A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity
Nature Genetics,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 3, 2025
Abstract
A
pan-transcriptome
describes
the
transcriptional
and
post-transcriptional
consequences
of
genome
diversity
from
multiple
individuals
within
a
species.
We
developed
barley
using
20
inbred
genotypes
representing
domesticated
by
generating
analyzing
short-
long-read
RNA-sequencing
datasets
tissues.
To
overcome
single
reference
bias
in
transcript
quantification,
we
constructed
genotype-specific
(RTDs)
integrated
these
into
linear
pan-genome
framework
to
create
pan-RTD,
allowing
categorization
as
core,
shell
or
cloud.
Focusing
on
core
(expressed
all
genotypes),
observed
significant
abundance
variation
among
tissues
between
driven
partly
RNA
processing,
gene
copy
number,
structural
rearrangements
conservation
promotor
motifs.
Network
analyses
revealed
conserved
co-expression
module::tissue
correlations
frequent
functional
diversification.
complement
pan-transcriptome,
comprehensive
cultivar
(cv.)
Morex
gene-expression
atlas
illustrate
how
combined
can
be
used
guide
biological
inquiry.
Язык: Английский
Candidate Gene for Kernel-Related Traits in Maize Revealed by a Combination of GWAS and Meta-QTL Analyses
Plants,
Год журнала:
2025,
Номер
14(6), С. 959 - 959
Опубликована: Март 19, 2025
Maize
kernel
traits
represent
crucial
agronomic
characteristics
that
significantly
determine
yield
potential.
Analyzing
the
genetic
basis
of
these
is
essential
for
improvement.
In
this
study,
we
utilized
1283
maize
inbred
lines
to
investigate
three
kernel-related
characteristics:
length
(KL),
width
(KW),
and
100-kernel
weight
(HKW).
We
conducted
a
genome-wide
association
study
(GWAS)
on
traits,
resulting
in
identification
29
associated
SNPs
six
candidate
genes.
Additionally,
compiled
quantitative
trait
loci
(QTL)
information
765
from
56
studies,
meta-analysis
QTL,
identified
65
meta-QTLs
(MQTLs).
Among
23
MQTLs,
found
25
functional
genes
reported
related
traits.
26
homologs
across
19
MQTLs
by
utilizing
affect
rice
grain
compared
significant
detected
with
physical
locations
3
were
located
within
MQTL
intervals,
another
10
proximity
being
less
than
2
Mb
away,
although
they
not
included
intervals.
The
results
provide
theoretical
foundation
elucidating
advancing
molecular
marker-assisted
breeding
selection.
Язык: Английский
Meta-analysis of QTLs for drought, heat, and salinity tolerance identifies high-confidence MQTLs and candidate genes in chickpea (Cicer arietinum L.)
Journal of Biosciences,
Год журнала:
2025,
Номер
50(2)
Опубликована: Март 22, 2025
Язык: Английский
Genetic dissection of yield and yield-related traits in mungbean based on QTL meta-analysis
Frontiers in Genetics,
Год журнала:
2025,
Номер
16
Опубликована: Май 8, 2025
As
an
important
food
crop
and
nutritional
source,
mungbean
has
prioritized
yield
improvement
as
a
key
objective
in
breeding
programs.
In
present
study,
we
conducted
QTL
meta-analysis
to
integrate
660
QTLs
related
yield-related
traits
published
over
the
past
20
years.
A
total
of
590
initial
were
mapped
onto
high-density
consensus
map,
resulting
identification
72
meta-QTLs
(MQTLs).
These
MQTLs
unevenly
distributed
across
11
linkage
groups
(LGs)
with
average
confidence
interval
(CI)
1.21
cM,
which
was
6.26-fold
narrower
than
CI
QTLs.
Among
these
MQTLs,
validated
genome-wide
association
study
(GWAS)
for
mungbean.
Orthologous
MQTL
analysis
revealed
that
22
collinear
19
common
bean
traits.
addition,
breeder's
screened
from
339
gene
models
identified
within
regions.
Twenty-two
orthologs
genes
such
seed
germination,
tiller
number,
plant
height
rice
Arabidopsis
regions
using
homology
analysis.
This
contributes
understanding
genetic
mechanisms
provides
new
ideas
Язык: Английский