The impact of genetic selection for increased production on fitness traits of small ruminants
Small Ruminant Research,
Год журнала:
2025,
Номер
unknown, С. 107491 - 107491
Опубликована: Март 1, 2025
Язык: Английский
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
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 diversity and runs of homozygosity (ROH): A portrait of the quantitative academic publication dynamic and scientific metadata
Research Square (Research Square),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 10, 2024
Abstract
Background
Autozygosity
is
the
homozygous
state
of
identical-by-descent
(IBD)
alleles,
which
can
result
from
several
phenomena.
The
increase
in
inbreeding
(F)
leads
to
different
negative
effects
such
as
a
reduction
genetic
variance,
with
individual
performance
(inbreeding
depression)
and
lower
population
viability.
Nowadays,
among
alternative
methods
estimate
inbreeding,
F
estimated
Run
Homozygosity
(FROH)
considered
most
powerful.
This
study
aimed
provide
systematic
review
comprehensive
understanding
structure
dynamics
genomic
diversity
impact
ROH
studies
over
last
decade,
highlighting
directions
opportunities
for
future
research.
Results
406
publications
were
identified
on
WoS
core
collection
applied
bibliometric
analysis
available
R
environment.
revealed
an
increased
number
per
year.
China,
Italy,
United
States
are
countries
that
published
topic,
main
contributions
journals
Animals
Frontiers
Genetics.
highlights
growing
interest
functional
ROHs
driven
by
computational
tools
capable
characterizing
these
regions.
Noteworthy
PLINK
software
detectRUNS
package,
utilizing
sliding
window
methodology
SNP
genome.
Beyond
global
crisis
loss,
challenges
encompass
ecological
issues,
habitat
fragmentation,
isolated
populations,
well
availability
variation
species
domesticated
humans,
forms
foundation
our
food
supply.
Conclusion
A
progress
research
breeds
homozygosity
(ROH)
diversity,
advancement
technology
international
collaboration.
Asia,
America
Europe
lead
knowledge
production.
Advances
like
mean
quest
more
accurate
analysis.
Emerging
topics
migration
correlation
indicate
increasing
focus
standards.
Challenges
include
refining
analytical
techniques
exploring
regions
high
heterozygosity,
promising
directions.
Язык: Английский
Genomic analysis revealed hotspots of genetic adaptation and risk of disappearance in the Brazilian goat populations
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 4, 2024
Abstract
We
accessed
a
50K
Illumina
SNP
genotype
dataset
from
two
important
goat
breeds
of
the
Brazilian
semi-
arid
region
to
analyze
abundance
and
length
runs
homozygosity
(ROH).
This
analysis
aims
elucidate
importance
adaptation
history
in
genome
populations
measure
genomic
inbreeding.
Heterozygosity-rich
regions
(HRR)
or
high
genetic
variability
provide
clues
about
how
diversity
might
be
associated
with
increased
fitness,
avoiding
deleterious
homozygous
alleles.
Overall,
22,872
ROH
were
identified.
The
average
number
per
individual
ranged
74.73
(Anglo-Nubian
commercial
breed)
173.85
(Marota
landrace).
Analysis
distribution
according
their
size
showed
that,
for
both
breeds,
majority
short
(<2.0
Mb)
category
(65.6%).
ROH-based
inbreeding
(F
)
revealed
low
levels
Anglo-Nubian
(0.0627)
Marota
(0.1419),
likely
due
reduction
effective
population
over
generations
landrace.
defined
islands
HRR
identified
common
goat,
where
genes
related
various
traits
such
as
embryonic
development,
body
growth,
lipid
homeostasis,
brain
functions
are
located.
These
results
indicate
that
many
have
therefore
been
under
selective
pressure
these
reared
different
purposes.
Язык: Английский
The relationship between genomic and estimated inbreeding in the population of Holstein cattle in Sverdlovsk region.
Agrarian Bulletin of the,
Год журнала:
2024,
Номер
24(09), С. 1158 - 1171
Опубликована: Окт. 2, 2024
Abstract.
The
purpose
of
this
paper
is
to
study
the
inbreeding
change
Holstein
cattle
in
Sverdlovsk
region
and
show
correlation
between
genomic
estimated
inbreeding.
Methods.
was
conducted
six
farms
included
512
cows
heifers
with
date
birth
from
2007
2022
12
breeding
bulls.
Chips
GGP
Bovine
150K
(Neogen,
USA)
50K
(Illumina,
were
used
for
genotyping.
Genome
estimates
F
--het
function
PLINK
v1.9.
Homozygosity
coefficient
FROH
calculated
“sliding
window”
package
detectRUNS;
FPED
taken
SELEX
database,
where
it
by
pedigrees
Wright-Kislovsky
formula.
Scientific
novelty.
comparison
different
age
groups
estimation
correlations
pedigree
first
time.
Results.
Our
studies
that
coefficients
increase
radically
younger
older
groups.
breed
bulls
highest
value
At
same
time
heterozygosity
level,
sMLH
tends
decrease
age.
In
addition,
a
strong
pedegree
birth,
as
well
weak
(which
have
each
other)
established.
Язык: Английский
Dynamic evolution of satellite DNAs drastically differentiates the genomes ofTriboliumsibling species
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 2, 2024
ABSTRACT
Tandemly
repeated
sequences,
known
as
satellite
DNAs
(satDNAs),
belong
to
the
most
rapidly
evolving
elements
in
eukaryotic
genomes.
Notwithstanding
their
plentitude
and
diverse,
yet
often
inconsistent
functions,
evolutionary
dynamics
of
satDNAs
way
they
model
genomes
are
still
poorly
understood.
In
this
study,
we
explored
satDNA
satDNA-rich
by
focusing
on
two
insect
species
from
genus
Tribolium
,
so
closely
related
that
can
produce
sterile
hybrids.
We
identified
135
freemani
satellitome,
accounting
for
38.7%
genome.
By
comparing
satellitome
T.
with
castaneum
deciphered
origins
predominant,
species-specific
major
satellites,
which
evolved
different
repetitive
present
both
Importantly,
discovered
centromeric
regions
share
an
orthologous
organization,
characterized
minor
satDNAs.
The
male
sex
chromosome,
lacks
but
contains
a
minor-like
satDNA,
further
heightened
question
might
be
centromere-competent.
analyzing
long-range
organization
regions,
arrays
exhibit
strong
tendency
toward
macro-dyad
symmetry,
suggesting
secondary
structures
these
may
more
important
than
primary
sequence
itself.
also
found
evidence
extrachromosomal
circular
DNAs,
thus
responsible
expansion
homogenization
between
non-homologous
chromosomes.
Throughout
genome,
numerous
low-copy-number
siblings,
some
associated
transposable
elements,
highlighting
transposition
mechanism
spreading.
These
findings
demonstrate
genomic
proportions
locations
subject
DNA
turnover
mechanisms.
While
dynamic
evolution
has
undeniably
played
role
shaping
differentiating
it
remains
determined
whether
differences
profiles
cause
or
consequence
speciation.
Язык: Английский
Analysis of the genetic diversity of Ayrshire cattle in Russia. Message 2. Genome analysis based on data on the distribution of ROH patterns in Ayrshire cows
Ecological genetics,
Год журнала:
2023,
Номер
21(3), С. 235 - 248
Опубликована: Дек. 5, 2023
BACKGROUND:
The
analysis
of
ROH
distribution
is
an
important
focus
genetic
resource
conservation
programs
cattle.
Characterization
ROH-islands
allows
to
identify
factors
affecting
productivity
traits
dairy
cattle.
AIM:
was
analyze
intra-breed
diversity
and
population
structure
Ayrshire
cattle,
based
on
data
homozygosity
patterns,
as
well
loci
associated
with
selection
intensity
utility
traits.
MATERIALS
AND
METHODS:
were
obtained
using
whole
genome
genotyping
Illumina
BovineSNP50
(50K)
DNA
chips
(Illumina
Inc.,
USA).
object
the
study
cows
(600
cows),
which
belonged
farms
different
levels
breeding
work.
RESULT:
results
our
studies
showed
a
generally
similar
level
inbredness
analyzed
cattle
herds.
homogeneity
confirmed
by
large
number
animals
(72.83%)
FROH
values
between
0.10
0.20.
Cluster
revealed
consolidated
groups
individuals,
due
their
ancestral
origins.
discovered
ROH-patterns
included
268
genes,
32
involved
in
regulation
synthesis
protein
fat
milk
components.
may
be
used
for
Russia.
CONCLUSIONS:
Russian
distinguished
unique
qualities
composition
architecture,
while
maintaining
insignificant
traces
gene
pool.
Язык: Английский