Introgressions lead to reference bias in wheat RNA-seq analysis
BMC Biology,
Год журнала:
2024,
Номер
22(1)
Опубликована: Март 7, 2024
Abstract
Background
RNA-seq
is
a
fundamental
technique
in
genomics,
yet
reference
bias,
where
transcripts
derived
from
non-reference
alleles
are
quantified
less
accurately,
can
undermine
the
accuracy
of
quantification
and
thus
conclusions
made
downstream.
Reference
bias
analysis
has
to
be
explored
complex
polyploid
genomes
despite
evidence
that
they
often
mosaic
wild
relative
introgressions,
which
introduce
blocks
highly
divergent
genes.
Results
Here
we
use
hexaploid
wheat
as
model
polyploid,
using
both
simulated
experimental
data
show
alignment
suffers
widespread
largely
driven
by
introgressed
This
leads
underestimation
gene
expression
incorrect
assessment
homoeologue
balance.
By
incorporating
models
ten
genome
assemblies
into
pantranscriptome
reference,
present
novel
method
reduce
readily
scaled
capture
more
variation
new
transcriptome
becomes
available.
Conclusions
study
shows
presence
introgressions
lead
analysis.
Caution
should
exercised
researchers
non-sample
for
methods,
such
one
presented
here,
considered.
Язык: Английский
Septoria tritici blotch resistance gene Stb15 encodes a lectin receptor-like kinase
Nature Plants,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 14, 2025
Abstract
Septoria
tritici
blotch
(STB),
caused
by
the
Dothideomycete
fungus
Zymoseptoria
,
is
one
of
most
damaging
diseases
bread
wheat
(
Triticum
aestivum
)
1
and
target
costly
fungicide
applications
2
.
In
line
with
fungus’s
apoplastic
lifestyle,
STB
resistance
genes
isolated
to
date
encode
receptor-like
kinases
(RLKs)
including
a
wall-associated
kinase
Stb6
cysteine-rich
Stb16q
3,4
Here
we
used
genome-wide
association
studies
on
diverse
panel
300
whole-genome
shotgun-sequenced
landraces
(WatSeq
consortium
5
identify
99-kb
region
containing
six
candidates
for
Stb15
gene.
Mutagenesis
transgenesis
confirmed
gene
encoding
an
intronless
G-type
lectin
RLK
as
The
characterization
exemplifies
unexpected
diversity
RLKs
conferring
Z.
in
wheat.
Язык: Английский
Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 23, 2025
Abstract
Changes
in
gene
expression
are
crucial
for
crop
breeding,
yet
population
genomics
has
primarily
focused
on
sequence
polymorphisms
rather
than
diversity.
The
strategy
of
using
single
genome
reference
RNA-seq
analysis
could
not
handle
introgression
bias,
especially
hexaploidy
wheat.
Here,
we
conducted
328
wheat
lines,
including
representative
diverse
landraces
and
elite
cultivars
from
China
the
United
States,
to
investigate
role
variation
shaping
agronomic
traits.
Using
pan-genome
resources,
identified
20,615
more
transcripts
‘Chinese
Spring’
alone.
We
constructed
a
pan-gene
atlas
regulatory
map
through
eQTL
analysis,
demonstrating
that
genes
introgressed
wild
relatives
were
under
tight
genetic
control.
Genes
responding
environmental
stress
show
higher
activity
after
into
genome,
how
long-term
breeding
selection
impacted
regulation
targeted
introgression.
Multi-omics
modeling
231
high-confidence
candidate
34
field
traits
seedling
resistance
phenotypes
8
powdery
mildew
isolates.
More
one
fifth
those
candidates
have
no
homolog
genome.
By
utilizing
indexed
KN9204
EMS
library,
80%
showed
significant
trait
difference
between
type
mutant
lines.
Furthermore,
directional
shifts
which
changed
by
improvement
demonstrated
distinct
adaptations
local
environments.
Our
study
correct
bias
reads
mapping
studies
revealed
patterns
within
their
mechanisms,
highlighted
impact
world’s
most
important
crop.
Язык: Английский
Wheat genomics: genomes, pangenomes, and beyond
Trends in Genetics,
Год журнала:
2024,
Номер
40(11), С. 982 - 992
Опубликована: Авг. 26, 2024
Язык: Английский
Identification of candidate genes for adult plant stripe rust resistance transferred from Aegilops ventricosa 2NvS into wheat via fine mapping and transcriptome analysis
Theoretical and Applied Genetics,
Год журнала:
2024,
Номер
137(5)
Опубликована: Май 1, 2024
Язык: Английский
A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance
Theoretical and Applied Genetics,
Год журнала:
2024,
Номер
137(4)
Опубликована: Март 27, 2024
Abstract
Key
message
A
bread
wheat
panel
reveals
rich
genetic
diversity
in
Turkish,
Pakistani
and
Iranian
landraces
novel
resistance
loci
to
diverse
powdery
mildew
isolates
via
subsetting
approaches
association
studies.
Wheat
breeding
for
disease
relies
on
the
availability
use
of
resources.
More
than
800,000
accessions
are
globally
conserved
gene
banks,
but
they
mostly
uncharacterized
presence
genes
their
potential
agriculture.
Based
selective
reduction
previously
assembled
collections
allele
mining
resistance,
we
a
trait-customized
755
geographically
with
focus
landraces,
called
LandracePLUS
panel.
Population
structure
analysis
this
based
TaBW35K
SNP
array
revealed
an
increased
compared
632
genotyped
earlier
study
17
high-quality
sequenced
accessions.
The
additional
found
here
originated
from
landraces.
We
characterized
ten
fungal
pathogen
mildew.
Performing
genome-wide
studies
dividing
further
by
targeted
approach
distinct
geographical
origin,
detected
several
known
already
cloned
genes,
including
Pm2a
gene.
In
addition,
identified
22
putatively
that
represent
useful
sources
research
mildew-wheat
pathosystem.
Our
shows
value
assembling
utilizing
range
races
detect
loci.
It
highlights
importance
integrating
different
origins
into
future
Язык: Английский
A pangenome and pantranscriptome of hexaploid oat
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 27, 2024
Oat
grain
is
a
traditional
human
food
rich
in
dietary
fiber
that
contributes
to
improved
health.
Interest
the
crop
has
surged
recent
years
owing
its
use
as
basis
for
plant-based
milk
analogs.
an
allohexaploid
with
large,
repeat-rich
genome
was
shaped
by
subgenome
exchanges
over
evolutionary
timescales.
In
contrast
many
other
cereal
species,
genomic
research
oat
still
at
early
stage,
and
surveys
of
structural
diversity
gene
expression
variability
are
scarce.
Here,
we
present
annotated
chromosome-scale
sequence
assemblies
33
wild
domesticated
oats
along
atlas
across
six
tissues
different
developmental
stages
23
accessions.
We
describe
interplay
subgenomes,
accessions
tissues.
Gene
loss
hexaploid
accompanied
compensatory
up-regulation
remaining
homeologs,
but
this
process
constrained
divergence.
Chromosomal
rearrangements
have
significantly
impacted
breeding.
A
large
pericentric
inversion
associated
flowering
explains
distorted
segregation
on
chromosome
7D
homeologous
exchange
between
chromosomes
2A
2C
semidwarf
mutant
risen
prominence
Australian
elite
varieties.
The
pangeome
will
promote
adoption
approaches
understanding
evolution
adaptation
accelerate
their
improvement.
Язык: Английский
Multiomics plasticity in seed traits of pan-genome wheat cultivars
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 21, 2024
Abstract
The
molecular
basis
of
cultivar-level
variations
in
polyploid
wheat
that
enables
environmental
adaptation
while
maintaining
yield
and
quality
remains
poorly
understood.
We
conducted
a
detailed
phenotypic
assessment
multiomics
analysis
nine
pan-genome
cultivars
grown
under
control
drought
conditions.
aimed
to
investigate
the
subgenome-level
variations,
cultivar
differences
biochemical
mechanisms
affecting
plant
fitness
moderate
stress.
Intrinsic
water
use
efficiency,
grain
yield,
protein
content
differed
among
cultivars,
supporting
plasticity
stress
responses.
Biased
proteome
metabolome
abundance
changes
response
during
vegetative
stage
indicate
different
strategies
for
utilization
homeologous
isoforms
assigned
A,
B,
D
subgenomes.
Drought
effects
were
detected
at
level,
but
significant
observed
central
carbon
pathway
metabolites
micronutrient
profiles.
subgenomic
localization
seed
storage
proteins
highlight
nutrient
reservoir
accumulation
emphasizes
enhanced
role
S-rich
prolamins
response.
Subgenomic
define
phenotypes
by
producing
molecules
accumulate
enable
underlying
trade-offs
between
yield-
or
quality-related
traits.
These
can
be
used
select
crops
with
increased
resistance
without
compromising
yield.
Язык: Английский