Research Square (Research Square),
Год журнала:
2022,
Номер
unknown
Опубликована: Окт. 25, 2022
Abstract
Transposable
elements
are
an
important
source
of
genome
variability.
Here,
we
analyze
their
contribution
to
gene
expression
variability
in
crops
by
performing
a
TE
insertion
polymorphism
(TIP)-eQTL
mapping
using
data
from
rice
varieties
the
O.
sativa
ssp.
indica
and
japonica
subspecies.
Our
shows
that
insertions
associated
with
changes
many
genes
known
be
targets
domestication
breeding.
An
fraction
these
were
already
present
wild
ancestors,
have
been
differentially
selected
populations.
Taken
together,
show
small
signal
transduction
induced
accompany
adaptation
National Science Review,
Год журнала:
2024,
Номер
11(6)
Опубликована: Май 3, 2024
Transposable
elements
(TEs)
are
ubiquitous
genomic
components
and
hard
to
study
due
being
highly
repetitive.
Here
we
assembled
232
chromosome-level
genomes
based
on
long-read
sequencing
data.
Coupling
the
with
15
existing
assemblies,
developed
a
pan-TE
map
comprising
both
cultivated
wild
Asian
rice.
We
detected
177
084
high-quality
TE
variations
inferred
their
derived
state
using
outgroups.
found
TEs
were
one
source
of
phenotypic
variation
during
rice
domestication
differentiation.
identified
1246
genes
whose
expression
was
associated
but
not
single-nucleotide
polymorphisms
(SNPs),
such
as
Transposable
elements
(TEs)
are
an
important
source
of
genome
variability.
Here,
we
analyze
their
contribution
to
gene
expression
variability
in
rice
by
performing
a
TE
insertion
polymorphism
quantitative
trait
locus
mapping
using
data
from
208
varieties
the
Oryza
sativa
ssp.
indica
and
O.
japonica
subspecies.
Our
show
that
insertions
associated
with
changes
many
genes
known
be
targets
domestication
breeding.
An
fraction
these
were
already
present
wild
ancestors,
have
been
differentially
selected
populations.
Taken
together,
our
results
small
signal
transduction
induced
accompany
adaptation
Transposable
elements
(TEs)
are
an
important
source
of
genome
variability.
Here,
we
analyze
their
contribution
to
gene
expression
variability
in
rice
by
performing
a
TE
insertion
polymorphism
quantitative
trait
locus
mapping
using
data
from
208
varieties
the
Oryza
sativa
ssp.
indica
and
O.
japonica
subspecies.
Our
show
that
insertions
associated
with
changes
many
genes
known
be
targets
domestication
breeding.
An
fraction
these
were
already
present
wild
ancestors,
have
been
differentially
selected
populations.
Taken
together,
our
results
small
signal
transduction
induced
accompany
adaptation
Vavilov Journal of Genetics and Breeding,
Год журнала:
2025,
Номер
29(1), С. 61 - 71
Опубликована: Март 3, 2025
Chickpea
is
the
second
most
important
legume
crop,
which
used
as
a
food
by
people
in
different
parts
of
world
due
to
its
high
nutritive
value.
Omics
technologies
have
revolutionized
characterization
chickpea
genetic
diversity
considering
single-nucleotide
polymorphisms,
while
structural
variants
and
transposons
been
overlooked.
The
specific
contribution
phenotypic
diversification
crop
species
still
poorly
documented,
therefore
important.
We
focused
on
landraces
collected
before
“green
revolution”,
they
are
valuable
source
can
be
broaden
base
modern
cultivars.
Analyzing
190
genomes,
we
found
42,324
new
transposon
insertion
sites
from
83
families
showed
that
such
highly
polymorphic.
Most
insertions
were
caused
mobilization
retrotransposons
(67
%
insertions);
among
DNA
transposons,
highest
number
was
for
superfamilies
MuDR,
PIF,
hAT,
CMC,
TcMar.
also
demonstrated
an
uneven
distribution
along
chromosomes.
Analysis
localization
relative
genes
their
elements
has
shown
largest
all
falls
introns
smallest,
exons.
sites,
until
recently
overlooked
population
genomics,
factor
diversifies
phenotypes
GWAS
markers
replacing
SNPs.
Comparative
analysis
geographic
regions
Ethiopian
accessions
many
unique
sites.
Our
results
highlight
role
implications
breeding
improved
varieties
adapted
global
climate
change.
Frontiers in Plant Science,
Год журнала:
2025,
Номер
16
Опубликована: Апрель 14, 2025
Introduction
The
rice
improvement
process,
driven
by
modern
breeding
techniques,
represents
the
second
revolutionary
advancement
in
agronomic
traits,
following
domestication.
Advances
pan-genomes
and
enhanced
capacity
for
analyzing
structural
variations
have
increasingly
highlighted
their
role
genetic
improvement.
Transposable
element
(TE)
variants
been
previously
reported
to
influence
genomic
diversity
during
domestication,
but
contribution
from
landraces
improved
varieties
remains
unclear.
Methods
Here,
we
combined
a
high-quality
pan-TE
variation
map,
transcriptome
profiles,
phenotypic
data
100
92
investigate
of
TE
rice.
Results
total
number
length
were
significantly
greater
than
those
landraces,
particularly
Ty3-retrotransposons,
LTR
Copia
Helitron
elements.
Comparing
varieties,
4,334
selective
TEs
detected
within
or
near
3,070
genes
that
enriched
basic
metabolism
development
stress
resistance.
Among
14,076
differentially
expressed
between
two
groups,
expression
level
3,480
(24.7%)
associated
with
variations.
Combining
haplotype
analysis,
demonstrated
potential
patterns
how
affect
gene
thereby
participate
important
traits
Discussion
Collectively,
our
results
highlight
contributions
shaping
basis
will
facilitate
exploration
superior
advance
molecular
efforts
Abstract
Transposable
elements
(TEs)
constitute
a
major
portion
of
plant
genomes
and
play
key
roles
in
shaping
genome
architecture,
regulating
gene
expression,
driving
evolution.
In
this
study,
we
generated
comprehensive
curated
TE
library
for
the
woodland
strawberry
(Fragaria
vesca)
by
integrating
two
bioinformatic
pipelines
(EDTA
DeepTE).
Our
annotation
revealed
that
TEs
account
approximately
37%
F.
vesca
genome.
Analysis
TE-derived
inverted
repeats
(IRs)
miniature
inverted-repeat
transposable
(MITEs)
demonstrated
their
association
with
24-nt
small
interfering
RNA
(siRNA)
production
differential
DNA
methylation
patterns
across
tissues,
suggesting
role
epigenetic
regulation
particularly
during
fruit
ripening.
This
MITE-mediated
regulatory
mechanism
was
confirmed
evaluating
expression
chromatin
organization
at
FvH4_7g18570,
which
encodes
alcohol
acyl
transferase
(FvAAT1).
Three
MITEs
located
upstream
or
downstream
FvAAT1
coding
sequence
were
shown
to
influence
epigenetically
expression.
Furthermore,
analyzed
210
re-sequenced
accessions
from
European
germplasm
collection
identify
annotate
insertion
deletion
polymorphisms.
A
principal
component
analysis
(PCA)
based
on
these
polymorphisms
subpopulation
structures
reflect
geographic
origins.
genome-wide
study
(GWAS)
uncovered
significant
associations
between
specific
economically
important
traits,
including
aroma-related
volatile
compounds
size.
Among
them,
hAT
MITE
near
FvH4_2g00610
correlated
increased
levels
γ-decalactone,
desirable
aroma
compound
strawberries.
These
findings
underscore
functional
significance
as
contributors
phenotypic
diversity
through
novel
functions.
By
into
population-genomic
studies,
work
provides
valuable
insights
development
quality
traits.
It
also
highlights
potential
harnessing
TE-mediated
variation
breeding
initiatives
editing
strategies
improve
quality.
Frontiers in Plant Science,
Год журнала:
2023,
Номер
14
Опубликована: Фев. 7, 2023
The
protein
kinase
(PK)
superfamily
constitutes
one
of
the
largest
and
most
conserved
families
in
eukaryotic
genomes,
comprising
core
components
signaling
pathways
cell
regulation.
Despite
its
remarkable
relevance,
only
a
few
have
been
studied
Hevea
brasiliensis.
A
comprehensive
characterization
global
expression
analysis
PK
superfamily,
however,
is
currently
lacking.
In
this
study,
with
aim
providing
novel
inferences
about
mechanisms
associated
stress
response
developed
by
PKs
retained
throughout
evolution,
we
identified
characterized
entire
set
PKs,
also
known
as
kinome,
present
genome.
Different
RNA-sequencing
datasets
were
employed
to
identify
tissue-specific
patterns
potential
correspondences
between
different
rubber
tree
genotypes.
addition,
coexpression
networks
under
several
abiotic
conditions,
such
cold,
drought
latex
overexploitation,
elucidate
associations
tissues/stresses.
total
1,809
genes
using
current
reference
genome
assembly
at
scaffold
level,
1,379
latest
chromosome-level
combined
into
single
2,842
PKs.
These
proteins
further
classified
20
groups
122
families,
exhibiting
high
compositional
similarities
among
family
members
two
phylogenetically
close
species
Manihot
esculenta
Ricinus
communis.
Through
joint
investigation
tandemly
duplicated
kinases,
transposable
elements,
gene
patterns,
events,
provided
insights
understanding
regulation
which
can
often
lead
significant
reduction
yield.
