Copy number variants selected during pig domestication inferred from whole genome resequencing
Frontiers in Veterinary Science,
Год журнала:
2024,
Номер
11
Опубликована: Март 5, 2024
Over
extended
periods
of
natural
and
artificial
selection,
China
has
developed
numerous
exceptional
pig
breeds.
Deciphering
the
germplasm
characteristics
these
breeds
is
crucial
for
their
preservation
utilization.
While
many
studies
have
employed
single
nucleotide
polymorphism
(SNP)
analysis
to
investigate
local
characteristics,
copy
number
variation
(CNV),
another
significant
type
genetic
variation,
been
less
explored
in
understanding
resources.
In
this
study,
we
examined
CNVs
18
Wanbei
pigs
(WBP)
using
whole
genome
resequencing
data
with
an
average
depth
12.61.
We
identified
a
total
8,783
(~30.07
Mb,
1.20%
genome)
WBP,
including
8,427
deletions
356
duplications.
Utilizing
fixation
index
(Fst),
determined
that
164
were
within
top
1%
Fst
value
defined
as
under
selection.
Functional
enrichment
analyses
genes
associated
selected
revealed
linked
reproduction
(
SPATA6
,
CFAP43
CFTR
BPTF
),
growth
development
NR6A1
SMYD3
VIPR2
immunity
PARD3
FYB2
).
This
study
enhances
our
genomic
offers
theoretical
foundation
future
breeding
breed.
Язык: Английский
Whole-genome selective sweep analysis of Danish Large White and Chinese indigenous pig populations
Animal Biotechnology,
Год журнала:
2025,
Номер
36(1)
Опубликована: Март 1, 2025
Язык: Английский
Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs
Genes,
Год журнала:
2022,
Номер
13(11), С. 2026 - 2026
Опубликована: Ноя. 3, 2022
Single
nucleotide
polymorphism
was
widely
used
to
perform
genetic
and
evolution
research
in
pigs.
However,
little
is
known
about
the
effect
of
copy
number
variation
(CNV)
on
characteristics
This
study
performed
a
genome-wide
comparison
CNVs
between
Wannan
black
pigs
(WBP)
Asian
wild
boars
(AWB),
using
whole
genome
resequencing
data.
By
Manta,
we
detected
total
28,720
that
covered
approximately
1.98%
pig
length.
We
identified
288
selected
(top
1%)
by
performing
Fst
statistics.
Functional
enrichment
analyses
for
genes
located
were
found
be
muscle
related
(NDN,
TMOD4,
SFRP1,
SMYD3),
reproduction
(GJA1,
CYP26B1,
WNT5A,
SRD5A2,
PTPN11,
SPEF2,
CCNB1),
residual
feed
intake
(RFI)
(MAP3K5),
ear
size
(WIF1).
provides
essential
information
further
basis
complex
phenotypic
direction
protection
utilization
pig.
Язык: Английский
Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars
Genes,
Год журнала:
2023,
Номер
14(2), С. 472 - 472
Опубликована: Фев. 12, 2023
Copy
number
variation
(CNV)
has
been
widely
used
to
study
the
evolution
of
different
species.
We
first
discovered
CNVs
in
24
Anqingliubai
pigs
and
6
Asian
wild
boars
using
next-generation
sequencing
at
whole-genome
level
with
10×
depth
understand
relationship
between
genetic
production
traits
domestic
pigs.
A
total
97,489
were
identified
divided
into
10,429
copy
regions
(CNVRs),
occupying
32.06%
porcine
genome.
Chromosome
1
had
most
CNVRs,
chromosome
18
least.
Ninety-six
CNVRs
selected
VST
1%
based
on
signatures
all
sixty-five
genes
regions.
These
strongly
correlated
distinguishing
groups
by
enrichment
Gene
Ontology
Kyoto
Encyclopedia
Genes
Genomes
pathways,
such
as
growth
(CD36),
reproduction
(CIT,
RLN),
detoxification
(CYP3A29),
fatty
acid
metabolism
(ELOVL6).
The
QTL
overlapping
associated
meat
traits,
growth,
immunity,
which
was
consistent
CNV
analysis.
Our
findings
increase
understanding
evolved
genome
structural
variations
pigs,
provide
new
molecular
biomarkers
guide
breeding
efficient
use
available
resources.
Язык: Английский
Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes
Genes,
Год журнала:
2024,
Номер
15(5), С. 623 - 623
Опубликована: Май 14, 2024
Genetic
variation
facilitates
the
evolution,
environmental
adaptability,
and
biodiversity
of
organisms.
Danish
Large
White
(LW)
pigs
have
more
desirable
phenotypes
compared
with
local
Chinese
pigs,
which
difficulty
adapting
to
modern
swine
industry.
However,
genome-wide
mutational
differences
between
these
pig
breeds
are
yet
be
evaluated.
Therefore,
this
study
aimed
evaluate
genomic
identify
breed-specific
SNPs
in
LW
pigs.
Here,
43
LW,
15
Diqing
Tibetan
(DQZ),
Diannan
small-ear
(DN)
whose
genomes
were
re-sequenced
5×
depth
selected.
This
was
followed
by
a
conjoined
analysis
our
previous
resequencing
data
24
Anqing
six-end
white
(AQ)
six
Asian
wild
(SS)
In
total,
39,158,378
13,143,989
insertion–deletions
obtained
all
breeds.
The
number
lowest,
287,194
1289
non-synonymous
Functional
indicated
that
mutations
mainly
associated
reproductive
performance,
feed
intake,
conversion
ratio
These
findings
provide
theoretical
basis
for
genetic
improvements
Язык: Английский
Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing
Genes,
Год журнала:
2024,
Номер
15(2), С. 233 - 233
Опубликована: Фев. 12, 2024
Baoshan
pigs
(BS)
are
a
local
breed
in
Yunnan
Province
that
may
face
inbreeding
owing
to
its
limited
population
size.
To
accurately
evaluate
the
level
of
BS
pig
population,
we
used
whole-genome
resequencing
identify
runs
homozygosity
(ROH)
regions
pigs,
calculated
coefficient
based
on
pedigree
and
ROH,
screened
candidate
genes
with
important
economic
traits
from
ROH
islands.
A
total
22,633,391
SNPS
were
obtained
whole
genome
201
ROHs
detected
532,450
after
quality
control.
The
number
medium-length
(1–5
Mb)
was
highest
(98.43%),
long
(>5
lowest
(1.57%),
mainly
occurred
distant
generations.
FROH,
0.018
±
0.016,
FPED,
pedigree,
0.027
0.028,
which
positively
correlated.
Forty
islands
identified,
containing
507
891
QTLs.
Several
associated
growth
development
(IGFALS,
PTN,
DLX5,
DKK1,
WNT2),
meat
(MC3R,
ACSM3,
ECI1,
CD36,
ROCK1,
CACNA2D1),
reproductive
(NPW,
TSHR,
BMP7).
This
study
provides
reference
for
protection
utilization
pigs.
Язык: Английский
Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink
BMC Genomic Data,
Год журнала:
2024,
Номер
25(1)
Опубликована: Июль 10, 2024
Abstract
The
recent
chromosome-based
genome
assembly
and
the
newly
developed
70K
single
nucleotide
polymorphism
(SNP)
array
for
American
mink
(
Neogale
vison
)
facilitate
identification
of
genetic
variants
underlying
complex
traits
in
this
species.
objective
study
was
to
evaluate
association
between
consensus
runs
homozygosity
(ROH)
with
growth
feed
efficiency
mink.
A
subsample
two
populations
n
=
2,986)
were
genotyped
using
Affymetrix
Mink
SNP
array.
identified
ROH
segments
included
simultaneously,
concatenated
into
regions,
ROH-based
studies
carried
out
linear
mixed
models
considering
a
genomic
relationship
matrix
11
implemented
ASReml-R
version
4.
In
total,
298,313
across
all
individuals,
an
average
length
coverage
4.16
Mb
414.8
Mb,
respectively.
After
merging
segments,
196
regions
detected
used
genome-wide
analysis.
Thirteen
significantly
P
<
0.01)
associated
traits.
Several
candidate
genes
within
significant
are
known
their
involvement
body
size
development,
including
MEF2A
,
ADAMTS17
POU3F2
TYRO3
.
addition,
we
found
ten
defined
as
islands,
frequencies
over
80%
population.
These
islands
harbored
12
annotated
genes,
some
which
related
immune
system
processes
such
DTX3L
PARP9
PARP14
CD86
HCLS1
This
is
first
explore
associations
homozygous
Our
findings
shed
light
on
effects
traits,
that
can
be
utilized
developing
sustainable
breeding
program
Язык: Английский
Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data
Animals,
Год журнала:
2022,
Номер
13(1), С. 13 - 13
Опубликована: Дек. 20, 2022
Wanbei
pig
(WBP)
is
one
of
the
indigenous
resources
in
China
and
has
many
germplasm
characteristics.
However,
research
on
its
genome
lacking.
To
assess
genomic
variation,
population
structure,
selection
signatures,
we
resequenced
18
WBP
for
first
time
performed
a
comprehensive
analysis
with
data
10
Asian
wild
boars.
In
total,
590.03
Gb
approximately
41
million
variants
were
obtained.
Polymorphism
level
(θπ)
ratio
genetic
differentiation
(fixation
index)-based
cross
approaches
applied,
539
regions,
which
harbored
176
genes,
selected.
Functional
selected
genes
revealed
that
they
associated
lipid
metabolism
(SCP2,
APOA1,
APOA4,
APOC3,
CD36,
BCL6,
ADCY8),
backfat
thickness
(PLAG1,
CACNA2D1),
muscle
(MYOG),
reproduction
(CABS1).
Overall,
our
results
provide
valuable
resource
characterizing
uniqueness
basis
future
breeding.
Язык: Английский
Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study
Animals,
Год журнала:
2024,
Номер
14(10), С. 1419 - 1419
Опубликована: Май 9, 2024
Copy
number
variation
(CNV)
is
an
important
structural
used
to
elucidate
complex
economic
traits.
In
this
study,
we
sequenced
25
Wannan
spotted
pigs
(WSPs)
detect
their
CNVs
and
identify
selection
signatures
compared
with
those
of
10
Asian
wild
boars.
A
total
14,161
were
detected
in
the
WSPs,
accounting
for
0.72%
porcine
genome.
The
fixation
index
(Fst)
was
signatures,
195
top
1%
Fst
value
selected.
Eighty
genes
identified
selected
CNV
regions.
Functional
GO
KEGG
analyses
revealed
that
within
these
are
associated
key
traits
such
as
reproduction
(GAL3ST1
SETD2),
fatty
acid
composition
(PRKG1,
ACACA,
ACSL3,
UGT8),
immune
system
(LYZ),
ear
size
(WIF1),
feed
efficiency
(VIPR2).
findings
study
contribute
novel
insights
into
genetic
underlying
WSP
characteristics
provide
essential
information
protection
utilization
populations.
Язык: Английский
Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data
Genes,
Год журнала:
2022,
Номер
13(12), С. 2310 - 2310
Опубликована: Дек. 8, 2022
As
a
distinguished
Chinese
indigenous
pig
breed
that
exhibits
disease
resistance
and
high
meat
quality,
the
Anqing
six-end-white
(AQ)
represents
valuable
germplasm
resource
for
improving
quality
of
breeding
industry.
In
this
study,
24
AQ
pigs
were
distantly
blood-related
6
Asian
Wild
Boar
(AWB)
selected
10×
deep-genome
resequencing.
The
signatures
selection
analyzed
to
explore
genetic
basis
their
characteristics
identify
excellent
germplasm-related
functional
genes
based
on
NGS
data.
A
total
49,289,052
SNPs
6,186,123
indels
detected
across
genome
in
30
pigs.
Most
variations
synonym
mutations
existed
intergenic
region.
We
identified
275
regions
(top
1%)
harboring
85
by
applying
crossover
approach
differentiation
(FST)
polymorphism
levels
(π
ratio).
Some
found
be
positively
pigs'
breeding.
SMPD4
DDX18
involved
immune
response
pseudorabies
virus
(PRV)
porcine
reproductive
respiratory
syndrome
(PRRSV).
BCL6
P2RX6
biological
regulation
T
cells
phagocytes.
SLC7A4
SPACA4
related
performance.
MSTN
HIF1A
fat
deposition
muscle
development.
Moreover,
138
overlapping
ROH
islands
Additionally,
we
QTLs
with
most
back
thickness,
color,
pH
value,
fatty
acid
content,
cells,
parasitic
immunity,
bacterial
immunity.
Based
enrichment
analysis
mapping,
conducted
further
research
molecular
traits
(disease
quality).
These
results
are
reliable
conserving
resources
exploiting
markers
Язык: Английский