PLANT PHYSIOLOGY,
Journal Year:
2024,
Volume and Issue:
195(4), P. 2500 - 2514
Published: April 30, 2024
Over
the
past
10,000
years,
tomato
species
have
undergone
both
unintentional
and
intentional
selection
to
enhance
their
favorable
traits
for
human
consumption
manufacturing.
These
processes
significantly
influenced
genomes
of
played
a
critical
role
in
improving
varieties.
In
this
review,
we
summarize
recent
advances
genome
sequencing,
explore
impact
human-driven
selection,
recapitulate
key
genes
associated
with
important
agronomic
breeding.
We
provide
several
examples
genomics-guided
breeding
highlight
potential
resources
facilitating
improvement.
Furthermore,
elaborate
progress
strategies
through
design
present
how
such
efforts
can
help
future
enhancements
align
demands
sustainability
evolving
societies.
Science China Life Sciences,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 8, 2025
Abstract
Epigenetic
mechanisms
are
integral
to
plant
growth,
development,
and
adaptation
environmental
stimuli.
Over
the
past
two
decades,
our
comprehension
of
these
complex
regulatory
processes
has
expanded
remarkably,
producing
a
substantial
body
knowledge
on
both
locus-specific
genome-wide
patterns.
Studies
initially
grounded
in
model
Arabidopsis
have
been
broadened
encompass
diverse
array
crop
species,
revealing
multifaceted
roles
epigenetics
physiological
agronomic
traits.
With
recent
technological
advancements,
epigenetic
regulations
at
single-cell
level
large-scale
population
emerging
as
new
focuses.
This
review
offers
an
in-depth
synthesis
regulations,
detailing
catalytic
machinery
functions.
It
delves
into
intricate
interplay
among
various
elements
their
collective
influence
modulation
Furthermore,
it
examines
breakthroughs
technologies
for
modifications
integration
strategies
improvement.
The
underscores
transformative
potential
bolstering
performance,
advocating
development
efficient
tools
fully
exploit
agricultural
benefits
insights.
aBIOTECH,
Journal Year:
2025,
Volume and Issue:
6(1), P. 116 - 132
Published: Jan. 23, 2025
Abstract
Plant
metabolites
are
crucial
for
the
growth,
development,
environmental
adaptation,
and
nutritional
quality
of
plants.
metabolomics,
a
key
branch
systems
biology,
involves
comprehensive
analysis
interpretation
composition,
variation,
functions
these
metabolites.
Advances
in
technology
have
transformed
plant
metabolomics
into
sophisticated
process
involving
sample
collection,
metabolite
extraction,
high-throughput
analysis,
data
processing,
multidimensional
statistical
analysis.
In
today’s
era
big
data,
field
is
witnessing
an
explosion
acquisition,
offering
insight
complexity
dynamics
metabolism.
Moreover,
multiple
omics
strategies
can
be
integrated
to
reveal
interactions
regulatory
networks
across
different
molecular
levels,
deepening
our
understanding
biological
processes.
this
review,
we
highlight
recent
advances
challenges
emphasizing
roles
technique
improving
crop
varieties,
enhancing
value,
increasing
stress
resistance.
We
also
explore
scientific
foundations
its
applications
medicine,
ecological
conservation.
Genome biology,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: April 5, 2024
Abstract
Background
DNA
methylation
is
an
essential
epigenetic
modification.
However,
its
contribution
to
trait
changes
and
diversity
in
the
domestication
of
perennial
fruit
trees
remains
unknown.
Results
Here,
we
investigate
variation
during
pear
improvement
using
whole-genome
bisulfite
sequencing
41
accessions.
Contrary
significant
decrease
rice
domestication,
detect
a
global
increase
improvement.
We
find
this
specific
significantly
correlated
with
downregulation
Demeter-like1
(
DML1
,
encoding
demethylase)
due
human
selection.
identify
total
5591
differentially
methylated
regions
(DMRs).
Methylation
CG
CHG
contexts
undergoes
co-evolution
DMRs
have
higher
genetic
than
selection
sweep
regions,
especially
introns.
Approximately
97%
are
not
associated
any
SNPs,
these
starch
sucrose
metabolism
phenylpropanoid
biosynthesis.
also
perform
correlation
analysis
between
gene
expression.
genes
close
hypermethylated
that
ripening.
further
verify
function
hyper-DMR-associated
gene,
CAMTA2
demonstrate
overexpression
tomato
callus
inhibits
Conclusions
Our
study
describes
pattern
tree
suggests
increased
plays
role
early
ripening
fruits.
The Plant Journal,
Journal Year:
2025,
Volume and Issue:
121(2)
Published: Jan. 1, 2025
Rice
(Oryza
sativa
L.)
subspecies
japonica
and
indica
show
distinct
morphological
genetic
differentiation.
However,
the
differences
in
genome-wide
DNA
methylation
its
effects
on
gene
expression
metabolic
levels
between
rice
remain
unclear.
In
this
study,
we
investigated
methylation,
transcriptomes
metabolomes
of
12
representative
accessions,
to
reveal
differentiation
subspecies.
We
detected
83
327
differentially
methylated
regions
(DMRs)
14
903
DMR-associated
genes
two
Indica
showed
significantly
lower
CG,
CHG,
CHH
compared
with
rice.
Subsequently,
identified
5596
expressed
subspecies,
predominantly
enriched
pathways
related
carbohydrate
amino
acid
metabolism.
By
integrating
transcriptomic
data,
a
significant
correlation
was
established
patterns
level
key
agronomic
Furthermore,
multi-omics
analyses
that
metabolism
pathways,
especially
tricarboxylic
(TCA)
cycle
metabolites,
are
remarkable
These
results
provide
foundation
for
future
studies
domestication
improvement.
The Plant Journal,
Journal Year:
2025,
Volume and Issue:
121(3)
Published: Feb. 1, 2025
SUMMARY
The
genus
Echinochloa
(Poaceae)
contains
problematic
weeds
worldwide
and
two
domesticated
orphan
crops.
In
this
study,
through
sequencing
DNA
methylomes
transcriptomes,
we
aimed
to
reveal
the
epigenome
changes
their
relationship
with
gene
expression
in
species
during
polyploidization
domestication.
Compared
hexaploid
crop
bread
wheat,
found
common
distinctive
methylation
patterns
crus‐galli
.
More
diverse
were
uncovered
hexaploidization
of
E.
,
suggesting
more
plasticity
weed
genome,
which
might
contribute
its
environmental
adaptation.
addition,
less
observed
cultivated
species,
as
compared
rice,
indicating
incomplete
domestication
Our
results
provide
new
insights
into
plant
from
an
epigenomic
perspective.
Horticulture Research,
Journal Year:
2024,
Volume and Issue:
11(7)
Published: May 14, 2024
Abstract
Blueberry
belongs
to
the
Vaccinium
genus
and
is
a
highly
popular
fruit
crop
with
significant
economic
importance.
It
was
not
until
early
twentieth
century
that
they
began
be
domesticated
through
extensive
interspecific
hybridization.
Here,
we
collected
220
accessions
from
various
geographical
locations,
including
154
United
States,
14
China,
eight
Australia,
29
Europe
other
countries,
comprising
164
corymbosum,
15
ashei,
10
lowbush
blueberries,
seven
half-high
others.
We
present
whole-genome
variation
map
of
reconstructed
hundred-year
molecular
history
hybridization
blueberry.
focused
on
two
major
blueberry
subgroups,
northern
highbush
(NHB)
southern
(SHB)
identified
candidate
genes
contribute
their
distinct
traits
in
climate
adaptability
quality.
Our
analysis
unveiled
role
gene
introgression
darrowii
V.
ashei
into
SHB
driving
differentiation
between
NHB,
potentially
facilitating
SHB’s
adaptation
subtropical
environments.
Assisted
by
genome-wide
association
studies,
our
suggested
VcTBL44
as
pivotal
regulator
governing
firmness
SHB.
Additionally,
conducted
bisulfite
sequencing
nine
NHB
12
cultivars,
characterized
regions
are
differentially
methylated
subgroups.
In
particular,
discovered
β-alanine
metabolic
pathway
were
enriched
for
DNA
methylation
changes.
study
provides
high-quality
genetic
epigenetic
maps
blueberry,
which
offer
valuable
insights
resources
future
breeding.
Plant Cell Reports,
Journal Year:
2024,
Volume and Issue:
43(6)
Published: May 22, 2024
Abstract
Key
message
Identification
of
selenium
stress-responsive
expression
and
molecular
docking
serine
acetyltransferase
(SAT)
O
-acetyl
(thiol)
lyase
(OASTL)
in
Cardamine
hupingshanensis.
A
complex
coupled
with
is
the
key
enzyme
that
catalyzes
selenocysteine
(Sec)
synthesis
plants.
The
functions
SAT
OASTL
genes
were
identified
some
plants,
but
it
still
unclear
whether
are
involved
metabolic
pathway
hupingshanensis
.
In
this
study,
genome-wide
identification
comparative
analysis
ChSAT
s
ChOASTL
performed.
eight
divided
into
three
branches,
thirteen
four
branches
by
phylogenetic
sequence
alignment,
indicating
evolutionary
conservation
gene
structure
its
association
other
plant
species.
qRT-PCR
showed
differentially
expressed
different
tissues
under
various
levels,
suggesting
their
important
roles
Sec
synthesis.
ChSAT1;2
ChOASTLA1;2
silenced
VIGS
system
to
investigate
involvement
metabolites
C.
findings
contribute
understanding
stress
provide
a
reference
for
further
exploration
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
15
Published: Feb. 20, 2025
Top
removal
is
a
widely
utilized
method
in
production
process
of
tobacco,
but
little
known
regarding
the
way
it
impacts
protein
and
metabolic
regulation.
In
this
study,
we
investigated
underlying
processes
alterations
cigar
tobacco
leaves
with
without
top
removal,
using
combined
proteomic
metabolomic
approach.
The
results
revealed
that:
(1)
Topping
significantly
affected
superoxide
anion
(O2
-)
levels,
dismutase
(SOD)
activity,
malondialdehyde
(MDA)
content,
(2)
proteome,
385
differentially
expressed
proteins
(DEPs)
were
identified,
228
upregulated
156
downregulated.
Key
pathways
enriched
included
flavonoid
biosynthesis,
porphyrin
chlorophyll
metabolism,
cysteine
methionine
amino
acid
biosynthesis
metabolism.
A
network
161
nodes
interconnected
by
102
altered
was
established,
(3)
metabolome,
247
different
metabolites
(DEMs)
120
128
downregulated
metabolites,
mainly
comprising
lipids
lipid-like
molecules,
phenylpropanoids
polyketides,
organic
acids
derivatives,
heterocyclic
compounds,
(4)
KEGG
pathway
enrichment
upregulation
such
as
chalcone
synthase
(CHS),
isomerase
(CHI),
naringenin
3-dioxygenase
(F3H),
3'-monooxygenase
(F3'H),
along
like
pinocembrin,
kaempferol,
trifolin,
rutin,
quercetin,
enhancing
'flavonoid'
'flavone
flavonol'
biosynthesis.
This
study
sheds
light
on
responses
after
topping.
