Nature Communications,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: Sept. 22, 2023
The
role
of
de
novo
evolved
genes
from
non-coding
sequences
in
regulating
morphological
differentiation
between
species/subspecies
remains
largely
unknown.
Here,
we
show
that
a
rice
gene
GSE9
contributes
to
grain
shape
difference
indica/xian
and
japonica/geng
varieties.
evolves
previous
region
wild
Oryza
rufipogon
through
the
acquisition
start
codon.
This
is
inherited
by
most
japonica
varieties,
while
original
sequence
(absence
codon,
gse9)
present
majority
indica
Knockout
varieties
leads
slender
grains,
whereas
introgression
background
results
round
grains.
Population
evolutionary
analyses
reveal
gse9
are
derived
Or-I
Or-III
groups,
respectively.
Our
findings
uncover
genetic
divergence
subspecies,
provide
target
for
precise
manipulation
shape.
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
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: April 17, 2024
Abstract
Poaceae
members
shared
a
whole-genome
duplication
called
rho.
However,
little
is
known
about
the
evolutionary
pattern
of
rho-derived
duplicates
among
lineages
and
implications
in
adaptive
evolution.
Here
we
present
phylogenomic/phylotranscriptomic
analyses
363
grasses
covering
all
12
subfamilies
report
nine
previously
unknown
duplications.
Furthermore,
duplications
from
single
were
mapped
to
multiple
nodes
on
species
phylogeny;
was
likely
by
woody
bamboos
with
possible
gene
flow
herbaceous
bamboos;
recent
paralogues
tetraploid
Oryza
are
implicated
tolerance
seawater
submergence.
Moreover,
rho
showing
differential
retention
include
those
functions
environmental
adaptations
or
morphogenesis,
including
ACOT
for
aquatic
environments
(Oryzoideae),
CK2β
cold
responses
(Pooideae),
SPIRAL1
rapid
cell
elongation
(Bambusoideae),
PAI1
drought/cold
(Panicoideae).
This
study
presents
profile
evidence
mechanisms
that
contribute
losses.
Plant Biotechnology Journal,
Journal Year:
2024,
Volume and Issue:
22(5), P. 1198 - 1205
Published: Feb. 27, 2024
Plants
have
evolved
a
multi-layered
immune
system
to
fight
off
pathogens.
However,
activation
is
costly
and
often
associated
with
growth
development
penalty.
In
crops,
yield
the
main
breeding
target
usually
affected
by
high
disease
resistance.
Therefore,
proper
balance
between
defence
critical
for
achieving
efficient
crop
improvement.
This
review
highlights
recent
advances
in
attempts
designed
alleviate
trade-offs
resistance
crops
mediated
(R)
genes,
susceptibility
(S)
genes
pleiotropic
genes.
We
also
provide
an
update
on
strategies
optimizing
growth-defence
breed
future
desirable
yield.
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.
PLANT PHYSIOLOGY,
Journal Year:
2024,
Volume and Issue:
195(2), P. 1401 - 1413
Published: Jan. 29, 2024
Abstract
Plant
domestication
are
evolutionary
experiments
conducted
by
early
farmers
since
thousands
years
ago,
during
which
the
crop
wild
progenitors
artificially
selected
for
desired
agronomic
traits
along
with
dramatic
genomic
variation
in
course
of
moderate
to
severe
bottlenecks.
However,
previous
investigations
mainly
focused
on
small-effect
variants,
while
changes
gene
contents
rarely
investigated
due
lack
population-level
assemblies
both
and
its
relatives.
Here,
we
applied
comparative
analyses
discover
gain
loss
grapevine
using
long-read
representative
population
samples
domesticated
grapevines
(V.
vinifera
ssp.
vinifera)
their
sylvestris).
Only
∼7%
families
were
shared
16
Vitis
genomes
∼8%
specific
each
accession,
suggesting
variations
genomes.
Compared
progenitors,
accessions
exhibited
an
increased
presence
genes
associated
asexual
reproduction,
showcased
a
higher
abundance
related
pollination,
revealing
transition
from
sexual
reproduction
clonal
propagation
processes.
Moreover,
harbored
fewer
disease-resistance
than
progenitors.
The
SVs
occurred
frequently
aroma
between
indicating
rapid
diversification
these
domestication.
Our
study
provides
insights
resources
biological
studies
breeding
programs
grapevine.
National Science Review,
Journal Year:
2024,
Volume and Issue:
11(4)
Published: Feb. 5, 2024
ABSTRACT
For
sessile
plants,
gene
expression
plays
a
pivotal
role
in
responding
to
salinity
stress
by
activating
or
suppressing
specific
genes.
However,
our
knowledge
of
genetic
variations
governing
response
salt
remains
limited
natural
germplasm.
Through
transcriptome
analysis
the
Global
Mini-Core
Rice
Collection
consisting
panel
202
accessions,
we
identified
22
345
and
27
610
quantitative
trait
loci
associated
with
7787
9361
eGenes
under
normal
salt-stress
conditions,
respectively,
leveraging
super
pan-genome
map.
Notably,
combined
genome-wide
association
studies,
swiftly
pinpointed
potential
candidate
STG5—a
major
salt-tolerant
locus
known
as
qSTS5.
Intriguingly,
STG5
is
required
for
maintaining
Na+/K+
homeostasis
directly
regulating
transcription
multiple
members
OsHKT
family.
Our
study
sheds
light
on
how
variants
influence
dynamic
changes
provides
valuable
resource
mining
genes
future.
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.
Molecular Horticulture,
Journal Year:
2025,
Volume and Issue:
5(1)
Published: Jan. 24, 2025
Abstract
Kiwifruit
is
an
economically
and
nutritionally
important
horticultural
fruit
crop
worldwide.
The
genomic
data
of
several
kiwifruit
species
have
been
released,
providing
unprecedented
opportunity
for
pan-genome
analysis
to
comprehensively
investigate
the
inter-
intra-species
genetic
diversity
facilitate
utilization
breeding.
Here,
we
generated
a
super
using
15
high-quality
assemblies
eight
Actinidia
species.
For
gene-based
pan-genome,
total
61,465
gene
families
were
identified,
softcore
dispensable
genes
enriched
in
biological
processes
like
response
endogenous
stimulus,
hormone
cell
wall
organization
or
biogenesis.
Then,
structural
variations
(SVs)
against
A.
chinensis
‘Donghong’
identified
then
used
construct
graph-based
genome.
Further
population-scale
SVs
based
on
resequencing
from
112
individuals
20
revealed
extensive
which
probably
contributed
phenotypic
among
SV
hotspot
regions
found
environmental
adaptation.
Furthermore,
systematically
resistance
analogs
(RGAs)
pan-RGA
dataset
reveal
potentially
involved
disease
.
pan-genomic
obtained
here
useful
evolutionary
functional
studies
,
facilitates
breeding
design.
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.
