Rice,
as
one
of
the
most
important
staple
crops,
its
genetic
improvement
plays
a
crucial
role
in
agricultural
production
and
food
security.
Although
extensive
research
has
utilized
single
nucleotide
polymorphisms
(SNPs)
data
to
explore
basis
agronomic
traits
rice
improvement,
reports
on
other
types
variations,
such
insertions
deletions
(INDELs),
are
still
limited.
In
this
study,
we
extracted
INDELs
from
resequencing
148
improved
varieties.
We
identified
938,585
found
that
length
variation
increases,
number
variations
decreases,
with
89.0%
being
2–10
bp.
The
highest
was
chromosome
1,
while
least
10.
were
unevenly
distributed
across
genome,
generating
total
33
hotspot
regions.
47.0%
located
within
2
kb
upstream
downstream
genes.
Using
phenotypic
five
(heading
date,
flag
leaf
length,
width,
panicle
number,
plant
height)
along
INDEL
perform
genome-wide
association
study
(GWAS),
6,331
significant
loci
involving
157
cloned
Haplotype
analysis
candidate
genes
revealed
affecting
functional
genes,
OsMED25
OsRRMh
related
heading
MOC2
height.
Our
work
analyzed
patterns
associated
traits.
These
results
will
provide
valuable
material
resources
for
rice.
Plants,
Год журнала:
2024,
Номер
13(4), С. 490 - 490
Опубликована: Фев. 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.
Plant Biotechnology Journal,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 5, 2025
Summary
With
advances
in
long‐read
sequencing
and
assembly
techniques,
haplotype‐resolved
(phased)
genome
assemblies
are
becoming
more
common,
also
the
field
of
plant
genomics.
Computational
tools
to
effectively
explore
these
phased
genomes,
particularly
for
polyploid
currently
limited.
Here
we
describe
a
new
strategy
adopting
pangenome
approach.
To
analyse
both
intra‐
intergenomic
variation
assemblies,
have
made
software
package
PanTools
ploidy‐aware
by
updating
graph
representation
adding
several
novel
functionalities
assess
synteny
gene
retention,
profile
repeats
calculate
synonymous
nonsynonymous
mutation
rates.
Using
PanTools,
constructed
analysed
comprising
one
diploid
four
tetraploid
potato
cultivars,
five
apple
species.
Both
pangenomes
show
high
allelic
diversity
terms
absence/presence,
SNPs,
indels
larger
structural
variants.
Our
findings
that
visualizations
useful
discover
introgressions
detect
likely
misassemblies
genomes.
is
available
at
https://git.wur.nl/bioinformatics/pantools
.
Heliyon,
Год журнала:
2025,
Номер
11(3), С. e42348 - e42348
Опубликована: Янв. 29, 2025
Foxtail
millet
is
part
of
the
group
but
less
popular
than
sorghum
and
pearl
millet.
Nevertheless,
potential
this
plant
considered
promising
for
diversifying
food
nutrition,
health
products,
feed,
biofuel,
several
other
uses,
as
indicated
by
various
publications,
including
review
articles.
However,
studies,
analyses,
development
trends
foxtail
are
lacking,
current
status
future
projections
cannot
be
systematically
identified.
Bibliometric
analysis
offers
a
method
to
clarify
state
interaction
study
topic
systematic
analysis.
Therefore,
conducted
bibliometric
examine
development,
interaction,
research
regarding
publication
trends,
countries
involved,
keywords.
Publications
related
were
first
mined
from
Scopus
database
analyzed
using
Biblioshiny
R
Studio
VOSviewer
software,
with
2091
documents
identified
being
associated
A
significant
occurred
in
2012
when
entire
genome
was
explored.
The
main
that
focus
on
developing
China
India.
focused
optimizing
omics-based
approaches
support
use
its
potential,
especially
efforts
involving
climate
change
tolerance
systems.
innovation,
exploration,
will
continue
develop
along
submarginal
land
public
problems,
Indonesia,
which
has
fourth
largest
population
globally.
Genes,
Год журнала:
2024,
Номер
15(8), С. 1072 - 1072
Опубликована: Авг. 14, 2024
Light
is
one
of
the
most
important
factors
regulating
plant
gene
expression
patterns,
metabolism,
physiology,
growth,
and
development.
To
explore
how
light
may
induce
or
alter
transcript
splicing,
we
conducted
RNA-Seq-based
transcriptome
analyses
by
comparing
samples
harvested
as
etiolated
seedlings
grown
under
continuous
dark
conditions
vs.
light-treated
green
seedlings.
The
study
aims
to
reveal
differentially
regulated
protein-coding
genes
novel
long
noncoding
RNAs
(lncRNAs),
their
light-induced
alternative
association
with
biological
pathways.
We
identified
14,766
expressed
genes,
which
4369
showed
splicing.
observed
that
mapped
plastid-localized
methyl-erythritol-phosphate
(MEP)
pathway
were
light-upregulated
compared
cytosolic
mevalonate
(MVA)
genes.
Many
these
also
undergo
These
pathways
provide
crucial
metabolite
precursors
for
biosynthesis
secondary
metabolic
compounds
needed
chloroplast
biogenesis,
establishment
a
successful
photosynthetic
apparatus,
photomorphogenesis.
In
chromosome-wide
survey
transcriptome,
intron
retention
predominant
splicing
event.
addition,
1709
lncRNA
transcripts
in
our
data.
This
provides
insights
on
light-regulated
rice.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 6, 2024
With
advances
in
long-read
sequencing
and
assembly
techniques,
haplotype-resolved
(phased)
genome
assemblies
are
becoming
more
common,
also
the
field
of
plant
genomics.
Computational
tools
to
effectively
explore
these
phased
genomes,
particularly
for
polyploid
genomes
currently
limited.
Here
we
describe
a
new
strategy
adopting
pangenome
approach.
To
analyze
both
intra-
intergenomic
variation
assemblies,
have
made
software
package
PanTools
ploidy-aware
by
updating
graph
representation
adding
several
novel
functionalities
assess
synteny
gene
retention,
profile
repeats
calculate
synonymous
nonsynyonymous
mutation
rates.
Using
PanTools,
constructed
analyzed
comprising
one
diploid
four
tetraploid
potato
cultivars,
five
apple
species.
Both
pangenomes
show
high
allelic
diversity
terms
absence/presence,
SNPs,
indels
larger
structural
variants.
Our
findings
that
visualizations
useful
discover
introgressions
detect
likely
misassemblies
genomes.
is
available
at
https://git.wur.nl/bioinformatics/pantools.
Frontiers in Microbiology,
Год журнала:
2024,
Номер
15
Опубликована: Авг. 6, 2024
Bacterial
exopolysaccharides
(EPS)
have
emerged
as
one
of
the
key
players
in
field
heavy
metal-contaminated
environmental
bioremediation.
This
study
aimed
to
characterize
and
evaluate
metal
biosorption
potential
EPS
produced
by
a
novel
