What are the Strategies for Genetic Conservation in Animal Populations in the Neotropics?
Published: Jan. 1, 2025
Language: Английский
Whole‐genome sequencing of alpaca revealed variants in KIT gene potentially associated with the white coat phenotype
Animal Genetics,
Journal Year:
2023,
Volume and Issue:
54(6), P. 816 - 817
Published: Oct. 1, 2023
The
association
between
variants
on
ASIP,
KIT
and
MC1R
genes
fleece
color
has
been
described
for
alpaca
(Chandramohan
et
al.,
2015;
Feeley
2016;
Jones
2019;
Pallotti
2020;
Tan
2022).
However,
the
genetics
behind
white
coat
phenotype
in
this
species
is
still
unknown.
In
regard,
were
associated
with
gray-
blue-eyed
phenotypes
(Jones
2022)
owing
to
its
important
role
melanogenesis
(Roskoski,
2005).
Moreover,
previous
segregation
analysis
suggested
that
inheritance
of
was
due
a
single
gene
which
completely
dominant
over
black
brown
pigmentation
(Valbonesi
2011).
present
study,
KITLG,
MITF
genes,
known
be
involved
different
domestic
(Linderholm
&
Larson,
2013),
analyzed
find
alpaca.
Six
Peruvian
alpacas
belonging
two
test-cross
families
studied:
huacaya
male
×
pigmented
suri
female
gave
birth
one
huacaya,
respectively
(Table
1).
animals
raised
at
experimental
station
INIA
(the
National
Institute
Agronomic
Innovation)
located
Quimsachata,
Peru.
Sampling
genomic
performed
as
reported
al.
(2023).
Briefly,
DNA
extracted
from
skin
biopsies
underwent
whole-genome
sequencing
an
Illumina
NovaSeq
6000
System,
150
2
bp
mode
average
depth
30×.
After
quality
control
alignment
VicPac3
reference
genome,
called
using
standard
joint-call
gatk
(McKenna
2010)
pipeline.
All
annotated
SNPeff
(Cingolani
2012)
filtered
according
phenotype.
No
segregating
identified
KITLG
MITF.
On
contrary,
segregated
1):
alpacas,
family
1,
heterozygous
(G/A)
c.35G>A
(p.Arg12His)
variant,
while
alpaca,
2,
heterozygotes
(G/C)
c.982G>C
(p.Val328Leu)
variant.
Conversely,
all
showed
homozygous
G/G
genotype.
protein
functional
domains
predicted
interproscan
(Quevillon
2005)
mutations
N-terminal
region
signal
peptide
extracellular
region,
are
essential
binding
appropriate
ligand
consequent
activation
addition,
such
results
may
suggest
proposed
by
studies
Although
these
must
validated
larger
sample,
our
findings
refine
current
understanding
new
potential
starting
point
further
Stefano
Pallotti:
Conceptualization;
data
curation;
formal
analysis;
writing
–
original
draft;
review
editing.
Marco
Antonini:
Writing
Valerio
Napolioni:
supervision;
Carlo
Renieri:
authors
declare
they
have
no
competing
interests.
Alpaca
obtained
2008
guidelines
Animal
Ethics
Committee
University
Camerino.
protocols
approved
aforementioned
committee.
FASTQ
files
de
novo
WGS
six
used
study
available
NCBI
SRA
(Sequence
Read
Archive)
repository
under
project
no.
PRJNA1020284.
Language: Английский
Identificación bioinformática de Polimorfismos de Nucleótido Simple (PNSs) en genes de proteínas asociadas a queratinas en alpacas (<i>Vicugna pacos</i>)
Revista Peruana de Biología,
Journal Year:
2024,
Volume and Issue:
31(1), P. e24889 - e24889
Published: March 15, 2024
El
objetivo
del
presente
trabajo
fue
identificar
polimorfismos
de
nucleótido
simple
(PNSs)
en
genes
proteínas
asociadas
a
las
queratinas
(KRTAPs)
alpacas
(Vicugna
pacos).
Se
realizó
el
estudio
un
total
34
KRTAPs
que
se
encuentran
anotados
genoma
referencia
VicPac3.1
la
base
datos
National
Center
for
Biotechnology
Information
(NCBI).
alpaca,
nueve
genomas
(NCBI)
y
reads
300
bibliotecas
representación
reducida
ADN
usaron
para
comparar
secuencias
e
PNSs
mediante
uso
BLASTN.
halló
frecuencia
alelo
menor
(MAF)
tasa
genotipificacion
(TG)
PNSs,
los
programas
KGD
PLINK.
Así
como,
Illumina
Score
cada
PNS,
programa
Design
Studio.
seleccionaron
marcadores
con
MAF
≥
0.05,
TG
45%
por
PNS
basado
0.6.
identificaron
67
ubicados
regiones
intrónicas,
exónicas
y/o
no
traducidas
queratinas,
cumplen
dichos
parámetros.
De
estos,
35
fueron
incluidos
una
micromatriz
76
mil
alpaca
32
validados
población
936
alpacas.
Whole genome sequencing analysis of alpaca suggests TRPV3 as a candidate gene for the suri phenotype
BMC Genomics,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: Feb. 16, 2024
Abstract
Background
Alpaca
is
a
domestic
South
American
camelid
probably
arising
from
the
domestication
of
two
wild
camelids,
vicugna
and
guanaco.
Two
phenotypes
are
described
for
alpaca,
known
as
huacaya
suri.
Huacaya
fleece
characterized
by
compact,
soft,
highly
crimped
fibers,
while
suri
longer,
straight,
less
crimped,
lustrous.
The
gene
variants
determining
these
still
unknown,
although
previous
studies
suggested
dominant
inheritance
Based
on
that,
aim
this
study
was
identification
alpaca
coat
through
whole
genome
sequencing
(WGS)
analysis.
Results
sample
used
includes
test-cross
families,
×
huacaya,
which
produced
offspring,
one
with
phenotype
phenotype.
analyzed
expanded
addition
WGS
data
six
vicugnas
guanacos;
because
we
assumed
absence
linked
to
in
species.
analysis
variant
segregation
phenotype,
coupled
filtering
present
species,
disclosed
presence
all
samples
premature
termination
codon
(PTC)
TRPV3
(transient
receptor
potential
cation
channel
subfamily
V
member
3),
be
involved
hair
growth
cycling,
thermal
sensation,
cold
tolerance
adaptation
several
Mutations
were
previously
associated
alteration
structure
leading
an
impaired
formation
canal
shaft
mouse.
This
PTC
,
due
G
>
T
substitution
(p.Glu475*),
results
loss
290
amino
acids
canonical
translated
protein,
plausibly
physiological
dysfunction.
Conclusion
suggest
that
may
arise
explain
some
features
such
its
longer
fibre
lower
number
cuticular
scales
compared
huacaya.
Language: Английский
Genetic Structure of the Population of Suri alpaca from Peru
Journal of Animal Health and Production,
Journal Year:
2023,
Volume and Issue:
11(4)
Published: Jan. 1, 2023
The
objective
of
the
study
was
to
evaluate
genetic
structure
Suri
alpaca
population,
from
Quimsachata
Research
and
Production
Center
Illpa-Puno
Experimental
Station
National
Institute
Agrarian
Innovation,
Peru.Data
1350
alpacas
born
1993
2015
(636
males
714
females)
were
analyzed
using
method
genealogical
analysis
method.ENDOG
program
v.4.8
used
for
calculation
following
parameters
such
as:
average
inbreeding
coefficient
(F),
relatedness
(AR),
effective
numbers
founders
(
),
number
ancestors
generation
interval
(GI)
pedigree
completeness,
ENDOG
used.The
F
AR
0.06%
0.40%,
respectively,The
that
gave
rise
reference
population
288,
132.The
338
animals.The
generational
5.53
years,
being
higher
in
gametic
pathways:
sire-daughter
sire-son.The
completeness
level
by
maternal
pathway
72.07%and
paternal
46.0%.In
conclusion,
Germplasm
long.The
small
magnitude,
so
mating
practices
appropriate
during
evaluation
period.
Language: Английский