A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study
BMC Genomics,
Год журнала:
2024,
Номер
25(1)
Опубликована: Окт. 31, 2024
The
concept
of
pangenomics
and
the
importance
structural
variants
is
gaining
recognition
within
plant
genomics
community.
Due
to
advancements
in
sequencing
computational
technology,
it
has
become
feasible
sequence
entire
genome
numerous
individuals
a
single
species
at
reasonable
cost.
Pangenomes
have
been
constructed
for
many
major
diploid
crops,
including
rice,
maize,
soybean,
sorghum,
pearl
millet,
peas,
sunflower,
grapes,
mustards.
However,
pangenomes
polyploid
are
relatively
scarce
available
only
few
crops
wheat,
cotton,
rapeseed,
potatoes.
Язык: Английский
Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustris L.)
Ecology and Evolution,
Год журнала:
2025,
Номер
15(3)
Опубликована: Март 1, 2025
ABSTRACT
Northern
Wild
Rice
(NWR;
Zizania
palustris
L.)
is
an
aquatic,
annual
grass
with
significant
ecological,
cultural,
and
economic
importance
to
the
Great
Lakes
region
of
North
America.
In
this
study,
we
assembled
genotyped
a
diverse
collection
839
NWR
individuals
using
genotyping‐by‐sequencing
(GBS)
obtained
5955
single‐nucleotide
polymorphisms
(SNPs).
This
consisted
samples
from
12
wild
populations
collected
across
Minnesota
Western
Wisconsin,
some
which
were
over
two
time
points;
representative
cultivated
varieties
breeding
populations;
aquatica
outgroup.
Using
these
data,
characterized
genetic
diversity,
relatedness,
population
structure
broad
genotypes.
We
found
that
clustered
primarily
by
their
geographical
location,
clustering
patterns
likely
influenced
historical
ecosystem
management.
Cultivated
genetically
distinct
populations,
suggesting
limited
gene
flow
between
semi‐domesticated
crop
its
counterparts.
The
first
genome‐wide
scans
putative
selection
events
in
suggest
undergoing
heavy
pressure
for
traits
conducive
irrigated
paddy
conditions.
Overall,
study
presents
large
set
SNP
markers
use
studies
provides
new
insights
into
flow,
history,
complexity
NWR.
Язык: Английский
Polyploidy in potatoes: challenges and possibilities for climate resilience
Trends in Genetics,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 1, 2025
Solanum
section
Petota
Dumort.
consists
of
tuber-bearing
species
(i.e.,
the
cultivated
potatoes
and
their
wild
relatives)
that
have
both
asexual
sexual
propagation,
variation
in
ploidy,
reproductive
isolation.
These
undergone
adaptation
to
a
diversity
climates,
altitudes,
photoperiods,
geographical
range.
The
defies
characterization
with
biological
concept
due
interspecies
hybridization,
allo-
auto-polyploidy,
phenotypic
plasticity.
Genetic
studies,
more
recently
genome
sequencing
pangenome
analyses,
are
fostering
greater
understanding
genetic
processes
shape
evolution
speciation
section,
shedding
light
on
phylogeny
providing
insights
utilization
potato
crop
relatives
breeding
for
climate-resilient
varieties.
Язык: Английский
Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustrisL.)
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Авг. 26, 2022
Abstract
Northern
Wild
Rice
(NWR;
Zizania
palustris
L.)
is
an
aquatic,
annual
grass
with
significant
ecological,
cultural,
and
economic
importance
to
the
Great
Lakes
region
of
North
America.
In
this
study,
we
assembled
genotyped
a
diverse
collection
839
NWR
individuals
using
genotyping-by-sequencing
(GBS)
obtained
5,955
single-nucleotide
polymorphisms
(SNPs).
Our
consisted
samples
from
12
wild
populations
collected
across
Minnesota
Western
Wisconsin,
some
which
were
over
two
time
points;
representative
cultivated
varieties
breeding
populations;
aquatica
outgroup.
Using
these
data,
characterized
genetic
diversity,
relatedness,
population
structure
broad
genotypes.
We
found
that
clustered
primarily
by
their
geographical
location,
clustering
patterns
likely
influenced
historical
ecosystem
management.
Cultivated
genetically
distinct
populations,
suggesting
limited
gene
flow
between
semi-domesticated
crop
its
counterparts.
The
first
genome-wide
scans
putative
selection
events
in
suggest
undergoing
heavy
pressure
for
traits
conducive
irrigated
paddy
conditions.
Overall,
study
presents
large
set
SNP
markers
use
studies
provides
new
insights
into
flow,
history,
complexity
NWR.
Язык: Английский