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- Small RNAs as
big players in
plant abiotic
stress
responses and
nutrient
deprivation.: Trends Plant
Sci, Vol. 12,
No. 7. (July
2007), pp.
301-309.Abioti
c stress is
one of the
primary causes
of crop losses
worldwide.
Much progress
has been made
in unraveling
the complex
stress
response
mechanisms,
particularly
in the
identification
of stress
responsive
protein-coding
genes. In
addition to
protein coding
genes,
recently
discovered
microRNAs
(miRNAs) and
endogenous
small
interfering
RNAs (siRNAs)
have emerged
as important
players in
plant stress
responses.
Initial clues
suggesting
that small
RNAs are
involved in
plant stress
responses stem
from studies
showing stress
regulation of
miRNAs and
endogenous
siRNAs, as
well as from
target
predictions
for some
miRNAs.
Subsequent
studies have
demonstrated
an important
functional
role for these
small RNAs in
abiotic stress
responses.
This review
focuses on
recent
advances, with
emphasis on
integration of
small RNAs in
stress
regulatory
networks.
Source: Trends Plant Sci, Vol. 12, No. 7. (July 2007), pp. 301-309. - The effects of
artificial
selection on
the maize
genome.: Science, Vol.
308, No. 5726.
(27 May 2005),
pp.
1310-1314.Dome
stication
promotes rapid
phenotypic
evolution
through
artificial
selection. We
investigated
the genetic
history by
which the wild
grass teosinte
(Zea mays ssp.
parviglumis)
was
domesticated
into modern
maize (Z. mays
ssp. mays).
Analysis of
single-nucleot
ide
polymorphisms
in 774 genes
indicates that
2 to 4% of
these genes
experienced
artificial
selection. The
remaining
genes retain
evidence of a
population
bottleneck
associated
with
domestication.
Candidate
selected genes
with putative
function in
plant growth
are clustered
near
quantitative
trait loci
that
contribute to
phenotypic
differences
between maize
and teosinte.
If we assume
that our
sample of
genes is
representative
,
approximately
1200 genes
throughout the
maize genome
have been
affected by
artificial
selection.
Source: Science, Vol. 308, No. 5726. (27 May 2005), pp. 1310-1314. - Single feature
polymorphism
discovery in
rice.: PLoS ONE, Vol.
2 (2007)The
discovery of
nucleotide
diversity
captured as
single feature
polymorphism
(SFP) by using
the expression
array is a
high-throughpu
t and
effective
method in
detecting
genome-wide
polymorphism.
The efficacy
of such method
was tested in
rice, and the
results
presented in
the paper
indicate high
sensitivity in
predicting
SFP. The
sensitivity of
polymorphism
detection was
further
demonstrated
by the fact
that no
biasness was
observed in
detecting SFP
with either
single or
multiple
nucleotide
polymorphisms.
The high
density SFP
data that can
be generated
quite
effectively by
the current
method has
promise for
high
resolution
genetic
mapping
studies, as
physical
location of
features are
well-defined
on rice
genome.
Source: PLoS ONE, Vol. 2 (2007) - Genome-Wide
Association
Mapping in
Arabidopsis
Identifies
Previously
Known
Flowering Time
and Pathogen
Resistance
Genes.: PLoS Genet,
Vol. 1, No. 5.
(11 November
2005)There is
currently
tremendous
interest in
the
possibility of
using
genome-wide
association
mapping to
identify genes
responsible
for natural
variation,
particularly
for human
disease
susceptibility
. The model
plant
Arabidopsis
thaliana is in
many ways an
ideal
candidate for
such studies,
because it is
a highly
selfing
hermaphrodite.
As a result,
the species
largely exists
as a
collection of
naturally
occurring
inbred lines,
or accessions,
which can be
genotyped once
and phenotyped
repeatedly.
Furthermore,
linkage
disequilibrium
in such a
species will
be much more
extensive than
in a
comparable
outcrossing
species. We
tested the
feasibility of
genome-wide
association
mapping in A.
thaliana by
searching for
associations
with flowering
time and
pathogen
resistance in
a sample of 95
accessions for
which
genome-wide
polymorphism
data were
available. In
spite of an
extremely high
rate of false
positives due
to population
structure, we
were able to
identify known
major genes
for all
phenotypes
tested, thus
demonstrating
the potential
of genome-wide
association
mapping in A.
thaliana and
other species
with similar
patterns of
variation. The
rate of false
positives
differed
strongly
between
traits, with
more clinal
traits showing
the highest
rate. However,
the false
positive rates
were always
substantial
regardless of
the trait,
highlighting
the necessity
of an
appropriate
genomic
control in
association
studies.
Source: PLoS Genet, Vol. 1, No. 5. (11 November 2005) - Prediction of
plant microRNA
targets.: Cell, Vol.
110, No. 4.
(23 August
2002), pp.
513-520.We
predict
regulatory
targets for 14
Arabidopsis
microRNAs
(miRNAs) by
identifying
mRNAs with
near
complementarit
y.
Complementary
sites within
predicted
targets are
conserved in
rice. Of the
49 predicted
targets, 34
are members of
transcription
factor gene
families
involved in
developmental
patterning or
cell
differentiatio
n. The
near-perfect
complementarit
y between
plant miRNAs
and their
targets
suggests that
many plant
miRNAs act
similarly to
small
interfering
RNAs and
direct mRNA
cleavage. The
targeting of
developmental
transcription
factors
suggests that
many plant
miRNAs
function
during
cellular
differentiatio
n to clear key
regulatory
transcripts
from daughter
cell lineages.
Source: Cell, Vol. 110, No. 4. (23 August 2002), pp. 513-520.
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