iScience,
Journal Year:
2020,
Volume and Issue:
23(6), P. 101241 - 101241
Published: June 1, 2020
As
one
of
the
most
extensively
cultivated
crops,
maize
(Zea
mays
L.)
has
been
studied
by
researchers
and
breeders
for
over
a
century.
With
advances
in
high-throughput
detection
various
omics
data,
wealth
multi-dimensional
multi-omics
information
accumulated
its
wild
relative,
teosinte.
Integration
this
potential
to
accelerate
genetic
research
generate
improvements
agronomic
traits.
To
end,
we
constructed
ZEAMAP,
comprehensive
database
incorporating
multiple
reference
genomes,
annotations,
comparative
genomics,
transcriptomes,
open
chromatin
regions,
interactions,
high-quality
variants,
phenotypes,
metabolomics,
maps,
mapping
loci,
population
structures,
populational
DNA
methylation
signals
within
inbred
lines.
ZEAMAP
is
user
friendly,
with
ability
interactively
integrate,
visualize,
cross-reference
different
datasets.
The Plant Cell,
Journal Year:
2022,
Volume and Issue:
35(1), P. 67 - 108
Published: Aug. 26, 2022
We
present
unresolved
questions
in
plant
abiotic
stress
biology
as
posed
by
15
research
groups
with
expertise
spanning
eco-physiology
to
cell
and
molecular
biology.
Common
themes
of
these
include
the
need
better
understand
how
plants
detect
water
availability,
temperature,
salinity,
rising
carbon
dioxide
(CO2)
levels;
environmental
signals
interface
endogenous
signaling
development
(e.g.
circadian
clock
flowering
time);
this
integrated
controls
downstream
responses
stomatal
regulation,
proline
metabolism,
growth
versus
defense
balance).
The
plasma
membrane
comes
up
frequently
a
site
key
transport
events
mechanosensing
lipid-derived
signaling,
aquaporins).
Adaptation
extremes
CO2
affects
hydraulic
architecture
transpiration,
well
root
shoot
morphology,
ways
not
fully
understood.
Environmental
adaptation
involves
tradeoffs
that
limit
ecological
distribution
crop
resilience
face
changing
increasingly
unpredictable
environments.
Exploration
diversity
within
among
species
can
help
us
know
which
represent
fundamental
limits
ones
be
circumvented
bringing
new
trait
combinations
together.
Better
defining
what
constitutes
beneficial
resistance
different
contexts
making
connections
between
genes
phenotypes,
laboratory
field
observations,
are
overarching
challenges.
Plant Biotechnology Journal,
Journal Year:
2022,
Volume and Issue:
20(9), P. 1807 - 1818
Published: June 1, 2022
Seed
size
is
one
of
the
most
important
agronomic
traits
determining
yield
crops.
Cloning
key
genes
controlling
seed
and
pyramiding
their
elite
alleles
will
facilitate
improvement.
To
date,
few
have
been
identified
in
soybean,
a
major
crop
that
provides
half
plant
oil
quarter
protein
globally.
Here,
through
genome-wide
association
study
over
1800
soybean
accessions,
we
determined
natural
allelic
variation
at
GmST05
(Seed
Thickness
05)
predominantly
controlled
thickness
germplasm.
Further
analyses
suggested
two
haplotypes
differed
significantly
transcriptional
level.
Transgenic
experiments
demonstrated
positively
regulated
influenced
contents,
possibly
by
regulating
transcription
GmSWEET10a.
Population
genetic
diversity
analysis
variations
were
selected
during
geographical
differentiation
but
not
fixed.
In
summary,
determines
levels
influences
quality
making
it
an
gene
resource
for
molecular
breeding.
Cell,
Journal Year:
2023,
Volume and Issue:
186(11), P. 2313 - 2328.e15
Published: May 1, 2023
Hybrid
potato
breeding
will
transform
the
crop
from
a
clonally
propagated
tetraploid
to
seed-reproducing
diploid.
Historical
accumulation
of
deleterious
mutations
in
genomes
has
hindered
development
elite
inbred
lines
and
hybrids.
Utilizing
whole-genome
phylogeny
92
Solanaceae
its
sister
clade
species,
we
employ
an
evolutionary
strategy
identify
mutations.
The
deep
reveals
genome-wide
landscape
highly
constrained
sites,
comprising
∼2.4%
genome.
Based
on
diploid
diversity
panel,
infer
367,499
variants,
which
50%
occur
at
non-coding
15%
synonymous
sites.
Counterintuitively,
with
relatively
high
homozygous
burden
can
be
better
starting
material
for
inbred-line
development,
despite
showing
less
vigorous
growth.
Inclusion
inferred
increases
genomic-prediction
accuracy
yield
by
24.7%.
Our
study
generates
insights
into
incidence
properties
their
far-reaching
consequences
breeding.
Trends in Genetics,
Journal Year:
2024,
Volume and Issue:
40(10), P. 891 - 908
Published: Aug. 7, 2024
Harnessing
cutting-edge
technologies
to
enhance
crop
productivity
is
a
pivotal
goal
in
modern
plant
breeding.
Artificial
intelligence
(AI)
renowned
for
its
prowess
big
data
analysis
and
pattern
recognition,
revolutionizing
numerous
scientific
domains
including
We
explore
the
wider
potential
of
AI
tools
various
facets
breeding,
collection,
unlocking
genetic
diversity
within
genebanks,
bridging
genotype–phenotype
gap
facilitate
This
will
enable
development
cultivars
tailored
projected
future
environments.
Moreover,
also
hold
promise
refining
traits
by
improving
precision
gene-editing
systems
predicting
effects
gene
variants
on
phenotypes.
Leveraging
AI-enabled
breeding
can
augment
efficiency
programs
holds
optimizing
cropping
at
grassroots
level.
entails
identifying
optimal
inter-cropping
crop-rotation
models
agricultural
sustainability
field.
Science,
Journal Year:
2024,
Volume and Issue:
385(6704)
Published: July 4, 2024
Understanding
how
numerous
quantitative
trait
loci
(QTL)
shape
phenotypic
variation
is
an
important
question
in
genetics.
To
address
this,
we
established
a
permanent
population
of
18,421
(18K)
rice
lines
with
reduced
structure.
We
generated
reference-level
genome
assemblies
the
founders
and
genotyped
all
18K-rice
through
whole-genome
sequencing.
Through
high-resolution
mapping,
96
high-quality
candidate
genes
contributing
to
16
traits
were
identified,
including
Journal of Integrative Plant Biology,
Journal Year:
2024,
Volume and Issue:
66(3), P. 484 - 509
Published: March 1, 2024
ABSTRACT
Brassica
napus
,
commonly
known
as
rapeseed
or
canola,
is
a
major
oil
crop
contributing
over
13%
to
the
stable
supply
of
edible
vegetable
worldwide.
Identification
and
understanding
gene
functions
in
B.
genome
crucial
for
genomic
breeding.
A
group
genes
controlling
agronomic
traits
have
been
successfully
cloned
through
functional
genomics
studies
.
In
this
review,
we
present
an
overview
progress
made
including
availability
germplasm
resources,
omics
databases
genes.
Based
on
current
progress,
also
highlight
main
challenges
perspectives
field.
The
advances
contribute
better
genetic
basis
underlying
complex
will
expedite
breeding
high
quality,
resistance
yield
varieties.
Plants,
Journal Year:
2024,
Volume and Issue:
13(4), P. 490 - 490
Published: Feb. 8, 2024
Climate
change
disrupts
food
production
in
many
regions
of
the
world.
The
accompanying
extreme
weather
events,
such
as
droughts,
floods,
heat
waves,
and
cold
snaps,
pose
threats
to
crops.
concentration
carbon
dioxide
also
increases
atmosphere.
United
Nations
is
implementing
climate-smart
agriculture
initiative
ensure
security.
An
element
this
project
involves
breeding
climate-resilient
crops
or
plant
cultivars
with
enhanced
resistance
unfavorable
environmental
conditions.
Modern
agriculture,
which
currently
homogeneous,
needs
diversify
species
cultivated
plants.
Plant
programs
should
extensively
incorporate
new
molecular
technologies,
supported
by
development
field
phenotyping
techniques.
Breeders
closely
cooperate
scientists
from
various
fields
science.
International Journal of Molecular Sciences,
Journal Year:
2025,
Volume and Issue:
26(4), P. 1466 - 1466
Published: Feb. 10, 2025
The
advancement
of
multi-omics
tools
has
revolutionized
the
study
complex
biological
systems,
providing
comprehensive
insights
into
molecular
mechanisms
underlying
critical
traits
across
various
organisms.
By
integrating
data
from
genomics,
transcriptomics,
metabolomics,
and
other
omics
platforms,
researchers
can
systematically
identify
characterize
elements
that
contribute
to
phenotypic
traits.
This
review
delves
recent
progress
in
applying
approaches
elucidate
genetic,
epigenetic,
metabolic
networks
associated
with
key
plants.
We
emphasize
potential
these
integrative
strategies
enhance
crop
improvement,
optimize
agricultural
practices,
promote
sustainable
environmental
management.
Furthermore,
we
explore
future
prospects
field,
underscoring
importance
cutting-edge
technological
advancements
need
for
interdisciplinary
collaboration
address
ongoing
challenges.
bridging
this
aims
provide
a
holistic
framework
advancing
research
plant
biology
agriculture.
Nature Communications,
Journal Year:
2025,
Volume and Issue:
16(1)
Published: March 3, 2025
Diversified
reproductive
systems
can
be
observed
in
the
plant
kingdom
and
applied
crop
breeding;
however,
their
impacts
on
genomic
variation
breeding
remain
unclear.
Grapevine
(Vitis
vinifera
L.),
a
widely
planted
fruit
tree,
underwent
shift
from
dioecism
to
monoecism
during
domestication
involves
crossing,
self-pollination,
clonal
propagation
for
its
cultivation.
In
this
study,
we
discover
that
types,
namely,
selfing,
cloning,
dramatically
impact
landscapes
grapevine
based
comparative
population
genetics
of
wild
complex
pedigree
Pinot
Noir.
The
are
divergent,
which
show
interesting
patterns
purging
Hill-Robertson
interference.
Selfing
reduces
heterozygosity,
while
cloning
increases
it,
resulting
"double
U-shaped"
site
frequency
spectrum
(SFS).
Crossing
conceal
selfing
purges
most
deleterious
structural
burdens.
Moreover,
close
leakage
large-effect
variations
repulsion
phases
maintains
heterozygous
regions
4.3%
genome
after
successive
nine
generations.
Our
study
provides
new
insights
into
genetic
basis
crops
by
variants
integrating
beneficial
through
various
systems.
Effects
Here,
authors
report
types
analyses
