Plants,
Journal Year:
2024,
Volume and Issue:
13(24), P. 3476 - 3476
Published: Dec. 11, 2024
Single-cell
and
spatial
transcriptomics
technologies
have
significantly
advanced
our
understanding
of
the
molecular
mechanisms
underlying
crop
biology.
This
review
presents
an
update
on
application
these
in
improvement.
The
heterogeneity
different
cell
populations
within
a
tissue
plays
crucial
role
coordinated
response
organism
to
its
environment.
enables
dissection
this
heterogeneity,
offering
insights
into
cell-specific
transcriptomic
responses
plants
various
environmental
stimuli.
Spatial
complement
single-cell
approaches
by
preserving
context
gene
expression
profiles,
allowing
for
situ
localization
transcripts.
Together,
facilitate
discovery
novel
genes
regulatory
networks
that
can
be
targeted
genetic
manipulation
breeding
strategies
aimed
at
enhancing
yield,
quality,
resilience.
highlights
significant
findings
from
recent
studies,
discusses
expanding
roles
technologies,
explores
future
opportunities
their
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 3, 2024
Summary
Cis
-regulatory
elements
(CREs)
precisely
control
spatiotemporal
gene
expression
in
cells.
Using
a
spatially
resolved
single-cell
atlas
of
with
chromatin
accessibility
across
ten
soybean
tissues,
we
identified
103
distinct
cell
types
and
303,199
accessible
regions
(ACRs).
Nearly
40%
the
ACRs
showed
cell-type-specific
patterns
were
enriched
for
transcription
factor
(TF)
motifs
defining
diverse
identities.
We
de
novo
TF
explored
conservation
regulatory
networks
underpinning
legume
symbiotic
nitrogen
fixation.
With
comprehensive
developmental
trajectories
endosperm
embryo,
uncovered
functional
transition
three
sub-cell
endosperm,
13
sucrose
transporters
sharing
DOF11
motif
that
co-up-regulated
late
peripheral
key
embryo
cell-type
specification
regulators
during
embryogenesis,
including
homeobox
promotes
cotyledon
parenchyma
identity.
This
resource
provides
valuable
foundation
analyzing
programs
tissues
life
stages.
New Crops,
Journal Year:
2024,
Volume and Issue:
1, P. 100025 - 100025
Published: May 12, 2024
Cells
of
multicellular
plants
possess
inherent
heterogeneity.
Recent
progress
in
single-cell
RNA
sequencing
(scRNA-seq)
allows
researchers
to
classify,
characterize,
and
distinguish
individual
cells
at
the
transcriptome
level,
enabling
identification
rare
cell
populations
with
functional
importance.
However,
scRNA-seq
obscures
spatial
information
about
cells.
Spatial
transcriptomics
approaches
have
substantially
improved
our
capacity
detect
distribution
transcripts
throughout
tissues,
yet
it
remains
challenging
characterize
whole-transcriptome-level
data
for
single
spatially.
In
this
review,
we
offer
a
concise
overview
experimental
computational
procedures
strategies
required
integrate
transcriptomics.
We
demonstrate
their
impact
on
plant
fundamental
biology,
discuss
advantages
current
challenges,
provide
an
outlook
future.
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
16
Published: Feb. 12, 2025
Maize
ear
leaves
have
important
roles
in
photosynthesis,
nutrient
partitioning
and
hormone
regulation.
The
morphological
structural
variations
observed
maize
are
numerous
contribute
significantly
to
the
yield.
Nevertheless,
research
on
fine-scale
morphology
of
is
less,
particularly
quantitative
methods
characterize
two-dimensional
(2D)
space
absent.
This
makes
it
challenging
accurately
identify
2D
leaf
shape
their
cultivars.
Therefore,
this
study
presents
semantic
feature
extraction
atlas
construction,
with
silking
stage
association
analysis
population
serving
as
an
example.
A
three-dimensional
(3D)
digitizer
was
employed
obtain
data
from
1,431
belonging
518
inbred
lines.
then
processed
using
mesh
subdivision
planar
parameterization
create
models
area-preserving
characteristics.
Additionally,
averaged
all
lines
were
constructed,
29
features
quantified.
Based
this,
11
extracted
through
clustering
correlation
analysis.
comprehensive
indicator
L
2
D
based
proposed,
a
constructed
accordance
ordering.
Inbred
line
identification
achieved
atlas.
results
can
determine
probability
that
corresponding
true
ranked
within
top
10
predicted
0.706,
20
0.810,
45
0.900.
enables
generation
matching
features.
methodology
presented
offers
novel
insights
into
construction
for
It
also
provides
theoretical
technical
foundation
drawing
Research Square (Research Square),
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 12, 2025
Abstract
In
wheat,
inflorescence
architecture
critically
determines
yield
potential,
yet
its
structural
complexity
and
asynchronous
development
have
hindered
cellular-resolution
studies
of
spikelet
floret
formation.
Here,
we
integrate
spatial
transcriptomics,
high-sensitivity
multiplexed
error-robust
fluorescence
in
situ
hybridization
(MERFISH),
snRNA-seq
across
six
developmental
stages
to
generate
a
spatiotemporal
atlas
the
wheat
inflorescence.
We
identified
20
cell
types,
spatially
resolved
into
three
categories:
1)
proliferating
cells
within
spikelet,
marked
by
active
division;
2)
supporting
along
central
axis,
including
pith,
cortex,
vasculature;
3)
developmental
located
both
inside
at
base
spikelets.
The
multi-omics
approach
enabled
identification
rare
type
ovary.
Trajectory
inference
revealed
that
spikelets
florets
originate
from
two
temporally
distinct
sub-clusters
proliferating
cells
(R7),
each
defined
high
expression
regulators.
These
findings
challenge
conventional
model
sequential
meristem
transitions
(inflorescence-spikelet-floret)
in
wheat.
Integration
time-series
snATAC-seq
delineated
cellular
transcriptional
regulatory
networks
(cTRNs)
governing
formation,
mediated
auxin
cytokinin
signaling,
driven
MADS-box
transcription
factors.
Cell
identity
was
maintained
type-specific
accessible
chromatin
regions
(csACRs),
which
are
enriched
for
SNPs
associated
with
spike-related
traits.
For
instance,
csACRs
WFZPDUO1
promoters
affect
TaNAC30
binding,
regulating
supernumerary
phenotypes.
Our
work
provides
mechanistic
framework
identifies
cTRN
nodes
as
potential
targets
optimizing
yield-related
architecture.
