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Genetic structure and admixture in sheep from terminal breeds in the United States

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Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross‐validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.
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Genetic structure and admixture in sheep from terminal breeds in the
United States
K. M. Davenport* , C. Hiemke
, S. D. McKay
, J. W. Thorne*
,§
, R. M. Lewis
, T. Taylor** and
B. M. Murdoch*
*Department of Animal and Veterinary Science, University of Idaho, Moscow, ID 83844, USA.
Niman Ranch and Mapleton Mynd
Shropshires, Stoughton, MA 53589, USA.
Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405,
USA.
§
Texas A&M AgriLife Extension, San Angelo, TX 76901, USA.
Department of Animal Science, University of NebraskaLincoln, Lincoln,
NE 68583, USA. **Department of Animal Science, Arlington Research Station, University of WisconsinMadison, Arlington, WI 53911,
USA.
Summary Selection for performance in diverse production settings has resulted in variation across
sheep breeds worldwide. Although sheep are an important species to the United States, the
current genetic relationship among many terminal sire breeds is not well characterized.
Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep
(n=248) sampled from different flocks were genotyped using the Applied Biosystems Axiom
Ovine Genotyping Array (50K), and additional Shropshire sheep (n=26) using the Illumina
Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozy-
gosity, inbreeding coefficients, eigenvalues, pairwise Wright’s F
ST
estimates and an identity
by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35
and was consistent with data reported in other US and Australian sheep. Suffolk from two
different regions of the United States (Midwest and West) clustered separately in eigenvalue
plots and the rectangular cladogram. Further, divergence was detected between Suffolk
from different regions with Wright’s F
ST
estimate. Shropshire animals showed the greatest
divergence from other terminal breeds in this study. Admixture between breeds was
examined using ADMIXTURE, and based on cross-validation estimates, the best fit number of
populations (clusters) was K=6. The greatest admixture was observed within Hampshire,
Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered
separately in comparison with sheep from other locations of the world. Understanding the
genetic relationships between terminal sire breeds in sheep will inform us about the
potential applicability of markers derived in one breed to other breeds based on relatedness.
Keywords genetic admixture, genetic relationships, sheep, terminal sheep breeds
Introduction
The production of lamb and wool is an important agricultural
industry in the United States, with approximately 5 million
sheep and 80 000 operations (USDA ERS 2019). According to
the American Sheep Industry National Animal Health Mon-
itoring System’s most recent study, 81.6% of operations raise
sheep for meat purposes (American Sheep Industry 2011).
The most popular breeds used formeat production include the
Suffolk, Hampshire, Shropshire, Oxford, and Southdown
(American Sheep Industry 2011). To make progress in their
own flocks, some US lamb and wool producers have imple-
mented quantitative genetic selection strategies using esti-
mated breeding values through the National Sheep
Improvement Program (NSIP) to identify and select animals
with desirable traits (Wilson & Morrical 1991; Notter 1998;
Lupton 2008). As this program is more widely utilized, the
improvement of product quality and yield of lamb and wool
products in the United States is anticipated to accelerate.
Previous research indicates that selection for various
traits such as wool or growth within breeds of sheep has led
to greater breed specialization across the world (Kijas et al.
2012; Zhang et al. 2013). However, many breeds of sheep
have retained greater heterozygosity in comparison with
other species, including cattle (Bovine HapMap Consortium
Address for correspondence
B. M. Murdoch, Department of Animal and Veterinary Science,
University of Idaho, Moscow, ID 83844, USA.
E-mail: bmurdoch@uidaho.edu
Accepted for publication 12 December 2019
doi: 10.1111/age.12905
284 ©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and
distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
et al. 2009; Kijas et al. 2012). Furthermore, sheep from
similar locations have been reported to have high levels of
admixture (Blackburn et al. 2011; Kijas et al. 2012).
The current genetic structure and level of admixture
among terminal sire breeds in the United States have not
been well characterized (Zhang et al. 2013). The objective of
this study was to examine population structure and
admixture in sheep from terminal breeds from US sheep
operations in collaboration with producers engaged with
NSIP. Understanding the genetic relationships between
terminal sire breeds in the United States will allow us to
better understand the genetic relatedness of these breeds of
sheep and assess the potential applicability of information
based on breed relatedness. Further, this study can help
elucidate how biological differences segregate in different
breeds, as well as between breeds of sheep.
Materials and methods
Sample collection and DNA isolation
A total of 248 sheep from terminal breeds of sheep including
Hampshire (n=45 from six flocks), Suffolk (n=68 from nine
flocks in the Midwest and n=37 from one flock, the
University of Idaho Suffolk flock, in the West), Oxford
(n=11 from two flocks) and Shropshire (n=44 from five
flocks), as well as wool/dual-purpose Rambouillet (n=43
from one flock), were genotyped for this study. Blood, semen
or tissue samples were collected by individual producers and
shipped to the University of Idaho and DNA was isolated using
the phenol chloroform method previously described (Sam-
brook et al. 1989).
Genotyping and quality control
Samples were genotyped using the Applied Biosystems
TM
Axiom
TM
Ovine Genotyping Array (50K) consisting of 51 572
SNPs (Thermo Fisher Scientific, catalog number 550898). A
subset of Shropshire samples (n=26) previously genotyped
on the Ovine Illumina SNP50 Bead Chip consisting of 54 241
SNPs (Illumina catalog number WG-420-1001) was also
included in this dataset. The genotypic data for these samples,
from each platform, were merged by SNP name and location
in PLINK version 1.90, with a total of 47 485 SNPs overlapping
between the two panels. Quality control of genotype data was
performed using PLINK version 1.90 specifically excluding
SNPs with a call rate of less than 0.90 and MAF less than
0.01, resulting in 45 864 SNPs remaining in the analyses
(Purcell et al. 2007; Chang et al. 2015).
Observed heterozygosity, inbreeding coefficients, and
F
ST
calculations
The observed heterozygosity was estimated for each animal
using PLINK version 1.90 and averaged by breed (Purcell et al.
2007; Chang et al. 2015). Inbreeding coefficients were
calculated for each animal based on the observed and expected
homozygosity in PLINK version 1.90, and the mean and 95%
confidence intervals were calculated with the Rpackage
‘rcompanion’ in Rversion 3.6.1. To remove redundancy and
provide a more accurate representation of variation, LD
pruning was performed using the --indep-pairwise function in
PLINK version 1.90 with an r
2
=0.5, a sliding window size of 50
SNPs and shifts of five SNPs (Visser et al. 2016; Gilbert et al.
2017). After LD pruning, 40 121 SNPs remained for further
analyses. Pairwise F
ST
was estimated in PLINK version 1.90
between breeds of sheep using the LD pruned dataset (Purcell
et al. 2007; Chang et al. 2015).
Eigenvalue analyses
Eigenvalues were calculated using the filtered SNP dataset
for terminal breeds only and then with Rambouillet in SNP
and Variation Suite version 8.7.2 (Golden Helix, Inc.,
www.goldenhelix.com). The top two eigenvalues were
plotted against each other in SNP and Variation Suite.
Hierarchical clustering
An identity by state matrix was calculatedfrom the LD pruned
dataset pairwise between all sheepusing the PLINK version 1.90
--distance flag (Purcell et al. 2007; Chang et al. 2015). The
matrix was read into Rversion 3.6.1 and hierarchical
clustering based on the identity by state matrix of Hamming
distances between each animal using the ‘hclust’ function.
The Bioconductor package ‘ctc’ was used in Rversion 3.6.1 to
write a Newick file to import into DENDROSCOPE 3 software
(Huson & Scornavacca 2012). A rectangular cladogram was
drawn from the Newick file in DENDROSCOPE version 3.5.9
(Huson & Scornavacca 2012). Individual branch labels were
colored according to producer-reported breed of sheep.
Admixture analysis
The program ADMIXTURE version 1.3.0 was implemented to
examine admixture between all samples using the LD pruned
genotypes in BED format (Alexander et al. 2009; Decker et al.
2014). The most probable number of Kgiven populations was
estimated using the lowest cross-validation error (Alexander
et al. 2009; Akanno et al. 2018). Euclidean distances were
calculated in Rversion 3.6.1 with the adegenet package and an
analysis of molecular variance (AMOVA) was performed with
the pegas package with 1000 permutations to statistically
examine differences between populations (McKay et al. 2008;
Paradis 2010; Jombart & Ahmed 2011).
International breed comparisons
Genotypes from 2819 sheep from 74 breeds across the
world were retrieved from the International Sheep Genome
©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
Genetic structure and admixture in sheep 285
Consortium Sheep HapMap Database and used in compar-
ison with US terminal breeds including the addition of n=5
Dorset and n=7 Southdown sheep from the United States.
The same set of 45 864 SNPs used with the US terminal
breeds was then merged with the same SNPs from the Sheep
HapMap dataset. Eigenvalues were calculated between US
terminal breeds and the same breeds from other locations in
the HapMap dataset, all US breeds in this study and the
same breeds present from other locations in the HapMap
dataset, and all US breeds in this study and the Sheep
HapMap dataset.
Results
Observed heterozygosity and inbreeding coefficient
To examine the relatedness of animals within each of the
breeds, observed heterozygosity and average inbreeding
coefficient were calculated. These statistics were calculated
based on observed and expected homozygosity, estimated
for each individual, and averaged for each breed (Table 1).
The Oxford animals exhibited the greatest (0.35) observed
heterozygosity and lowest inbreeding coefficients. Similar
observed heterozygosity was exhibited by Shropshire (0.34),
Western Suffolk (0.34), Suffolk (0.33) and Hampshire
(0.33). Shropshire had the lowest inbreeding coefficient
(0.09) in comparison with the Suffolk (0.13), Western
Suffolk (0.14) and Hampshire (0.14). The group with the
lowest observed heterozygosity (0.30) and highest inbreed-
ing coefficient (0.16) was Rambouillet.
Wright’s F
ST
Wright’s F
ST
was calculated pairwise between each group of
animals to examine differentiation between breeds (Table 2;
Wright 1965; Weir & Cockerham 1984; Lenstra et al.
2012). In general, values between 0 and 0.05 are catego-
rized as ‘little to no differentiation,’ values between 0.05
and 0.15 as ‘moderate differentiation’, values between 0.15
and 0.25 as ‘great differentiation’, and values above 0.25 as
‘very great differentiation’ between populations tested (Weir
& Cockerham 1984; Frankham et al. 2002). Rambouillet is
considered greatly differentiated from all terminal breeds.
Interestingly, Western Suffolk are considered moderately
differentiated from other terminal breeds. Little to no
difference was detected between Hampshire and Suffolk or
Hampshire and Shropshire. Furthermore, although Western
Suffolk and other Suffolk are not reported as different
breeds, they too exhibit moderate differentiation.
Eigenvalue analyses
To investigate how individuals from reported terminal
breeds the US group or cluster, eigenvalues were calculated
and plotted for all samples (Fig. 1). An eigenvalue plot for
only terminal breeds of sheep (Fig. 1a) as well as terminal
breeds and Rambouillet sheep (Fig. 1b) is displayed. In
Fig. 1a, the largest difference of eigenvalues is between
Western Suffolk and Shropshire and can be observed on the
x-axis of the plot shown. Further, the animals sampled for
the Shropshire breed exhibited the largest spread of eigen-
value points. Interestingly, all Suffolk did not group
together. Most of the Suffolk animals sampled cluster closely
with Hampshire animals; however, the Western Suffolk
flock clustered separately from Hampshire and other Suffolk
animals.
In Fig. 1b, Rambouillet animals cluster together, and the
entire breed clusters distinctly and away from the terminal
sheep breeds on the largest eigenvalue axis. Similar to
Fig. 1a, sheep cluster primarily by breed with the exception
of four Shropshire animals. The Suffolk samples do not all
group together, with Western Suffolk clustering separately
from other Suffolk animals. With these notable exceptions,
animals within a breed cluster together.
Hierarchical clustering based on identity by state
To examine how animals from breeds of sheep in the United
States are related to those from other breeds, hierarchical
Table 2 Pairwise F
ST1
between breeds of sheep.
Hampshire Suffolk
Western
Suffolk Oxford Shropshire
Hampshire 0
Suffolk 0.03 0
Western
Suffolk
0.09 0.07 0
Oxford 0.06 0.06 0.13 0
Shropshire 0.05 0.06 0.11 0.06 0
Rambouillet 0.17 0.17 0.23 0.18 0.16
1
Wright’s F
ST
values between 0 and 0.05 are categorized as no
differentiation, 0.060.15 as moderate differentiation, 0.160.25 as
great differentiation, and >0.26 as very great differentiation.
Table 1 The mean observed heterozygosity and average estimated
inbreeding coefficient including the 95% confidence interval for each
group.
Breed
Observed
heterozygosity
Inbreeding
coefficient
1
95% Confidence
interval for inbreeding
coefficient
Hampshire 0.33 0.14 0.120.15
Suffolk 0.33 0.13 0.120.15
Western
Suffolk
0.34 0.14 0.130.15
Oxford 0.35 0.05 0.010.09
Shropshire 0.34 0.09 0.040.11
Rambouillet 0.30 0.16 0.150.17
1
Inbreeding coefficients are reported as Fhat2 and calculated by:
(observed heterozygosity expected)/(total expected).
©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
Davenport et al.286
clustering was performed using an identity by state matrix.
A rectangular cladogram was constructed to visualize the
hierarchical clustering (Fig. 2). All Western Suffolk, Oxford
and Rambouillet animals clustered together by breed.
Rambouillet animals clustered in a distinct, separate branch
from all other breeds, which was consistent with the
eigenvalue plot. In general, most sheep were more identical
by state to other animals within the same breed with a few
notable exceptions.
Several reported Shropshire animals clustered with the
Hampshire branches; these were the same animals that
clustered with the Hampshire breed in the eigenvalue plots.
A branch of Shropshire animals also clustered closely with a
larger branch of Hampshire sheep. Additionally, Suffolk and
Hampshire animals overlapped and appeared to cluster
closely within the branches of the cladogram. Still, overall
most breeds clustered independently with the few excep-
tions mentioned before.
Admixture analysis
An admixture analysis was performed using the program
ADMIXTURE to investigate the extent of admixture between
different breeds of sheep in this study (Alexander et al. 2009;
Decker et al. 2014; Getachew et al. 2017). The analysis was
conducted using two to 10 given populations. The best fit of K
given populations was determined as K=6 based on the cross-
validation values calculated in ADMIXTURE (Fig. S1; Akanno et al.
2018). Further, the AMOVA analyses showed significant
(P<0.01) differences betweenthe K=6 assigned populations.
In the best fit K=6 plot, admixture was detected within
terminal breeds (Fig. 3). Admixture between terminal
breeds was observed in Hampshire, Oxford, Suffolk and
Shropshire, but the Western Suffolk population showed
little admixture with other terminal breeds except Suffolk.
Not surprisingly, the dual-purpose Rambouillet sheep were
different from the US terminal breeds examined.
Figure 1 Plot of calculated eigenvalues for
breeds of US sheep. (a) Eigenvalues plotted for
US terminal breeds of sheep. (b) Eigenvalues
plotted for US terminal breeds and Rambouil-
let sheep. Each point represents an individual
animal and points are colored by reported
breed.
©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
Genetic structure and admixture in sheep 287
Eigenvalue plots of US and international comparisons
To examine how US sheep compare with other sheep
across the world, genotyping data from this study were
merged with data from the Sheep HapMap (Kijas et al.
2012; Kijas 2013). Eigenvalues were calculated and
plotted with US terminal breeds including additional
Dorset and Southdown sheep from the United States, and
animals of the same breeds from the Sheep HapMap
dataset (Fig. 4a). Interestingly, the US terminal breeds
clustered closer to other breeds from the United States
than the same reported breed, including Suffolk and
Dorset, from other locations. When the genetic informa-
tion for wool breeds of sheep was included, they clustered
apart from the terminal breeds (Fig. 4b). Figure 4b also
shows the Irish Suffolk clustering closely with Suffolk from
the United States. Finally, when all samples were consid-
ered, the US terminal breeds clustered with similar breeds
from Australia and the UK (Fig. 4c). In summary, animals
clustered closest with those of similar geographic location
in the eigenvalue plots.
Discussion
The observed heterozygosity results from this study were
consistent with data reported in other breeds of sheep across
the world (Kijas et al. 2012; Ciani et al. 2014; Gaouar et al.
2017). More specifically, the observed heterozygosity in
most breeds was close to what was reported in Australian
sheep (Kijas et al. 2012; Al-Mamun et al. 2015). In addition,
the observed heterozygosity was consistent with other US
sheep including Suffolk, Rambouillet, Columbia, Polypay
and Targhee (Zhang et al. 2013). However, the breeds in
this study had lower observed heterozygosity when com-
pared with Boutsko, Karagouniko and Chios breeds from
Greece (Michailidou et al. 2018).
In our study, Oxford sheep exhibited the lowest average
inbreeding coefficient and highest observed heterozygosity,
similar to Finnsheep (Li et al. 2011). This is probably
because these sheep were selected based on pedigree
diversity from NSIP, whereas Western Suffolk had one of
the highest inbreeding coefficients and was only represented
by one flock. However, to our surprise, the inbreeding
coefficient for Western Suffolk was similar to that of Suffolk,
which included animals from 10 separate flocks. Perhaps
this is because these animals are the result of and
representative of the breeding strategies of purebred flocks.
Other work in 97 sheep breeds across the world includ-
ing Ethiopian sheep reported inbreeding coefficients
between 0.07 and 0.16 and observed heterozygosity
between 0.061 and 0.343, which are similar to our results
(Edea et al. 2017; Zhang et al. 2018).
Figure 2 Rectangular cladogram of individuals clustered based on identity by state and colored by reported breed.
Figure 3 ADMIXTURE model clustering output with K= 6 populations. Each bar represents an individual animal for each terminal breed and Rambouillet,
and the six colors represent each Kpopulation cluster.
©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
Davenport et al.288
Despite similarity in inbreeding coefficient and heterozy-
gosity estimates, Western Suffolk shows moderate differen-
tiation from Suffolk whereas Hampshire, Oxford, Shropshire
and Suffolk show little to moderate differentiation from each
other. The Western Suffolk consists of representatives from
a ‘closed flock’, which may explain the divergence from the
more broadly sampled Suffolk. The lack of differentiation
observed between the Suffolk, Hampshire and Shropshire is
not surprising considering the prevalence of crossbreeding
in many US terminal breed flocks. It is worth noting that the
Southdown is thought to be a common ancestor for
Hampshire, Shropshire and Oxford breeds (Ryder 1964).
These points are strongly supported by the results of the
ADMIXTURE analysis. Furthermore, these results concur with
previous research that reported a Wright’s F
ST
=0.1621
between Suffolk and Rambouillet; these breeds differ in
origin as the Rambouillet breed was derived from Merino
bloodlines (Dickinson & Lush 1933; Zhang et al. 2013).
Differences between breed groups can be visualized in the
eigenvalue plots, where sheep cluster primarily by reported
breed with the exception of a few animals. The separation of
Suffolk from Western Suffolk is apparent, which is consis-
tent with previous work that identified regional differences
in Suffolk from the United States (Kuehn et al. 2008). The
Figure 4 Eigenvalue plots of US sheep in this
study compared with other breeds across the
world as part of the Sheep HapMap study. (a)
Eigenvalue plot of US terminal breeds and
Dorset and Suffolk HapMap breeds. (b)
Eigenvalue plot of all US sheep in this study
compared with HapMap terminal and wool
sheep. (c) Eigenvalue plot of US sheep in this
study compared with all breeds present in the
Sheep HapMap study.
©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
Genetic structure and admixture in sheep 289
Shropshire breed has a large spread of eigenvalues and a
few animals cluster with Oxford and Hampshire, suggesting
the occurrence of crossbreeding. The distinct clustering of
the Rambouillet away from other breeds clearly displays the
genetic difference between terminal and wool/dual-purpose
breeds in the United States.
The K=6 plot, supported by the AMOVA analysis, shows
that sheep cluster primarily by breed with some level of
admixture between all terminal breeds, with the exception
of Western Suffolk, which exhibits little admixture except
with other Suffolk. The observed admixture within Hamp-
shire, Suffolk, Oxford and Shropshire is potentially due to
the use of sires with composite influence from other breeds
in US commercial operations (Ercanbrack & Knight ;
Norberg & Sørensen 2007). Rambouillet sheep showed
little to no admixture with the US terminal breeds examined
in this study.
When US sheep were compared with other populations
across the world, sheep primarily clustered closest to other
animals in similar geographic locations rather than to the
same reported breeds in other parts of the world (Kijas et al.
2012). More specifically, Suffolk and Dorset animals clus-
tered closer to other US groups than to Suffolk from
Australia and Ireland, or Dorset from Australia or the UK.
This observation may be partially attributed to the differ-
ences in selection and breeding strategies and in production
systems across the world (Andersson 2012;
Curkovi
cet al.
2016; Wang et al. 2015). In addition, the difference
between terminal breeds and wool breeds is clear, suggest-
ing that there are genetic differences between breeds that
have been selected for alternative production objectives and
purposes (Blackburn et al. 2011; Zhang et al. 2013; Fariello
et al. 2014).
In summary, we characterized relationships between
sheep from terminal sire breed populations in the United
States. Internationally, there has been an increased empha-
sis on genetic selection of sheep for a variety of traits and
purposes. Marker-assisted selection is growing in popularity
as new technology is being rapidly developed, along with an
increase in the use of quantitative genetic programs that
calculate estimated breeding values. By better understand-
ing the population structure and admixture between
terminal breeds in the United States compared with breeds
across the world, we can improve the effectiveness of this
developing technology. Our research provides insight into
the current relatedness of the popular terminal breeds in the
United States and the framework for future analyses on a
larger scale.
Acknowledgements
This project was supported by Agriculture and Food
Research Initiative Hatch grant no. IDA01566 from the
USDA National Institute of Food and Agriculture. We would
like to thank Thermo Fisher Scientific for genotyping, and
Curt Stanley, Shane Kirtchen, Virginia Tech/Scott Greiner,
Hayden’s Hamps, North Dakota State University, Drewry,
Reombke, Adams, University of Wisconsin, Kindred Cross-
ing, Bingen, Mapleton Mynd, Knepp Shropshires, All Forage
Farm, Dr. Fred Groverman, Formo, Bishop, Bar-Zel Suffolks,
JMG Suffolks, Virginia Tech, Culham & Stevens, Reau
Suffolks, Double L Livestock and Dry Sandy for sample
contributions.
Data availability
Data (50K SNP) have been deposited in Open Science
Framework (https://osf.io/d7s59/?view_only=9c85566d
0ac542d89a62150524eaad0e).
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Supporting information
Additional supporting information may be found online in
the Supporting Information section at the end of the article.
Figure S1 ADMIXTURE cross-validation output plotted across
Kpopulations.
©2020 The Authors. Animal Genetics published by
John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 51, 284–291
Genetic structure and admixture in sheep 291
... The Hu sheep breed is highly regarded in China for its advantageous features of non-seasonal estrus, multiple births, tolerance to roughage, and suitability for domestic breeding [13,14]. Southdown sheep and Suffolk sheep have the characteristics of early development and easy fattening, and their rams are suitable for hybridization to obtain good growth and carcass characteristics [15][16][17]. Proteomics can be used to systematically characterize large-scale dynamic changes in protein expression [18], contributing to genomics and transcriptomics by deepening our understanding of complex biochemical processes at the molecular level [19]. Wang et al. used proteomics technology to screen the differential abundance proteins (DAPs) of more than 1000 Chinese Merino sheep at different embryonic stages, elucidating mechanisms involved in embryonic skeletal muscle growth, development, and maturation [20]. ...
... The Hu sheep breed is highly regarded in China for its advantageous features of nonseasonal estrus, multiple births, tolerance to roughage, and suitability for domestic breeding [13,14]. Southdown sheep and Suffolk sheep have the characteristics of early development and easy fattening, and their rams are suitable for hybridization to obtain good growth and carcass characteristics [15][16][17]. Proteomics can be used to systematically characterize large-scale dynamic changes in protein expression [18], contributing to genomics and transcriptomics by deepening our understanding of complex biochemical processes at the molecular level [19]. Wang et al. used proteomics technology to screen the differential abundance proteins (DAPs) of more than 1000 Chinese Merino sheep at different embryonic stages, elucidating mechanisms involved in embryonic skeletal muscle growth, development, and maturation [20]. ...
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Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.
... Hu sheep, a unique domestic sheep germplasm resource in China, which is known for its excellent characteristics, including perennial estrus, high fecundity, novel lactation performance and strong adaptability, is an important dam breed in commercial hybrid mutton sheep. 2 Southdown and Dorset are famous sheep breeds with perfect mutton production performance, which show the advantages of early growth, excellent mutton quality, easy to fatten and other characteristics, are considered to be the most popular breeds in mutton production, so as to usually utilized as the sire breeds in hybrid mutton sheep. 3,4 Therefore, we carried out economic hybriding with local Hu sheep as the female parent, Southdown and Dorset as the sire to produce Southhu (Southdown × Hu sheep, SH) and Dorhu (Dorset × Hu sheep, DH) sheep. ...
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The aim of this study was to analyze the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid mutton sheep using ASReml software, in order to provide theoretical basis for screening the optimal hybriding combinations and accelerating the breeding process of new breeds of specialized housed-feeding mutton sheep. We selected the wellgrown hybrid Southhu (Southdown × Hu sheep) and Dorhu (Dorset × Hu sheep) sheep as the research objects, constructed weight correction formulae for SH and DH sheep at 60 and 180 days; and used ASReml software to investigate the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid sheep. The results showed that the birth month and birth type were found significant for all traits (p < 0.001); the heritability of maternal effects ranged from 0.0709 to 0.1859. It was found that both SH and DH sheep emerged the potential for rapid early growth and development, early growth traits are significantly affected by maternal genetic effects, thereby the maternal effect should be taken into consideration for the purpose of improving accuracy in parameter estimations and therefore increasing the success of breeding programs.
... The average proportion of expected and observed homozygous SNPs for Rambouillet, Katahdin, and Dorper are reported in Table 1. The observed homozygosity was similar to previous estimates for Rambouillet [71] and was slightly higher than previous estimates for Katahdin and Dorper [72,73]. For each breed, the average F ROH estimate was higher than the average F estimate. ...
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... In addition, characterising the genetics of production breeds is also important to understand genetic relationships between breeds. The 50K chip has been used, for example, to characterise the genetic diversity of terminal sires in the US (Davenport et al. 2020) and the genetic diversity in New Zealand's composite flocks has also been characterised using a higher density 600K chip (Brito et al. 2017b). When combined the genotyping datasets from SNP arrays for sheep now probably capture a considerable amount of the genetic diversity represented by sheep breeds from across the globe. ...
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Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
... Duplicate markers designed for the same genomic position within a panel were filtered to retain the marker with the highest call rate (CR). Compatible markers were matched by marker name and genome position resulting in a consensus dataset of 44,431 markers in common between the genotype platforms (Davenport et al., 2020). Plink v1.9 was used to merge genotype array data and correct markers designed for opposite strands https://pngu.mgh.harvard.edu/purcell/plink/). Markers were filtered for quality control in the following order: non-autosomal markers (1,019 SNPs), markers with a call rate (CR) <90% (87 SNPs), markers with a minor allele frequency (MAF) <0.01 (1,407 SNPs) and markers with Hardy-Weinberg Equilibrium p-values <1e-50 (30 SNPs) were excluded, for a total of 41,888 high-quality autosomal SNPs retained for final analyses. ...
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