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A whole-genome radiation hybrid panel for goat

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Xiaoyong Du at Huazhong Agricultural University
Xiaoyong Du
J. E. Womack
J. E. Womack
J. E. Womack
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K. E. Owens
K. E. Owens
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Abstract

A 5000 rad goat–hamster panel of 121 whole-genome radiation hybrids was generated and preliminarily characterized. A normal diploid fibroblast culture from a male Boer goat was fused with a recipient thymidine kinase-deficient hamster cell line. The generated 121 radiation hybrids were grown and produced an average of 8.4 mg of DNA per radiation hybrid. A SINE-PCR test showed that almost all radiation hybrids retained goat DNA. The retention frequencies of the 121 hybrids were preliminarily estimated using a collection of 42 unlinked molecular markers. An optimized panel of therein 90 radiation hybrids (CHRH5000) with an average retention frequency of 34.2% was screened on the basis of interspersed repetitive DNA content and chromosome retention frequency. The development of this WG-RH panel will provide a fundamental tool for advanced goat genome mapping studies and for mammalian comparative mapping.
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Small
Ruminant
Research
105 (2012) 114–
116
Contents
lists
available
at
SciVerse
ScienceDirect
Small
Ruminant
Research
jou
rnal
h
omepa
g
e:
www.elsevier.com/locate/smallrumres
Short
communication
A
whole-genome
radiation
hybrid
panel
for
goat
X.Y.
Dua,
J.E.
Womackb,
K.E.
Owensb,
J.S.
Elliottb,
B.
Sayrec,
P.J.
Bottcherd,
D.
Milane,
M.
Garcia
Podestaf,
S.H.
Zhaoa,∗,
M.
Malekf,∗∗
aDepartment
of
Animal
Science
and
Technology,
Huazhong
Agricultural
University,
Wuhan
430070,
PR
China
bDepartment
of
Veterinary
Pathobiology,
College
of
Veterinary
Medicine,
Texas
A&M
University,
College
Station,
TX
77843,
USA
cDepartment
of
Biology,
Virginia
State
University,
Petersburg,
VA
23830,
USA
dAnimal
Production
and
Health
Division,
Food
and
Agriculture
Organization
of
the
United
Nations,
00153
Rome,
Italy
eToulouse,
INRA,
FR
(INRA),
Laboratoire
de
Génétique
Cellulaire
and
Biométrie
et
Intelligence
Artificielle,
Castanet-Tolosan,
France
fFAO/IAEA
Agriculture
and
Biotechnology
Laboratory,
Department
of
Nuclear
Sciences
and
Applications,
International
Atomic
Energy
Agency,
Wagramer
Strasse
5,
P.O.
Box
100,
A-1400,
Austria
a
r
t
i
c
l
e
i
n
f
o
Article
history:
Received
23
July
2011
Received
in
revised
form
28
November
2011
Accepted
29
November
2011
Available online 21 April 2012
Keywords:
Radiation
hybrid
panel
Goat
Gene
mapping
CHRH5000
a
b
s
t
r
a
c
t
A
5000
rad
goat–hamster
panel
of
121
whole-genome
radiation
hybrids
was
generated
and
preliminarily
characterized.
A
normal
diploid
fibroblast
culture
from
a
male
Boer
goat
was
fused
with
a
recipient
thymidine
kinase-deficient
hamster
cell
line.
The
generated
121
radi-
ation
hybrids
were
grown
and
produced
an
average
of
8.4
mg
of
DNA
per
radiation
hybrid.
A
SINE-PCR
test
showed
that
almost
all
radiation
hybrids
retained
goat
DNA.
The
retention
fre-
quencies
of
the
121
hybrids
were
preliminarily
estimated
using
a
collection
of
42
unlinked
molecular
markers.
An
optimized
panel
of
therein
90
radiation
hybrids
(CHRH5000)
with
an
average
retention
frequency
of
34.2%
was
screened
on
the
basis
of
interspersed
repeti-
tive
DNA
content
and
chromosome
retention
frequency.
The
development
of
this
WG-RH
panel
will
provide
a
fundamental
tool
for
advanced
goat
genome
mapping
studies
and
for
mammalian
comparative
mapping.
© 2012 Elsevier B.V. All rights reserved.
1.
Introduction
The
goat
(Capra
hircus)
is
an
important
agricultural
species
with
centuries
of
phenotypic
observations,
trait
selection,
and
breed
differentiation.
Of
the
world’s
870
mil-
lion
goats
estimated,
95%
are
found
in
developing
countries
(FAO,
1997)
where
they
provide
reliable
access
to
meat,
milk,
skins,
and
fiber
for
the
livelihood
of
low
input
produc-
tion
systems.
However,
the
understanding
of
the
goat
at
the
genomic
level
lags
behind
other
livestock
species,
such
as
cattle,
pigs,
chickens,
and
sheep.
The
most
recent
genetic
and
cytogenetic
maps
in
the
goat
were
published
more
than
one
decade
ago
(Vaiman
et
al.,
1996;
Schibler
et
al.,
1998),
∗Corresponding
author.
Tel.:
+86
27
87284161;
fax:
+86
27
87280408.
∗∗ Corresponding
author.
Tel:
+431
2600
28358;
fax:
+431
2600
28222.
E-mail
addresses:
shzhao@mail.hzau.edu.cn
(S.H.
Zhao),
memalek@yahoo.com
(M.
Malek).
but
lacks
the
resolution
that
is
possible
for
ordering
mark-
ers
with
radiation
hybrid
(RH)
panels
(Cox
et
al.,
1990;
Faraut
et
al.,
2009).
Currently,
the
‘first-generation’
RH
panels
were
built
for
producing
whole-genome
maps
for
several
farm
animals,
e.g.,
cattle
(Womack
et
al.,
1997),
pigs
(Yerle
et
al.,
1998),
river
buffalo
(Amaral
et
al.,
2007)
and
sheep
(Wu
et
al.,
2007).
This
study
specifically
involves
the
development
of
a
tool,
WG-RH
panel,
for
high-resolution
mapping
of
the
goat
genome.
2.
Materials
and
methods
2.1.
Generation
of
Capra
hircus
radiation
hybrid
panel
The
construction
of
Capra
hircus
radiation
hybrid
panel
followed
the
protocols
well
developed
by
Womack
et
al.
(1997)
and
is
briefly
described
as
follow.
Skin
biopsies
were
obtained
from
one
adult
Boer
male
from
which
we
cultured
fibroblasts
and
performed
karyotypic
analysis.
Approx-
imately
108cells
were
irradiated
with
a
cobalt
60
source
for
a
total
dose
of
5000
rad.
The
donor
goat
fibroblast
cells
were
fused
with
the
0921-4488/$
–
see
front
matter ©
2012 Elsevier B.V. All rights reserved.
doi:10.1016/j.smallrumres.2011.11.023
X.Y.
Du
et
al.
/
Small
Ruminant
Research
105 (2012) 114–
116 115
Table
1
The
information
of
markers
were
typed
on
the
121
hamster-goat
radiation
hybrids.
Marker
Type
Chromosome
Retention
frequency
(%)
Reference
CSSM19 STS
CHI1q43
40
Vaiman
et
al.
(1996)
SOD1
Gene
CHI1q12.2
56
Schibler
et
al.
(1998)
MYL1
Gene
CHI2q41
32
Di
Meo
et
al.
(2006)
BMS2782
STS
CHI2q22-q23
26
Schibler
et
al.
(1998)
CSSM54 STS CHI3q22 45 Schibler
et
al.
(1998)
8-16R EST CHI3q37 51 Le
Provost
et
al.
(2000)
TGL159 STS
CHI4q34
37
Schibler
et
al.,
1998
TRG2
gene
CHI4q22
41
Antonacci
et
al.
(2007)
OarFCB005 STS
CHI5q21
46
Schibler
et
al.
(1998)
2-21revR
EST
CHI5q31
54
Le
Provost
et
al.
(2000)
GNRHR
gene
CHI6q31
39
Schibler
et
al.
(1998)
BM1329
STS
CHI6q15
42
Schibler
et
al.
(1998)
SLC27A1
gene
CHI7q11–12
36
Ordovas
et
al.
(2005)
BMS522
STS
CHI7q26
40
Tabet-Aoul
et
al.
(2000)
18-12rev EST CHI8q26 64 Le
Provost
et
al.
(2000)
TGLA010
STS
CHI8q15
41
Schibler
et
al.
(1998)
INRA127 STS
CHI9q13
49
Schibler
et
al.
(1998)
BM4208
STS
CHI9q25–26
40
Schibler
et
al.
(1998)
BMS528
STS
CHI10q13
52
Tabet-Aoul
et
al.
(2000)
MCM185 STS CHI10q35 49 Schibler
et
al.
(1998)
ILSTS028
STS
CHI11q27–28
47
Schibler
et
al.
(1998)
TGFA gene CHI11q13–14
49
Schibler
et
al.
(1998)
SRCRSP09
STS
CHI12q22
50
Schibler
et
al.
(1998)
SRCRSP01
STS
CHI13
41
Vaiman
et
al.
(1996)
ILSTS008
STS
CHI14q19
50
Schibler
et
al.
(1998)
LSCV05
STS
CHI15q25
39
Schibler
et
al.
(1998)
BMS538 STS CHI16q15 47 Tabet-Aoul
et
al.
(2000)
OarFCB48
STS
CHI17q15
52
Schibler
et
al.
(1998)
INRA063 STS
CHI18q22
40
Schibler
et
al.
(1998)
BMS0745
STS
CHI19q13
45
Schibler
et
al.
(1998)
TGLA304
STS
CHI20q13.3
53
Schibler
et
al.
(1998)
SRCRS5
STS
CHI21q14
45
Schibler
et
al.
(1998)
LSCV14
STS
CHI22q24
46
Schibler
et
al.
(1998)
OarCP73 STS CHI23q13
56
Schibler
et
al.
(1998)
ILSTS65
STS
CHI24q21
53
Schibler
et
al.
(1998)
BM4005 STS
CHI25q14
47
Schibler
et
al.
(1998)
LSCV52
STS
CHI26q21
45
Schibler
et
al.
(1998)
LSCV40
STS
CHI27q14
53
Schibler
et
al.
(1998)
RBP3
gene
CHI28q19
49
Schibler
et
al.
(1998)
OPCML
gene
CHI29q22
54
Schibler
et
al.
(1998)
XBM31 STS CHIXp12 45 Piumi
et
al.
(1998)
McM74
STS
CHIXq11
46
Piumi
et
al.
(1998)
recipient
hamster
A23
cells
(kindly
provided
by
David
Cox,
Stanford
Uni-
versity)
to
generate
goat–hamster
radiation
hybrids.
Each
hybrid
was
grown
to
confluent
cultures
in
two
900
cm2roller
bottles
to
produce
the
final
harvest.
DNA
extractions
from
cell
pellets
were
performed
by
phenol/chloroform/isoamyl
alcohol
protocol.
2.2.
Selection
of
molecular
markers
A
SINE-PCR
test
was
performed
in
each
clone
to
for
the
presence
of
goat
DNA.
One
primer
pair
(Forward:
5-CTGCAGCACGCCAGGACTTC;
Reverse:
5-AGCTCCGAGACTTTGGCCAC)
was
designed
according
to
a
goat
PstI
(Sheikh
et
al.,
2002)
SINE
sequence
(Accession
Number
X71732)
with
online
Primer
3.
The
retention
frequencies
of
the
radiation
hybrids
were
estimated
using
a
collection
of
unlinked
markers.
Initially
50
markers
including
goat
STS,
ESTs,
and
coding
genes
were
selected
according
to
their
expected
positions
on
all
29
goat
autosomes
and
Chromosome
X.
At
least
two
markers
at
large
intervals
on
the
larger
chromosomes
(Chromosome
1
to
11
and
Chromosome
X)
and
one
maker
for
the
other
chromosome
were
chosen.
These
markers
were
derived
from
the
integrated
cytogenetic
map
(Schibler
et
al.,
1998)
or
marker
assignment
studies
by
FISH
(Vaiman
et
al.,
1996;
Piumi
et
al.,
1998;
Le
Provost
et
al.,
2000;
Tabet-Aoul
et
al.,
2000;
Ordovas
et
al.,
2005;
Di
Meo
et
al.,
2006;
Antonacci
et
al.,
2007)
in
goat.
2.3.
Polymerase
chain
reaction
(PCR)
Markers
were
genotyped
on
DNA
of
the
obtained
radiation
hybrids
together
with
goat
and
hamster
control
DNA
by
PCR.
The
10
␮L
PCR
cocktail
contained
50
ng
DNA;
1.5
mM
MgCl2;
10
mM
Tris–HCl;
50
mM
KCl;
0.2
mM
dGTP,
dTTP,
dATP
and
dCTP;
10
pmol
each
primer
and
0.5
U
Taq
DNA
polymerase
(Applied
Biosystems).
PCR
reactions
were
performed
in
the
following
conditions:
94 ◦C
for
10
min;
35
cycles
of
94 ◦C
for
30
s,
51–63 ◦C
for
30
s
and
72 ◦C
for
30
s;
a
final
5
min
extension
at
72 ◦C.
PCR
products
were
separated
by
electrophoresis
on
2.0%
agarose
gels
and
scored
manually.
3.
Results
and
discussion
3.1.
Generation
of
Capra
hircus
radiation
hybrid
panel
The
karyotypic
analysis
showed
our
goat
sample
has
normal
chromosome
structure.
The
fusion
of
the
donor
goat
fibroblast
cells
with
the
recipient,
A23
generated
130
radi-
ation
hybrids
totally.
121
of
these
130
radiation
hybrids
were
grown
to
confluent
cultures
produced
an
average
of
8.4
mg
of
DNA
for
each
radiation
hybrid.
The
hybrid
DNA
harvest
ranged
from
18.5
to
2.4
mg,
sufficient
for
an
estimated
81,000
PCR
reactions,
assuming
50
ng
per
reac-
tion.
The
SINE-PCR
test
showed
that
All
of
121
RH
colonies
except
one
demonstrated
strong
amplification,
suggesting
retention
of
goat
chromosomes.
116 X.Y.
Du
et
al.
/
Small
Ruminant
Research
105 (2012) 114–
116
3.2.
Preliminary
characterization
of
the
radiation
hybrid
panel
Of
50
molecular
markers
we
selected,
42
(Table
1)
were
suitable
for
PCR
screening.
Using
the
genotype
of
these
markers
on
the
radiation
hybrids,
we
calculated
the
reten-
tion
frequencies
for
each
hybrid.
Among
the
121
hybrids
produced,
3
had
a
genome
retention
frequency
<
9%
(1–2
marker
retained/42),
90
ranged
between
9.5%
and
71.4%
(3–30
markers
retained/42),
and
18
hybrids
represented
the
frequency
>71.4%
(31–42
markers
retained/42).
Some
previous
simulation
studies
suggested
that
a
retention
frequency
of
50%
would
be
optimal
for
ordering
mark-
ers
(Lunetta
and
Boehnke,
1994;
Lunetta
et
al.,
1996).
To
optimizing
the
genome
coverage,
we
selected
a
subset
of
90
radiation
hybrids
with
moderate
retention
frequencies
(9.5–71.4%)
as
a
final
panel
(Capra
hircus
radiation
hybrid
Panel,
CHRH5000)
for
advanced
mapping
studies.
The
aver-
age
frequency
of
CHRH5000
was
34.2%
based
on
these
42
markers,
and
was
comparable
to
that
for
other
domestic
animals,
i.e.,
28%
in
BovR5
for
cattle
(Womack
et
al.,
1997),
25%
in
USUoRH5000
for
sheep
(Wu
et
al.,
2007),
27.3%
in
BBURH5000
for
river
buffalo
(Amaral
et
al.,
2008).
4.
Conclusion
WG-RH
panels
have
proven
to
be
highly
efficient
tools
for
mapping
genes
and
comparing
genome
architecture.
Our
study
developed
a
fundamental
tool
for
genomic
research
in
the
goat.
Dense
maps
of
over
1000
SNP
mark-
ers
on
chromosome
1
have
been
constructing
for
goat
(data
unpublished).
Because
the
goat
has
adapted
to
virtually
every
type
of
environment
and
have
many
biomedical
con-
ditions
similar
to
humans
and
other
ruminants,
this
will
be
also
a
valuable
resource
for
comparative
genomic
analysis
and
for
eventual
assembly
of
the
goat
sequence.
Acknowledgements
This
research
was
supported
by
the
IAEA’s
Coordinated
Research
Project,
The
project
of
China
Scholarship
Coun-
cil,
and
the
creative
team
project
of
Education
Ministry
of
China.
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... The sequence of each primer pair was first searched against ARS1 and all other unplaced scaffolds to ensure the primer's uniqueness using nucmer (v4.0.0) (Marçais et al., 2018) with the parameter "-c 10 -l 10." The goat RH panel includes 93 hybrid clones, one positive from a male goat (JEW105), one negative from a hamster cell line (A23), and blank control (water) (Du et al., 2012). For each primer pair, we had two PCR tests. ...
... The goat RH panel from a male Boer goat was used to validate and orient these Y scaffolds (Du et al., 2012). This goat RH panel has been used to validate the goat genome assembly of CHIR_1.0 version and ARS1 Dong et al., 2013Dong et al., , 2015. ...
The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat
Article
Full-text available
  • Jun 2021
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.
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... The sequence of each primer pair was first searched against ARS1 and all other unplaced scaffolds to ensure the primer's uniqueness using nucmer (v4.0.0) (Marçais et al., 2018) with the parameter "-c 10 -l 10." The goat RH panel includes 93 hybrid clones, one positive from a male goat (JEW105), one negative from a hamster cell line (A23), and blank control (water) (Du et al., 2012). For each primer pair, we had two PCR tests. ...
... The goat RH panel from a male Boer goat was used to validate and orient these Y scaffolds (Du et al., 2012). This goat RH panel has been used to validate the goat genome assembly of CHIR_1.0 version and ARS1 Dong et al., 2013Dong et al., , 2015. ...
The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat
Article
Full-text available
  • May 2021
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y‐linked scaffolds using existing data. A total of 11.5 Mb Y‐linked sequences were clustered into 33 scaffolds, and 187 protein‐coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole‐genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post‐Neolithic period.
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... PacBio contigs were first scaffolded using optical mapping data, and the resulting scaffolds were clustered using Hi-C data into chromosome-scale scaffolds. To assess quality, the resulting assembly was validated via statistical methods and comparison to a radiation hybrid (RH) map 34 (Supplementary Table 1) and previous assemblies (Supplementary Note). To maximize accuracy of the final reference assembly, the RH map was used to correct 21 inversions (consisting of 83 scaffolds) and 4 misplacements before final gap filling and polishing 35,36 . ...
... Our tiered approach to scaffolding provides several opportunities for resolving misassemblies and contig orientation mistakes made by prior steps (for more detail, see Supplementary Note). In order to resolve all conflicts from our final assembly, we used a consensus approach that used evidence from five different sources of information: (i) our long-read-based contig sequence, (ii) Irys optical maps, (iii) Hi-C scaffolding orientation quality scores, (iv) San Clemente goat Illumina HiSeq read alignments to the contigs, and (v) a previously generated RH map 34 (Fig. 1b). We found that 40 contigs did not align with the Irys optical map, and there were 102 Irys conflicts that needed resolution. ...
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Article
  • Apr 2017
  • Nat Genet
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a [sim]400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
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... The assessment of population structure, admixture analysis, and genetic diversity among different breeds has significant implications for animal breeding programs (Notter et al., 1999). Population structure and genomic diversity were analyzed in five long-tailed and short-tailed sheep breeds using a whole-genome radiation hybrid panel and Short Tandem Repeats (Du et al., 2012;Ginja et al., 2017). With the help of SNP and Variation Suite v.8.5.0., the genetic differentiation among populations was estimated, and it varied from 0.02 to 0.07, showing moderate differentiation among different breeds. ...
Trajectory of livestock genomics in South Asia: A comprehensive review
Article
  • Aug 2022
  • GENE
Livestock plays a central role in human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This paper discusses genomic studies on Cattle, Buffalo, Sheep, Goat, Pig, Horse, Camel, Yak, Mithun, and Poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancement.
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... This advance made the reference genome sequence of the domestic goat available for the first time. The knowledge of the caprine genomic map was preceded by the first 'Bacterial Artificial Chromosome Library' published for caprine [43]. Recently, a new, 'de novo' genetic assembly (ARS1) has been developed. ...
Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats (Capra hircus)
Article
Full-text available
  • Apr 2022
Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in ge-nomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.
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... Scaffold gaps were then filled where possible using mapped single-molecule data, and the final assembly was polished to achieve high consensus accuracy using mapped Illumina data. The resulting reference assembly, named ARS1, totals 2.92 Gbp of sequence with a contig NG50 of 19 Mbp and a scaffold NG50 of 87 Mbp, and was further validated via statistical methods and comparison to a radiation hybrid (RH) map 34 and previous assemblies (Supplementary Note 1). ...
Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes
Preprint
Full-text available
  • Jul 2016
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat ( Capra hircus ), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.
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... Radiation hybrid (RH) mapping [38] uses X-ray breakage of DNA to determine distance and order between DNA markers on the chromosome. This validation is useful because it spots errors in the scaffolds without the reference genome. ...
Scaffolding of long read assemblies using long range contact information
Article
Full-text available
  • Jul 2017
  • BMC GENOMICS
Background Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually does not reconstruct a full chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To increase the contiguity of the assembly to the chromosome level, different strategies are used which exploit long range contact information between chromosomes in the genome. Methods We develop a scalable and computationally efficient scaffolding method that can boost the assembly contiguity to a large extent using genome-wide chromatin interaction data such as Hi-C. Results we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies. We tested our methods on the human and goat genome assemblies. We compare our scaffolds with the scaffolds generated by LACHESIS based on various metrics. Conclusion Our new algorithm SALSA produces more accurate scaffolds compared to the existing state of the art method LACHESIS. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3879-z) contains supplementary material, which is available to authorized users.
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Genome mapping tools: current research and future prospects
Chapter
Full-text available
  • Jan 2021
The structure and function of every living organism in the biosphere are shaped and directed by its genome, respectively. The genome of an organism is an abode of all the genes and other DNA segments, known and yet to be known, responsible for its metabolism, survival, growth, development, interaction with the environment, defense, reproduction, senescence, etc. To exploit any species as a biological resource at molecular level to serve human kind in form of good(s) and/or service(s), primarily requires a thorough understanding of its genes and their locations in the genome. Genome mapping is a technique that aids in determining the location of genes, and/or its(or their) markers(s), of interest in relation to other gene(s), and/or its (or their) marker(s), within the genome. Since all the genes of commercial interest are nor present in the same individual/taxa, it is essential to move gene(s) of interest from available source(s) to the required target(s), which is made easy with the knowledge of genome map. Genome mapping has wider applications in modern molecular biology: from the applied areas, such as genetic improvement of organisms, to the fundamental research such as genome sequencing. It needs proper tools and techniques such as various kinds of markers and mapping populations. To choose an appropriate tool and method requires thorough knowledge of myriad basket of available genome mapping tools. This chapter brings a complete, comprehensive and updated information that is necessary to understand genome of interest and use appropriate mapping tools, such as markers and mapping populations, for mapping of genes of interest in the genome of an organism of interest, ultimately to help deriving useful product(s) and/or service(s) to meet various needs of humankind in the wake of everchanging environment and never-receding human populations. This chapter also offers future prospects of available genome mapping tools and opportunities to develop new tools in the light of advanced techniques available for DNA sequencing and rapid generation advancement of mapping populations.
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Progress in goat genome studies
Article
Full-text available
  • Oct 2019
The goat genome is the research basis for the protection and utilization of goat resources, which is important for breeding and improving goat breeds. At present, with the continuous improvement of goat reference genome, various important research progress in goat origin, evolution and adaptability has been achieved. In this review, we summarize the research progress in the goat genome in detail, encompassing goat genome structure, genome map (genetic, physical and comparative maps), goat high throughput sequencing and SNP chip development. We aim to provide a theoretical foundation for the development of goat genome selection.
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Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000 RAD and 15000 RAD
Article
Full-text available
  • Jan 2018
The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.
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A Genetic Linkage Map of the Male Goat Genome
Article
Full-text available
  • Sep 1996
  • GENETICS
This paper presents a first genetic linkage map of the goat genome. Primers derived from the flanking sequences of 612 bovine, ovine and goat microsatellite markers were gathered and tested for amplification with goat DNA under standardized PCR conditions. This screen made it possible to choose a set of 55 polymorphic markers that can be used in the three species and to define a panel of 223 microsatellites suitable for the goat. Twelve half-sib paternal goat families were then used to build a linkage map of the goat genome. The linkage analysis made it possible to construct a meiotic map covering 2300 cM, i.e., >SO% of the total estimated length of the goat genome. Moreover, eight cosmids containing microsatellites were mapped by fluorescence in situ hybridization in goat and sheep. Together with 11 microsatellite-containing cosmids previously mapped in cattle (and supposing conservation of the banding pattern between this species and the goat) and data from the sheep map, these results made the orientation of 15 linkage groups possible. Furthermore, 12 coding sequences were mapped either genetically or physically, providing useful data for comparative mapping.
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Mapping of 11 genes by FISH to BTA2, BBU2q, OAR2q and CHI2, and comparison with HSA2q
Article
Full-text available
Description/source: Comparative maps provide insight into the evolution of closely related species and are useful for studying the evolution of chromosome breakpoints and for identifying gene orthologues. 1 Assignment of loci to metaphase chromosomes using fluorescence in situ hybridization (FISH) results in low-resolution maps but allows anchoring of linkage and radiation hybrid (RH) maps to specific chromosome regions. Herein, we report the FISH localization of 11 type I loci to BTA2. Nine of these loci were mapped by FISH to R-banded chromosomes of river buffalo (BBU2q), sheep (OAR2q) and goat (CHI2), all of which are evolutionary homologues of BTA2. Six and seven of these loci were mapped for the first time to specific chromosomal regions of BTA2 and CHI2 respectively. Furthermore, eight of the genes are candidates for quantitative trait loci (QTL) influencing growth traits, based in part on an examination of the human bovine comparative map. 1 A direct comparison between the cytogenetic maps of BTA2 and HSA2q revealed at least nine conserved chromosomal segments that arose from complex chromosomal rearrangements. BAC library screening and selection of candidate genes: Primers used to screen genes from the bovine and ovine BAC libraries 2-4 are listed in Table S1. DNA sequencing of poly-merase chain reaction (PCR) products amplified from the BAC clones verified the presence of each gene with at least 90% nucleotide identity to the corresponding human sequence. Because growth-related QTL have been previously identified on BTA2, 5 candidate genes for QTL (GDF8, GCG, NEB, TTN, IGFBP2 MYL1, FN1 and ACADL) were selected from the corresponding region of the long arm of human chromosome 2. Cell cultures and FISH analysis: Fibroblast cell cultures for cattle and peripheral blood cultures for river buffalo, sheep and goat were established. Cultures were treated for early (cattle) or late (river buffalo, sheep and goat) BrdU incorporation to obtain G/Q and R-banding patterns respectively. Meiotic preparations were made from a bull testicle collected at the time of slaughter. Single-or two-colour FISH was used to map the BAC clones to bovine mitotic or pachytene chromosomes, respectively, while single-colour FISH was used for river buffalo, sheep and goat. At least 20 metaphases were studied for all probes and species. Figure 1 Comparative cytogenetic maps of BTA2, BBU2q, OAR2q and CHI2, as well as a comparison between the BTA2 and HSA2q cytogenetic maps. Type I and type II loci are reported in normal and italic characters respectively. Loci mapped in the present study are reported in large, bold characters. The remaining loci are from BOVMAP), as well as from earlier publications. 8-11 To facilitate the comparison of locus order and to visualize conserved syntenies between BTA2 and HSA2q, conserved chromosomal segments between the two species are numbered on the left (HSA2q) and right (BTA2) sides of the banded ideograms. Ten conserved syntenies were identified on BTA2 (nine from HSA2q and one from HSA1p). No loci on HSA2q24.1-q24.3 (arrow) have been mapped on BTA2 until now.
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Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library
Article
Full-text available
  • Jul 2000
Abstract In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC) library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57). This study allowed us, (i), to anchor all linkage groups on sheep chromosomes, (ii), to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii), to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.
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Cytogenetic mapping of 25 goat mammary gland Expressed Sequence Tags (ESTs)
Article
Full-text available
  • May 2000
Abstract Today, there is a shift towards a positional candidate approach in the molecular identification of genes. This study reports on an Expressed Sequence Tags (ESTs) mapping initiative in goats, based on sequence information gathered from a previous mammary gland cDNA systematic sequencing project. A total of 25 novel genes was localised cytogenetically on 16 goat chromosomes. Six of these ESTs were found to map to cattle milk QTL regions. These results made it possible to assess the use of ESTs as a shortcut to the molecular identification of some QTLs and as a valuable tool for comparative mapping.
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Cytogenetic mapping of 25 goat mammary gland Expressed Sequence Tags (ESTs)
Article
Full-text available
  • May 2000
  • GENET SEL EVOL
Abstract Today, there is a shift towards a positional candidate approach in the molecular identification of genes. This study reports on an Expressed Sequence Tags (ESTs) mapping initiative in goats, based on sequence information gathered from a previous mammary gland cDNA systematic sequencing project. A total of 25 novel genes was localised cytogenetically on 16 goat chromosomes. Six of these ESTs were found to map to cattle milk QTL regions. These results made it possible to assess the use of ESTs as a shortcut to the molecular identification of some QTLs and as a valuable tool for comparative mapping.
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A first generation whole genome RH map of the river buffalo with comparison to domestic cattle
Article
Full-text available
  • Jan 2009
  • BMC GENOMICS
The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species. A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0). We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.
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Radiation Hybrid Mapping: A Somatic Cell Genetic Method for Constructing High-Resolution Maps of Mammalian Chromosomes
Article
Full-text available
  • Nov 1990
Radiation hybrid (RH) mapping, a somatic cell genetic technique, was developed as a general approach for constructing long-range maps of mammalian chromosomes. This statistical method depends on x-ray breakage of chromosomes to determine the distances between DNA markers, as well as their order on the chromosome. In addition, the method allows the relative likelihoods of alternative marker orders to be determined. The RH procedure was used to map 14 DNA probes from a region of human chromosome 21 spanning 20 megabase pairs. The map was confirmed by pulsed-field gel electrophoretic analysis. The results demonstrate the effectiveness of RH mapping for constructing high-resolution, contiguous maps of mammalian chromosomes.
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Construction of a river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel and preliminary RH mapping of chromosomes 3 and 10
Article
  • Jun 2007
The buffalo (Bubalus bubalis) is a source of milk and meat, and also serves as a draft animal. In this study, a 5000-rad whole-genome radiation hybrid (RH) panel for river buffalo was constructed and used to build preliminary RH maps for BBU3 and BBU10 chromosomes. The preliminary maps contain 66 markers, including coding genes, cattle expressed sequence tags (ESTs) and microsatellite loci. The RH maps presented here are the starting point for mapping additional loci that will allow detailed comparative maps between buffalo, cattle and other species whose genomes may be mapped in the future. A large quantity of DNA has been prepared from the cell lines forming the river buffalo RH panel and will be made publicly available to the international community both for the study of chromosome evolution and for the improvement of traits important to the role of buffalo in animal agriculture.
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Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals
Article
  • Dec 2009
  • CYTOGENET GENOME RES
Radiation hybrid mapping has emerged in the end of the 1990 s as a successful and complementary approach to map genomes, essentially because of its ability to bridge the gaps between genetic and clone-based physical maps, but also using comparative mapping approaches, between 'gene-rich' and 'gene-poor' maps. Since its early development in human, radiation hybrid mapping played a pivotal role in the process of mapping animal genomes, especially mammalian ones. We review here all the different steps involved in radiation hybrid mapping from the constitution of panels to the construction of maps. A description of its contribution to whole genome maps with a special emphasis on domestic animals will also be presented. Finally, current applications of radiation hybrid mapping in the context of whole genome assemblies will be described.
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Multipoint Radiation Hybrid Mapping: Comparison of Methods, Sample Size Requirements, and Optimal Study Characteristics
Article
  • Jun 1994
There are several statistical methods available for analyzing radiation hybrid (RH) data, but little is known about the ordering accuracy we can expect under common study conditions. Using analytic methods and computer simulation, we compared the ordering accuracy of three multipoint statistical methods: minimum breaks (MB), maximum likelihood (ML), and maximum posterior probability (PP). For 8, 12, and 16 markers and all combinations of numbers of hybrids, retention patterns, and marker spacings considered, the probabilities that the true order is identified as the best order were considerably higher with the ML and PP methods than with the MB method. ML and PP performed similarly, but PP tended to give slightly greater support for the best order than did ML. Our results can be used as guidelines for determining sample size requirements and optimal marker spacing for future RH mapping experiments. For equally spaced markers, intermarker spacing of 30 to 50 cR gave the highest probability of correctly ordering all the markers. For randomly spaced markers, 10-20 cR average intermarker spacing resulted in the highest proportion of markers being placed in a 1000:1 framework map. Assuming equal retention in the analysis when a centromeric model would be more appropriate did not affect the ability of the ML method to accurately order the markers, but did influence the distance estimates obtained.
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