Nature Communications,
Journal Year:
2019,
Volume and Issue:
10(1)
Published: March 14, 2019
Abstract
Efficient
crop
improvement
depends
on
the
application
of
accurate
genetic
information
contained
in
diverse
germplasm
resources.
Here
we
report
a
reference-grade
genome
wild
soybean
accession
W05,
with
final
assembled
size
1013.2
Mb
and
contig
N50
3.3
Mb.
The
analytical
power
W05
is
demonstrated
by
several
examples.
First,
identify
an
inversion
at
locus
determining
seed
coat
color
during
domestication.
Second,
translocation
event
between
chromosomes
11
13
some
genotypes
shown
to
interfere
assignment
QTLs.
Third,
find
region
containing
copy
number
variations
Kunitz
trypsin
inhibitor
(
KTI
)
genes.
Such
findings
illustrate
this
assembly
analysis
large
structural
collections.
has
wide
applications
comparative
genomic
evolutionary
studies,
as
well
breeding
programs.
Frontiers in Plant Science,
Journal Year:
2014,
Volume and Issue:
5
Published: June 3, 2014
Soybean
production
is
greatly
influenced
by
abiotic
stresses
imposed
environmental
factors
such
as
drought,
water
submergence,
salt,
and
heavy
metals.
A
thorough
understanding
of
plant
response
to
stress
at
the
molecular
level
a
prerequisite
for
its
effective
management.
The
mechanism
tolerance
complex
requires
information
omic
understand
it
effectively.
In
this
regard,
enormous
progress
has
been
made
in
omics
field
areas
genomics,
transcriptomics,
proteomics.
emerging
ionomics
also
being
employed
investigating
soybean.
Omic
approaches
generate
huge
amount
data,
adequate
advancements
computational
tools
have
achieved
analysis.
However,
integration
omic-scale
address
genetics
physiological
questions
still
challenge.
review,
we
described
advances
view
conventional
modern
used
dissect
Emphasis
was
given
quantitative
trait
loci
(QTL)
mapping,
genome-wide
association
studies
(GWAS),
genomic
selection
(GS).
Comparative
genomics
candidate
gene
are
discussed
considering
identification
potential
loci,
genes,
biochemical
pathways
involved
This
review
provides
comprehensive
catalog
available
online
resources
soybean
utilization.
We
addressed
significance
phenomics
integrated
recognized
high-throughput
multi-dimensional
phenotyping
major
limiting
factor
improvement
Molecular Plant,
Journal Year:
2013,
Volume and Issue:
7(3), P. 541 - 553
Published: Oct. 12, 2013
A
high-density
single
nucleotide
polymorphism
(SNP)
array
is
critically
important
for
geneticists
and
molecular
breeders.
With
the
accumulation
of
huge
amounts
genomic
re-sequencing
data
available
technologies
accurate
SNP
detection,
it
possible
to
design
high-quality
rice
arrays.
Here
we
report
development
a
its
utility.
probes
were
designed
by
screening
more
than
10
000
loci
extracted
from
801
varieties
an
named
RiceSNP50
was
produced
on
Illumina
Infinium
platform.
The
contained
51
478
evenly
distributed
markers,
68%
which
within
genic
regions.
Several
hundred
plants
with
parent/F1
relationships
used
generate
cluster
file
calling.
Application
tests
showed
that
this
had
high
genotyping
accuracy,
could
be
different
objectives.
For
example,
core
collection
elite
clustered
fine
resolution.
Genome-wide
association
studies
(GWAS)
analysis
correctly
identified
characterized
QTL.
Further,
successfully
variety
verification
trait
introgression.
As
high-throughput
tool,
will
play
role
in
both
functional
genomics
breeding.
Plant Biotechnology Journal,
Journal Year:
2019,
Volume and Issue:
17(10), P. 1938 - 1953
Published: March 26, 2019
Summary
Tea
is
the
world's
widely
consumed
nonalcohol
beverage
with
essential
economic
and
health
benefits.
Confronted
increasing
large‐scale
omics‐data
set
particularly
genome
sequence
released
in
tea
plant,
construction
of
a
comprehensive
knowledgebase
urgently
needed
to
facilitate
utilization
these
data
sets
towards
molecular
breeding.
We
hereby
present
first
integrative
specially
designed
web‐accessible
database,
Plant
Information
Archive
(TPIA;
http://tpia.teaplant.org
).
The
current
release
TPIA
employs
comprehensively
annotated
plant
as
framework
incorporates
abundant
well‐organized
transcriptomes,
gene
expressions
(across
species,
tissues
stresses),
orthologs
characteristic
metabolites
determining
quality.
It
also
hosts
massive
transcription
factors,
polymorphic
simple
repeats,
single
nucleotide
polymorphisms,
correlations,
manually
curated
functional
genes
globally
collected
germplasm
information.
A
variety
versatile
analytic
tools
(e.g.
JBrowse,
blast,
enrichment
analysis,
etc.)
are
established
helping
users
perform
further
comparative,
evolutionary
analysis.
show
case
application
that
provides
novel
interesting
insights
into
phytochemical
content
variation
section
Thea
genus
Camellia
under
well‐resolved
phylogenetic
framework.
constructed
will
serve
central
gateway
for
global
community
better
understand
biology
largely
benefits
whole
industry.
Nature Communications,
Journal Year:
2019,
Volume and Issue:
10(1)
Published: March 14, 2019
Abstract
Efficient
crop
improvement
depends
on
the
application
of
accurate
genetic
information
contained
in
diverse
germplasm
resources.
Here
we
report
a
reference-grade
genome
wild
soybean
accession
W05,
with
final
assembled
size
1013.2
Mb
and
contig
N50
3.3
Mb.
The
analytical
power
W05
is
demonstrated
by
several
examples.
First,
identify
an
inversion
at
locus
determining
seed
coat
color
during
domestication.
Second,
translocation
event
between
chromosomes
11
13
some
genotypes
shown
to
interfere
assignment
QTLs.
Third,
find
region
containing
copy
number
variations
Kunitz
trypsin
inhibitor
(
KTI
)
genes.
Such
findings
illustrate
this
assembly
analysis
large
structural
collections.
has
wide
applications
comparative
genomic
evolutionary
studies,
as
well
breeding
programs.
