Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz)
Plants,
Год журнала:
2024,
Номер
13(6), С. 796 - 796
Опубликована: Март 12, 2024
Flowering
in
cassava
(Manihot
esculenta
Crantz)
is
crucial
for
the
generation
of
botanical
seed
breeding.
However,
genotypes
preferred
by
most
farmers
are
erect
and
poor
at
flowering
or
never
flower.
To
elucidate
genetic
basis
flowering,
293
diverse
accessions
were
evaluated
flowering-associated
traits
two
locations
seasons
Uganda.
Genotyping
using
Diversity
Array
Technology
Pty
Ltd.
(DArTseq)
platform
identified
24,040
single-nucleotide
polymorphisms
(SNPs)
distributed
on
18
chromosomes.
Population
structure
analysis
principal
components
(PCs)
kinships
showed
three
clusters;
first
five
PCs
accounted
49.2%
observed
variation.
Linkage
disequilibrium
(LD)
estimation
averaged
0.32
a
distance
~2850
kb
(kilo
base
pairs).
Polymorphism
information
content
(PIC)
minor
allele
frequency
(MAF)
0.25
0.23,
respectively.
A
genome-wide
association
study
(GWAS)
uncovered
53
significant
marker–trait
associations
(MTAs)
with
involving
27
loci.
Two
loci,
SNPs
S5_29309724
S15_11747301,
associated
all
traits.
Using
Phenotype_Variance_Explained
(PVE)
≥
5%,
44
candidate
genes
peak
SNP
sites
located
within
50
upstream
downstream,
branching
Eight
genes,
orthologous
to
Arabidopsis
other
plant
species,
had
known
functional
annotations
related
e.g.,
eukaryotic
translation
initiation
factor
myb
family
transcription
factor.
This
genomic
regions
cassava,
can
be
useful
marker-assisted
selection
overcome
hybridization
challenges,
like
unsynchronized
gene
validation.
Язык: Английский
Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies
Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Март 13, 2024
Cassava,
a
vital
global
food
source,
faces
threat
from
Cassava
Brown
Streak
Disease
(CBSD).
CBSD
results
two
viruses:
brown
streak
virus
(CBSV)
and
Ugandan
cassava
(UCBSV).
These
viruses
frequently
pose
challenges
to
the
traditional
symptom-based
1-5
phenotyping
method
due
its
limitations
in
terms
of
accuracy
objectivity.
Quantitative
polymerase
chain
reaction
(qPCR)
offers
precise
quantification,
although
high
costs
hinder
widespread
adoption.
In
this
research,
we
utilized
qPCR
measure
viral
titer/load
CBSV
UCBSV.
The
objectives
were
evaluate
titer
variability
within
Cycle
2
(C2)
population
different
environments,
establish
connections
between
titers
severity
scores
scoring
method,
perform
Genome-Wide
Association
Studies
(GWAS)
identify
genomic
regions
associated
with
UCBSV
titers,
investigate
functional
annotated
genes.
demonstrated
significantly
higher
prevalence
(50.2%)
clones
compared
(12.9%)
mixed
infections
some
cases.
Genotypic
effects,
particularly
concerning
UCBSV,
significant,
genotype-by-environment
effects
primarily
influencing
titer.
GWAS
identified
titers.
Twenty-one
SNP
markers
on
chromosomes
10,
13,
17,
18
exhibited
significant
associations
titer,
collectively
explaining
43.14%
phenotypic
variation.
Additionally,
25
1,
2,
4,
5,
8,
11,
12,
16,
explained
70.71%
No
shared
Gene
ontology
analysis
also
revealed
diverse
gene
functions,
especially
transport
catalytic
activities.
findings
enhance
our
understanding
prevalence,
genetics,
molecular
functions
plants,
offering
valuable
insights
for
targeted
breeding
strategies.
Язык: Английский
Genome‐wide association study for yield and quality of granulated cassava processed product
The Plant Genome,
Год журнала:
2024,
Номер
17(2)
Опубликована: Июнь 1, 2024
The
starchy
storage
roots
of
cassava
are
commonly
processed
into
a
variety
products,
including
granulated
products
(gari).
commercial
value
depends
on
the
yield
and
quality
directly
influencing
acceptance
new
varieties
by
farmers,
processors,
consumers.
This
study
aims
to
estimate
genetic
advance
through
phenotypic
selection
identify
genomic
regions
associated
candidate
genes
linked
with
gari
quality.
Higher
single
nucleotide
polymorphism
(SNP)-based
heritability
estimates
compared
broad-sense
were
observed
for
most
traits
highlighting
influence
factors
variation.
Using
genome-wide
association
analysis
188
clones,
genotyped
using
53,150
SNPs,
nine
SNPs
located
seven
chromosomes
significantly
peel
loss,
yield,
color
parameters
eba,
bulk
density,
swelling
index,
textural
properties
eba.
Future
research
will
focus
validating
understanding
functions
identified
their
traits.
Язык: Английский
Identification of Genomic Regions Associated with Flowering Traits in Cassava (<em>Manihot esculenta </em>Crantz)
Опубликована: Дек. 4, 2023
Flowering
in
cassava
is
crucial
for
generation
of
botanical
seed
breeding.
However,
most
farmer
preferred
genotypes
are
poor
at
flowering,
exhibit
great
disparity
time
and
amount
flowering
or
never
flower.
To
elucidate
the
genetic
basis
such
a
behaviour,
293
diverse
accessions
were
evaluated
traits
under
two
locations
seasons
Uganda.
Genotyping
by
Diversity
Array
Technology
Pty
Ltd.
(DArTseq)
platform
identified
24,040
single-nucleotide
polymorphisms
(SNPs)
distributed
on
18
chromosomes.
Population
structure
analysis
using
principal
components
(PC)
kinships
showed
clustering,
first
five
PCs
accounted
49.2%
observed
variation.
Linkage
disequilibrium
(LD)
estimation
was
averagely
0.32
distance
~2850kb
(kilo
base
pairs).
Polymorphism
information
content
(PIC)
minor
allele
frequency
(MAF)
0.25
0.23,
respectively.
Genome-wide
association
study
(GWAS)
uncovered
53
significant
marker-trait
associations
(MTA)
with
involving
27
loci.
Two
loci,
SNPs
S5_29309724
S15_11747301
associated
all
traits.
Using
Phenotype_Variance_Explained
(PVE)
≥
5%,
37
candidate
genes
peak
SNP
sites
located
within
50kb
upstream
downstream,
branching
Eight
genes,
orthologous
to
Arabidopsis
other
plant
species,
had
known
functional
annotations
related
e.g.
eukaryotic
translation
initiation
factor
myb
family
transcription
factor.
This
genomic
regions
cassava,
could
be
useful
marker-assisted
selection
overcome
hybridization
challenges
like
unsynchronized
gene
validation.
Язык: Английский
Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies
Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Март 18, 2024
Cassava
brown
streak
disease
(CBSD)
poses
a
substantial
threat
to
food
security.
To
address
this
challenge,
we
used
PlantCV
extract
CBSD
root
necrosis
image
traits
from
320
clones,
with
an
aim
of
identifying
genomic
regions
through
genome-wide
association
studies
(GWAS)
and
candidate
genes.
Results
revealed
strong
correlations
among
certain
traits,
such
as
necrotic
area
fraction
width
fraction,
well
between
the
convex
hull
percentage
necrosis.
Low
were
observed
scores
obtained
1-5
scoring
method
all
traits.
Broad-sense
heritability
estimates
ranged
low
moderate,
highest
estimate
0.42
for
necrosis,
while
narrow-sense
consistently
remained
low,
ranging
0.03
0.22.
Leveraging
data
30,750
SNPs
DArT
genotyping,
eight
on
chromosomes
1,
7,
11
identified
associated
both
ellipse
eccentricity
GWAS.
Candidate
gene
analysis
in
172.2kb
region
chromosome
1
24
potential
genes
diverse
functions,
including
ubiquitin-protein
ligase,
DNA-binding
transcription
factors,
RNA
metabolism
protein,
others.
Despite
our
initial
expectation
that
objectivity
would
yield
better
stronger
associations
than
method,
results
unexpectedly
lower.
Further
research
is
needed
comprehensively
understand
genetic
basis
these
their
relevance
cassava
breeding
management.
Язык: Английский
Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America
Scientific Reports,
Год журнала:
2024,
Номер
14(1)
Опубликована: Окт. 4, 2024
Cassava
(Manihot
esculenta
Crantz)
is
a
vital
carbohydrate
source
for
over
800
million
people
globally,
yet
its
production
in
East
Africa
severely
affected
by
cassava
brown
streak
disease
(CBSD).
Genebanks,
through
ex-situ
conservation,
play
pivotal
role
preserving
crop
diversity,
providing
crucial
resources
breeding
resilient
and
disease-resistant
crops.
This
study
genotyped
234
South
American
accessions
conserved
at
the
CIAT
genebank,
previously
phenotyped
CBSD
resistance
an
independent
group,
to
perform
genome-wide
association
analysis
(GWAS)
identify
genetic
variants
associated
with
resistance.
Our
GWAS
identified
35
single
nucleotide
polymorphism
(SNP)
markers
distributed
across
various
chromosomes,
severity
or
presence/absence
of
viral
infection.
Markers
were
annotated
within
near
genes
functions
related
pathogen
recognition
immune
response
activation.
Using
SNP
candidates,
we
screened
world's
largest
collection
higher
frequency
favorable
genotypes,
proposing
potential
CBSD.
results
provide
insights
into
genetics
highlight
importance
equip
breeders
raw
materials
needed
develop
new
varieties
resistant
pests
diseases.
Язык: Английский