Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 7, 2025
Abstract
Global
patterns
of
population
genetic
variation
through
time
offer
a
window
into
evolutionary
processes
that
maintain
diversity.
Over
time,
lineages
may
expand
or
contract
their
distribution,
causing
turnover
in
composition.
At
individual
loci,
migration,
drift,
environmental
change
(among
other
processes)
affect
allele
frequencies.
Museum
specimens
widely
distributed
species
unique
the
genetics
understudied
populations
and
changes
over
time.
Here,
we
sequenced
genomes
130
herbarium
91
new
field
collections
Arabidopsis
thaliana
combined
these
with
published
genomes.
We
sought
broader
view
genomic
diversity
across
species,
to
test
if
composition
is
changing
documented
extensive
previously
uncharacterized
range
Africa,
are
under
threat
from
anthropogenic
climate
change.
Through
did
not
find
dramatic
populations.
Instead,
found
pattern
every
100
years
same
magnitude
seen
when
comparing
Eurasian
185
km
apart,
potentially
due
combination
drift
selection.
only
mixed
signals
polygenic
adaptation
at
phenology
physiology
QTL.
genes
conserved
eudicots
show
altered
levels
directional
frequency
change,
variable
purifying
background
Our
study
highlights
how
museum
can
reveal
dimensions
wild
evolving
recent
history.
Язык: Английский
GWAS-Driven Identification of Genomic Regions Conferring Yield and Related Traits Under Drought Stress in Wheat
Опубликована: Май 12, 2025
Abstract
Drought
stress
highlights
the
urgent
need
to
create
drought-tolerant
wheat
varieties.
The
genome-wide
association
analysis
was
performed
identify
genetic
markers
linked
yield
traits
under
drought
stress.
A
diverse
panel
of
190
bread
genotypes
evaluated
both
well-watered
and
water-limited
conditions
throughout
three
growing
seasons
(2021–2024)
in
Bahawalpur,
Punjab,
Pakistan
using
an
alpha
lattice
design
with
replications.
Genotyping
a
37
K
SNP
array.
Genomic
prediction
models
were
developed
genomic
best
linear
unbiased
predictions
(g-BLUPs).
Heritability
highest
(0.88)
for
lowest
(0.53)
spikes
per
plant.
Overall
tolerance
indices
ranged
from
1.21
thousand
kernel
weight
0.42
grain
yield.
additive
main
effects
multiplicative
interaction
(AMMI)
model
principal
component
(PCA)
identified
10
high-yielding
conditions.
59
regions
significantly
associated
related
on
21
chromosomes
clustered
as
ten
QTLs.
significant
QTL
3A
5B
explained
phenotypic
variance
7.1%
5.08%.
(g-BLUP)
indicated
notable
accuracies,
large-effect
QTLs,
ranging
0.1
flag
leaf
length
0.53
biomass.
This
study
concluded
variation
conditions,
moderate
high
heritability.
It
identifies
elite
key
tolerance,
model,
g-BLUP,
aids
breeding
programs
developing
climate-resilient
Язык: Английский
Nonphotochemical quenching changes with abiotic stressor and developmental stages
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Май 18, 2025
Abstract
Nonphotochemical
quenching
(NPQ)
is
a
critical
photoprotective
mechanism
in
plants,
safeguarding
photosystem
II
(PSII)
and
PSI
from
photodamage
under
abiotic
stress.
However,
it
unclear
if
different
stressors
lead
to
similar
NPQ
phenotypes,
the
magnitude
of
natural
variation
(between
within
plant
species)
response
stress
unknown.
Testing
semi-high-throughput
leaf-disc
approach
for
examining
kinetics
parameters,
we
investigated
chilling,
drought
low
nitrogen
across
multiple
species
and/or
genotypes.
Our
results
show
substantial
phenotypes
species,
genotypes
treatments.
In
C3
crops,
tobacco
soybean,
parameters
generally
increased
chilling
drought,
while
C4
maize
sorghum,
traits
were
more
variable
including
decrease
parameters.
Low-N
revealed
genotype-
developmental
stage-specific
effects
on
NPQ,
potentially
reflecting
distinct
adaptive
strategies
regulatory
changes
response.
A
significant
effect
ecotype
treatment
was
detected
most
Arabidopsis
thaliana
,
however,
interaction
between
stronger
than
chilling.
Differential
regulation
could
be
associated
with
combination
proton
motive,
ATPase
synthase
activity,
redox
state.
findings
highlight
that
interpreting
relative
inherently
complex
demands
broader
integration
physiological
data
layers.
Язык: Английский
Estimating scale-specific and localized spatial patterns in allele frequency
Genetics,
Год журнала:
2024,
Номер
227(3)
Опубликована: Май 17, 2024
Abstract
Characterizing
spatial
patterns
in
allele
frequencies
is
fundamental
to
evolutionary
biology
because
these
contain
evidence
of
underlying
processes.
However,
the
scales
at
which
gene
flow,
changing
selection,
and
drift
act
are
often
unknown.
Many
processes
can
operate
inconsistently
across
space,
causing
nonstationary
patterns.
We
present
a
wavelet
approach
characterize
pattern
frequency
that
helps
solve
problems.
show
how
our
relatedness
multiple
scales,
i.e.
multilocus
genetic
dissimilarity.
also
develop
tests
differentiation
quantitative
trait
loci
(QTL).
With
simulation,
we
illustrate
methods
under
different
scenarios.
apply
natural
populations
Arabidopsis
thaliana
population
structure
identify
locally
adapted
scales.
find,
for
example,
flowering
time
QTL
significantly
elevated
300–1,300
km
Wavelet
transforms
offer
flexible
way
reveal
geographic
Язык: Английский
The Roles of Drift and Selection on Short Stamen Loss inArabidopsis thalianaalong an Elevational Gradient in the Spanish Pyrenees
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 14, 2024
Traits
that
have
lost
function
sometimes
persist
through
evolutionary
time.
These
traits
may
if
there
is
not
enough
standing
genetic
variation
for
the
trait
to
allow
a
response
selection,
selection
against
weak
relative
drift,
or
has
residual
function.
To
determine
processes
shaping
whether
nonfunctional
are
retained
lost,
we
investigated
short
stamens
in
16
populations
of
Arabidopsis
thaliana
along
an
elevational
cline
northeast
Spain.
We
found
stamen
number
from
retention
high
elevation
incomplete
loss
low
populations.
did
find
evidence
limited
constrains
at
elevations,
nor
divergent
on
between
and
elevations.
Finally,
identified
loci
associated
with
Spain
different
across
latitudes
previous
study.
Overall,
identify
mechanisms
contributing
but
underlying
similar
phenotypic
clines.
Язык: Английский
Genetic variation in phenology of wild Arabidopsis thaliana plants
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 3, 2024
Phenology
and
the
timing
of
development
are
often
under
selection,
but
at
same
time
influence
selection
on
other
traits
by
controlling
how
expressed
across
seasons.
Plants
exhibit
high
natural
genetic
variation
in
phenology
when
grown
controlled
environments,
many
molecular
mechanisms
underlying
have
been
dissected.
There
remains
considerable
diversity
germination
flowering
within
populations
wild
contribution
genetics
to
phenological
plants
is
largely
unknown.
We
obtained
collection
dates
naturally
inbred
Язык: Английский