Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes
Biomolecules,
Год журнала:
2023,
Номер
13(9), С. 1403 - 1403
Опубликована: Сен. 17, 2023
The
availability
of
multiple
sequenced
genomes
from
a
single
species
made
it
possible
to
explore
intra-
and
inter-specific
genomic
comparisons
at
higher
resolution
build
clade-specific
pan-genomes
several
crops.
crops
constructed
various
cultivars,
accessions,
landraces,
wild
ancestral
represent
compendium
genes
structural
variations
allow
researchers
search
for
the
novel
alleles
that
were
inadvertently
lost
in
domesticated
during
historical
process
crop
domestication
or
extensive
plant
breeding.
Fortunately,
many
valuable
associated
with
desirable
traits
like
disease
resistance,
abiotic
stress
tolerance,
architecture,
nutrition
qualities
exist
species,
relatives.
ancestors
landraces
can
be
introduced
back
high-yielding
varieties
modern
by
implementing
classical
breeding,
selection,
transgenic/gene
editing
approaches.
Thus,
pan-genomic
represents
great
leap
research
offers
new
avenues
targeted
breeding
mitigate
impact
global
climate
change.
Here,
we
summarize
tools
used
pan-genome
assembly
annotations,
web-portals
hosting
pan-genomes,
etc.
Furthermore,
highlight
few
discoveries
using
approach
future
potential
this
emerging
field
study.
Язык: Английский
A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes
Plants,
Год журнала:
2025,
Номер
14(9), С. 1399 - 1399
Опубликована: Май 6, 2025
Copy
number
variations
(CNVs),
as
an
important
structural
variant
in
genomes,
are
widely
present
plants,
affecting
their
phenotype
and
adaptability.
In
recent
years,
CNV
research
has
not
only
focused
on
changes
gene
copy
numbers
but
also
been
linked
to
complex
mechanisms
such
genome
rearrangements,
transposon
activity,
environmental
adaptation.
The
advancement
sequencing
technologies
made
the
detection
analysis
of
CNVs
more
efficient,
revealing
crucial
roles
plant
disease
resistance,
adaptability,
growth
development,
demonstrating
broad
application
potential
crop
improvement,
particularly
selective
breeding
genomic
selection.
By
studying
during
domestication
process,
researchers
have
gradually
recognized
role
evolution.
This
article
reviews
formation
methods
for
detection,
relationship
with
traits,
applications
improvement.
It
emphasizes
future
directions
involving
integration
multi-omics
provide
new
perspectives
structure
function
genomes.
Язык: Английский
Multi-omic applications for understanding and enhancing tropical fruit flavour
Plant Molecular Biology,
Год журнала:
2024,
Номер
114(4)
Опубликована: Июль 8, 2024
Abstract
Consumer
trends
towards
nutrient-rich
foods
are
contributing
to
global
increasing
demand
for
tropical
fruit.
However,
commercial
cultivars
in
the
breeding
pipeline
that
tailored
meet
market
at
risk
of
possessing
reduced
fruit
flavour
qualities.
This
stems
from
recurrent
prioritised
selection
superior
agronomic
traits
and
not
flavour,
which
may
turn
reduce
consumer
satisfaction.
There
is
realisation
quality
traits,
inclusive
must
be
equally
selected
for;
but
currently,
there
limited
tools
resources
available
select
particularly
species.
Although
sugars,
acids,
volatile
organic
compounds
known
define
specific
combinations
these,
result
defined
preferences,
remain
unknown
many
To
include
preferences
selective
breeding,
it
vital
determine
metabolites
underpin
them.
Then,
objective
quantitative
analysis
implemented
instead
solely
relying
on
human
sensory
panels.
lead
development
genetic
markers
through
integrated
omics
approaches
target
biosynthetic
pathways
active
compounds.
In
this
review,
we
explore
progress
able
strategically
consumer-preferred
profiles
new
Язык: Английский
Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation
Опубликована: Авг. 23, 2023
The
availability
of
multiple
sequenced
genomes
from
a
single
species
made
it
possible
to
explore
intra-
and
inter-specific
genomic
comparisons
at
higher
resolution
build
clade-specific
pangenomes
several
crops.
pan-genomes
crops
constructed
various
cultivars/accessions,
landraces,
wild
ancestral
represent
compendium
genes
structural
variations
allow
researchers
search
for
the
novel
alleles
that
were
inadvertently
lost
in
domesticated
during
historical
process
crop
domestication
or
extensive
plant
breeding.
Fortunately,
many
valuable
associated
with
desirable
traits
like
disease
resistance,
abiotic
stress
tolerance,
architecture,
nutrition
qualities
exist
species,
relatives.
novels
ancestors
landraces
can
be
introduced
back
high-yielding
varieties
modern
by
implementing
classical
breeding,
selection,
transgenic/gene
editing
approaches.
Thus,
pan-genomic
represents
great
leap
research
offers
new
avenues
targeted
breeding
mitigating
impact
global
climate
change.
Here
we
summarize
tools
used
pangenome
assembly
annotations,
web-portals
hosting
pangenomes.
Furthermore,
highlight
few
discoveries
using
approach
its
future
potential.
Язык: Английский
A test-tube vinification method for high-throughput characterisation of the oenological and aromatic potential of white wines
OENO One,
Год журнала:
2024,
Номер
58(1)
Опубликована: Фев. 29, 2024
The
quality
of
wine
largely
depends
on
aroma
perception,
but
the
genetic
basis
explaining
variations
compound
concentrations
in
wines
is
still
fragmentary.
To
unravel
links
between
and
hundreds
genotypes,
we
developed
a
small-scale,
high-throughput
test-tube
vinification
(TTV)
method
capable
producing
white
that
reveal
potential
at
scale
single
vine
stock.
We
evaluated
this
commercial
grapevine
varieties
(Riesling,
Gewurztraminer,
Chardonnay,
Chasselas,
Floreal,
Muscat
à
petits
grains
blancs)
genotypes
resulting
from
bi-parental
cross,
covering
wide
aromatic
palette.
produced
were
described
by
usual
oenological
parameters
GC-MS
profiling
volatile
compounds.
compared
obtained
with
TTV
to
larger
fermentation
volumes
(5–10
L).
Our
results
show
suitable
produce
very
small
scale,
i.e.,
less
than
100
mL
these
small-scale
faithfully
reflect
different
varieties,
as
would
volume
methods.
proposed
approach
assess
grape
material
harvested
vine.
This
wine-focused
direct
phenotyping
will
pave
way
for
better
understanding
determinism
aromas,
especially
molecules
are
not
directly
present
grapes,
such
thiols
1,1,6-trimethyl-1,2-dihydronaphthalene
(TDN).
Язык: Английский