,
Номер
22(1), С. 1008 - 1022
Опубликована: Сен. 27, 2023
The
Aosta
cattle
breeds
have
a
key
role
in
the
economy
of
Valley.
In
addition
to
meat
and
milk
production
these
autochthonous
are
important
for
their
cultural
value,
maintenance
mountain
environment.
knowledge
genetic
makeup
represents
fundamental
asset
managing
reproduction
population
order
maintain
existing
diversity
and,
as
possible
input,
apply
genomic
selection
small
population.
A
total
3195
cows
were
genotyped
with
GeneSeek
Genomic
Profiler®
(GGP)
Bovine
100K
by
Neogen
framework
DUALBREEDING-2
project.
Black-Chestnut
Chestnut-Herèn
resulted
be
unique
female
had
shorter
ROH
than
bulls
shared
ROH_islands
that
harbour
adaptative
functional
genes.
Allele
frequencies
major
genes
highlight
possibility
both
quality
variants
is
free
from
known
Mendelian
inheritance
diseases
found
cosmopolitan
(e.g.
BLAD,
CVM,
HCD).
Язык: Английский
MOCOS‐associated renal syndrome in a Brown Swiss cattle
Journal of Veterinary Internal Medicine,
Год журнала:
2023,
Номер
37(6), С. 2603 - 2609
Опубликована: Сен. 7, 2023
A
recessive
form
of
MOCOS-associated
xanthinuria
type
II
is
described
in
Tyrolean
grey
cattle.
similar
case
was
identified
a
5-month-old
Brown
Swiss
calf
with
hoof
overgrowth,
rough
coat,
urine
sediment,
and
pneumonia.To
characterize
the
disease
phenotype,
to
evaluate
its
genetic
etiology,
determine
prevalence
deleterious
allele
population.An
affected
calf,
parents,
65
441
dairy
cattle.The
animal
clinically
examined
necropsied.
Microarray
genotyping
used
genotypes
assess
frequency
MOCOS
control
cohort.Ultrasonography
revealed
hyperechoic
renal
pyramids
multifocal
distal
shadowing
echogenic
sediment
urinary
bladder.
Necropsy
suppurative
bronchopneumonia
urolithiasis.
Histology
numerous
nephroliths
chronic
lymphohistiocytic
interstitial
infiltrates,
fibrosis,
tubular
degeneration,
glomerulonephritis
sclerosis,
bilateral
hydronephrosis.
Dysplastic
changes
were
observed
corium
claw
cornea.
Genetic
testing
homozygous
presence
known
frameshift
variant
case.
Both
parents
heterozygous
carriers
genotyped
cattle
1.4%
(342/24337).The
findings
consistent
diagnosis
syndrome
The
low
breed.
However,
mating
should
be
avoided
prevent
further
losses.
Язык: Английский
Genetic parameters, genomic prediction, and identification of regulatory regions located on chromosome 14 for weight traits in Nellore cattle
Journal of Animal Breeding and Genetics,
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 27, 2024
Abstract
This
study
aimed
to
investigate
functional
variants
in
chromosome
14
(BTA14)
and
its
impact
genomic
selection
for
birth
weight
(BW),
weaning
(WW),
yearling
(YW)
Nellore
cattle.
Genetic
parameter
estimation
the
weighted
single‐step
best
linear
unbiased
prediction
(WssGBLUP)
analyses
were
performed.
Direct
additive
heritability
estimates
high
WW
YW,
moderate
BW.
Trait‐associated
distributed
across
multiple
regions
on
BTA14
observed
genome‐wide
association
studies
(WssGWAS)
results,
implying
a
polygenic
genetic
architecture
different
ages.
Several
genes
have
been
found
with
traits,
including
CUB
And
Sushi
domains
3
(
CSMD3
),
thyroglobulin
TG
diacylglycerol
O‐acyltransferase
1
DGAT1
)
genes.
The
variance
explained
per
SNP
was
higher
six
classes
of
gene
regulatory
(5UTR,
CpG
islands,
downstream,
upstream,
long
non‐coding
RNA,
transcription
factor
binding
sites
(TFBS)),
highlighting
their
importance
traits
A
marginal
increase
accuracy
when
selected
(SV)
information
considered
WssGBLUP
method,
probably
because
small
number
SV
available
BTA14.
identified
genes,
pathways,
functions
contribute
better
understanding
physiological
mechanisms
regulating
breed.
Язык: Английский
Assessment of genome complementarity in three beef-on-dairy crossbreds reveals sire-specific effects on production traits with comparable rates of genomic inbreeding reduction
BMC Genomics,
Год журнала:
2024,
Номер
25(1)
Опубликована: Ноя. 20, 2024
Crossbreeding
beef
bulls
with
dairy
cows
can
improve
the
economic
value
and
fitness
of
calves
not
entering
production
owing
to
increased
meat
yield
heterosis.
However,
outcrossing
might
reduce
dosage
alleles
that
confer
local
adaptation
or
result
in
a
higher
risk
dystocia
due
calf
size.
Given
clear
phenotypic
differences
between
breeds,
varying
phylogenetic
distances
genomic
variations
within
attainable
gains
will
strongly
depend
on
selection
sires
for
crossing.
Thus,
aim
this
study
was
assess
genome
complementarity
Angus
(AAN),
Limousin
(LIM),
Simmental
(SIM)
Brown
Swiss
(BSW)
by
quantifying
inbreeding
reduction
F1
crosses
identifying
genes
potentially
under
BSW-specific
be
affected
outcrossing.
Low-pass
sequencing
data
from
181
cows,
34
bulls,
301
their
progeny,
body
weight
carcass
composition
measurements
248
F1s
were
obtained.
The
high
levels
detected
BSW
substantially
reduced
crossbreds,
only
minor
sire
breeds.
In
585
candidate
identified,
overrepresenting
associated
milk,
carcass,
traits.
Only
few
differentiated
at
nonsynonymous
variants
including
four
tightly
clustered
(FAM184B,
NCAPG,
DCAF16,
LCORL)
nearly
fixed
alternate
but
mostly
heterozygous
homozygous
reference
AAN
LIM
bulls.
allele
these
significantly
correlated
protein
mass
F1s.
Some
highly
divergent
breeds
likely
strong
breed,
trade-offs
productions.
As
opposing
effects
still
segregate
cattle,
marker-assisted
mating
pairs
may
used
modulate
desired
phenotypes
simultaneously
decrease
inbreeding.
Язык: Английский