New Zealand Journal of Agricultural Research

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Application of new technologies in sheep breeding

H. T. Blair & D. J. Garrick

To cite this article: H. T. Blair & D. J. Garrick (2007) Application of new technologies
in sheep breeding, New Zealand Journal of Agricultural Research, 50:2, 89-102, DOI:
10.1080/00288230709510285

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New Zealand Journal of Agricultural Research, 2007, Vol. 50: 89-102 89
0028-8233/07/5002-0089 © The Royal Society of New Zealand 2007

Invited paper

Application of new technologies in sheep breeding

H. T. BLAIR1 INTRODUCTION
D. J. GARRICK1,2 Over a long period of time, farmers have changed
1
Institute of Veterinary the appearance and function of sheep in succes-
Animal and Biomedical Sciences sive generations through exploitation of selection
National Research Centre for Growth and opportunities. While there are few records about
Development the specifics of selection practices, it is clear that
Massey University genetic manipulation has happened because of the
Private Bag 11222 differences between modern-day sheep and their
Palmerston North 4442, New Zealand ancestral antecedents. The developing interest in
Department of Animal Sciences family or pedigree lines in the mid 18th century re-
Colorado State University sulted in more written records being kept, so we have
Fort Collins, CO 80523-1171 greater knowledge of the procedures used by Robert
USA Bakewell and others to "improve" their sheep. The
critical thinking of such early animal breeders must
be admired when it is considered that knowledge of
Abstract Genetically improved sheep make an genes, their impact and manner of inheritance, has
important contribution to farmer profitability. New been known for little more than 100 years.
Zealand sheep breeders have a good track record in Mendel proposed the existence of genes and
applying cost effective technologies to assist with the Fisher and others described how two or more genes
genetic improvement of their stock, with current an- might combine to produce quantitative effects. As
nual rates of genetic gain in the New Zealand sheep that knowledge has filtered out to livestock breeders,
industry likely to be between 0.1 and 0.2 genetic there has been widespread adoption of the principles
standard deviations. Several new technologies are of selection, albeit using imperfect knowledge of
discussed and their potential impact on improving the genotypes of candidate animals, to select those
genetic gain in the New Zealand sheep industry capable of favourably changing the form and/or
evaluated. While it might be possible to improve function of the next generation of offspring. The last
the rate of genetic gain to 0.5 genetic standard de- 50 years have seen dramatic changes in the scien-
viations by applying all available technologies, it is tific understanding of how genes work and interact.
more likely that improved rates will only reach about Furthermore, the time lag between the acquisition of
0.3 genetic standard deviations when cost effective- new knowledge and its availability to farmers has
ness is taken into account. decreased.
The purpose of this paper is to briefly review
Keywords genetic improvement; technology; the current state of affairs and then explore some
sheep likely technologies that will be available to, and
may impact on, the future of sheep breeding in New
Zealand. The task of looking forward has been at-
tempted before (Rae 1993); there are also two good
reviews that should be consulted: Dry (1938) and
Rae (1956). In 1990 the 50th Jubilee Proceedings
of the New Zealand Society of Animal Production
Conference also contained a number of papers that
A07003; Online publication date 5 April 2007 "looked forward". Blair & Garrick (1994) and Gar-
Received 6 October 2006; accepted 1 March 2007 rick & Snell (2005) considered the application of
90 New Zealand Journal of Agricultural Research, 2007, Vol. 50
new technologies in the New Zealand beef cattle
and dairy cattle industries, respectively. In this paper,
attention is focused on sheep meat production with
little mention of how new technologies might im-
pact on breeding sheep with "better" wool. It seems
unlikely that crossbred wool will again become an
important product for most farmers in the foresee-
able future. There will be exceptions; for example,
the extraction of speciality products from wool fi-
bres such as keratin proteins, but it is unlikely that
breeding will be required to change fibre attributes
for these products. If wool does again become more
important, the technologies discussed have equal
application to breeding for "better" wool.
SOME COMPONENTS OF GENETIC
IMPROVEMENT AND THEIR CURRENT
STATUS
There are many components that influence the ef-
fectiveness of a genetic improvement programme.
These are briefly explained in the following section
to give a framework for further discussion.
Breeding objective (also called selection
objective, breeding goal)
The first step in designing a genetic improvement
scheme is to establish the target or goal trait(s) that
affect the fitness for purpose of the animal system.
While these traits typically include those that have
direct impact on farm income or expenses, it is
also possible to consider traits that simply affect
farmer satisfaction. An estimate of the genetic merit
is required for each trait included in the breeding
goal. The estimated genetic merit is typically called
the breeding value (BV), estimated breeding value
(EBV) or expected progeny difference (EPD). To al-
low the controlled apportioning of selection pressure
when many traits are to be simultaneously changed,
either economic or relative economic values are
required for each trait.
Within-breed genetic improvement
The sheep industry is comprised of several distinct
breeding populations (typically breeds), and each
of these populations will be progressing at various
rates of genetic improvement. There are four fac-
tors that control the rate of genetic gain towards the
breeding goal:
—the selection differential is dictated by the pro-
portion of replacement males and females cho-
sen to become parents from the available pool of
replacements. As the proportion chosen becomes
smaller, selection becomes more intense and the se-
lection differential becomes larger allowing genetic
gain to increase. The standardised selection differ-
ential reflects the superiority of selected candidates
over the average of their cohort in standard deviation
units and ranges from 0.0 (if parents are chosen at
random) to 3.4 (if just the most elite 0.1% of avail-
able replacements are chosen to become parents).
Typical values for performance-recorded flocks in
the New Zealand sheep industry are between 1.3 and
1.7, averaged over both sexes.
—selection accuracy reflects the degree to which
the available phenotypic information predicts the
genetic merit of the animals being ranked. This
value can be expressed as a correlation and ranges
between 0 and 1.0, with an accuracy of one meaning
that the phenotype exactly predicts the genotype.
For traits that are controlled by many genes, an
accuracy near 1.0 is currently achieved only with
extensive progeny testing. In the New Zealand sheep
industry accuracy values on performance-recorded
selection candidates are typically between 0.2 and
0.4. A related value more commonly used in dairy
industries is the reliability, which is the square of
the accuracy. Reliabilities in the sheep industry thus
range between 0.04 and 0.16.
—variability measures how variable the trait under-
going selection is. The magnitude of the variation is
dependent on the trait, for example lamb weaning
weight has a phenotypic standard deviation of about
4 kg while number of lambs born per ewe has a
value of 0.6 lambs. The observed variation within a
cohort of animals is determined by both genetic and
environmental components. The greater the genetic
variation in the trait, the faster the potential rate of
genetic change.
—the generation interval reflects how fast the gen-
erations are turning over in the population that is
undergoing selection. The quicker that parents are
replaced with superior offspring, the faster the rate
of genetic gain. It is calculated as the average age of
all parents in the population when their offspring are
born. In the New Zealand sheep industry, generation
intervals are typically 3-4 years.
These four factors that control the rate of genetic
change are interdependent, so rather than seeking to
either maximise or minimise each factor, it is neces-
sary to consider them jointly to optimise the rate of
genetic change. In practice, the cost of achieving ge-
netic gain can vary widely according to the selection
strategies adopted, so the strategy associated with the
Blair & Garrick—New technologies in sheep breeding
highest rate of genetic gain is seldom the most cost
effective. Using the range of figures suggested above
for the standardised selection differential (1.3-1.7),
selection accuracy (0.2-0.4) and generation interval
(3-4), the maximum rate of annual genetic gain in
the New Zealand sheep industry is likely to be of the
order of 0.1-0.2 times the genetic standard deviation
of the trait(s) under selection pressure.
Industry structure
The way in which subpopulations (or flocks) in-
teract through the exchange of genetic material is
referred to as the industry structure. The majority
of genetic change is achieved in specialised flocks
called stud/nucleus/seedstock/pedigree flocks. The
genetic change in these flocks is then transferred
to commercial flocks through the sale of rams (or
sometimes semen). Efficient genetic gain in the
nucleus sector and its subsequent transfer to the
commercial sector requires ram buyers committed
to genetically improving their flocks (Garrick et
al. 1992). Sometimes there are either insufficient
numbers of rams or rams are too expensive from a
favoured stud to meet the demand from commercial
farmers. In these circumstances, some flocks called
multipliers might be added to the industry structure
(Stewart & Garrick 1996). These flocks procure rams
or semen from the favoured stud and "multiply"
the genetic material for sale to the commercial tier.
These so-called multiplier flocks do not modify the
long-term rate of genetic gain achieved by the indus-
try but can reduce the average cost of improvement
and dissemination of genotypes. The time it takes
for genetic change generated in the stud flocks to
be expressed in the commercial flocks is referred to
as "genetic lag". Where the genetic material passes
directly from a stud flock to commercial flocks, this
lag is two times the average generation interval in the
commercial flocks. However, if there is a multiplier
layer between the stud and commercial flocks, the
genetic lag can increase to as much as four times
the generation interval. However, if multipliers use
only the best nucleus rams, their involvement in gene
flow provides little or no increase in genetic lag. In
the New Zealand sheep industry, the genetic lag is
typically between 5 and 8 years.
Farmers can take advantage of the fact that the
sheep population in New Zealand is divided into
distinct breeding groups or breeds. They can opt
to either use only the same breed (straightbreed) or
to crossbreed between the various breeds suited to
their production system; these different options are
referred to as mating plans. Genetic improvement
91
within a breed utilises differences in additive gene
action between animals while crossbreeding utilises
both additive and non-additive gene action. Non-
additive gene action is the basis for hybrid vigour
or heterosis, and it can lead to substantial lifts in
performance above the average genetic merit of the
breeds being used in the cross.
TRACK RECORD FOR ADOPTING NEW
TECHNOLOGY
Before looking forward at which technologies might
be usefully employed to improve the genetic merit
of the national sheep flock, it is worthwhile to con-
template how well the New Zealand sheep industry
has historically accepted new technologies through
consideration of some examples.
Composite breeds
New Zealand sheep breeders have produced several
composite breeds that have had a significant impact
on New Zealand's sheep industry. The Corriedale
was the first of these, being established in the late
1800s. Throughout the 1900s, there were several
more composite breeds established, with the Poll
Dorset, Drysdale, Perendale, and Coopworth breeds
from the 1950s and 1960s having a significant influ-
ence in moving ram breeders from pedigree-based
to performance-based selection. The Drysdale and
Poll Dorset were somewhat unusual in that their
success was dependent on a single gene for hairy
fibres or polledness, respectively. More recently,
there has been a flurry of composite breeds enter-
ing the market as a consequence of the release of
several breeds new to New Zealand. It would seem
that New Zealand sheep breeders have been capable
users of crossbreeding to assist them in achieving
their production targets.
Statistical techniques
New Zealand has been fortunate in having a strong
quantitative breeding presence since Professor Al
Rae returned from Iowa State University in 1951 to
take up the Professorship of the Sheep Husbandry
Department at Massey Agricultural College. Pro-
fessor Rae and his students led the application of
statistics to the ranking of replacement breeding
stock in the New Zealand livestock sectors (Rae
1969). Initial genetic evaluations were based on Best
Linear Prediction (BLP), but as computing capacity
allowed, Best Linear Unbiased Prediction (BLUP)
(Garrick 1991) was introduced (Geenty 2000).
92 New Zealand Journal of Agricultural Research, 2007, Vol. 50
Computers
The New Zealand sheep industry was an early
adopter of computing to assist with the estimation
of breeding values from large datasets. Adoption
throughout the 1960s and 1970s was encouraged by
Professor Rae and a number of his former students at
both Massey and the Department of Agriculture. Ac-
cess to a computer in the Biometrics Section at Ru-
akura allowed the introduction of the National Flock
Recording Scheme in 1967 (Clarke 1967), with some
348 flocks joining in the first year (Wallace 1974).
While computers were initially only available to
education and research organisations, the uptake of
smaller desktop computers by leading ram breeders
grew rapidly in the 1980s. More recently, the avail-
ability of handheld computers for use in the field has
also been enthusiastically embraced.
Group breeding schemes, progeny testing and
sire referencing
The late 1960s saw the emergence of several Group
Breeding Schemes (GBS) in New Zealand, follow-
ing promotion of their benefits by Rae (1964,1974),
Hight & Rae (1970), and Hight et al. (1970). Rae
(1974) and James (1977) suggested that open-nucleus
breeding schemes could increase the rate of genetic
gain by 10-18% over closed, within-flock, selection
and breeding. The concepts and advantages of GBS
were enthusiastically received and implemented by
many forward-thinking ram breeders of that time and
arguably changed the nature of ram breeding in New
Zealand. One particularly successful and long-last-
ing scheme was implemented by (the then) Rotorua
Land Development District of the Lands and Survey
Department at their Waihora farm which initially
screened high performing ewes from some 308 700
ewes run under commercial conditions (Hight et al.
1975). While few GBS survive in their original form
some 40 years later, their impact can still be seen in a
number of informal relationships that exist amongst
influential ram breeders today. Changes in thinking
and technology, for example dispersed, open-nucleus
flocks and sire referencing schemes (Harvey et al.
1990), meant that by the mid 1980s a number of GBS
had morphed into sets of more loose arrangements
than were required by GBS.
Rae (1976, 1984) showed that the application of
progeny testing to improve lean meat production
could increase the rate of genetic gain by 40-50%
over using BVs based on individual selection. With
such significant gains to be harvested, it may seem
surprising at first that progeny testing has not been
more widely applied by terminal sire breeders in
New Zealand. However, there has been an excess of
supply of rams in New Zealand since the 1980s as
sheep numbers have dropped to their current levels.
In addition, most terminal sire flocks are relatively
small. Under these circumstances, it is perhaps un-
surprising that progeny testing was not more widely
adopted. However, the application of sire referencing
and the adoption of BLUP for genetic evaluations
has meant that a number of de facto progeny tests
have been occurring throughout the New Zealand
ram breeding sector. More recently, some breed-
ers have implemented formalised progeny testing
schemes as suggested by Professor Rae some 20
years ago (Johnson et al. 2002).
Reproductive technologies
Artificial insemination (AI) and embryo transfer
(ET) have been used as research tools for many
years. The use of AI to increase the selection differ-
ential has had a major impact on the dairy industry,
but has played only a minor role in the sheep in-
dustry. The Perendale Genetic Development Group
briefly used AI to reduce the genetic lag between
their nucleus flock and contributing flocks in 1983,
while in 1985 the New Zealand Ovine Sire Referenc-
ing Group used AI as a means of genetically linking
flocks together to enable sire referencing (Harvey
et al. 1990). ET has been used sporadically, mainly
to achieve the rapid multiplication of breeds newly
introduced into New Zealand. Neither AI or ET have
achieved widespread sustained application in the
New Zealand sheep breeding sector for the purpose
of routine genetic gain. However, both technologies
have played important roles in allowing the national
sheep population to evolve to where it is today.
Disease phenotypes
Analysis of large sheep datasets has shown that ei-
ther resistance, resilience or tolerance to a range of
important sheep diseases has a genetic component,
offering the opportunity for genetic improvement
via selection (Morris et al. 1995; Brandsma & Blair
1997; Bisset et al. 2001). Furthermore, a number of
experiments have demonstrated that selection can
be effective. However, basing selection on the clini-
cal signs of these diseases is often ineffective, time
consuming, expensive, or causes an animal welfare
problem. Consequently, significant scientific effort
has been invested in discovering indicator traits such
as gamma glutamyltransferase (GGT) for facial ec-
zema(e.g., Towers & Stratton 1978) andELISAtests
for worm burden (e.g., Douch et al. 1995). There
has been modest uptake of these new phenotypes
Blair & Garrick—New technologies in sheep breeding
by ram breeders. At least some of the resistance to
widespread adoption of these phenotypes is the as-
sociated cost when spread over a large number of
potential sale animals, of which only a proportion
are sold. The cost of testing those animals not sold
has to be shared amongst those that are sold.
DNA technologies
One of the early commercial DNA tests in New
Zealand with significant industry uptake was offered
by the Equine Blood Typing and Research Centre
at Massey University in 2001 to Suffolk breeders
wishing to identify animals carrying the so-called
spider gene (West et al. 1995). Some 3400 tests have
been completed (J. Cahill pers. comm.), with about
300 being requested in 2006, down from a peak of
about 950 in 2003. The test has been very successful
at reducing the incidence of the mutation in the New
Zealand Suffolk population. While the test remains
a requirement for transfers between studs, for sheep
that are exported and donors of semen and embryos,
the number of animals tested is likely to remain low.
Similar gene tests for undesirable mutations will be
offered in the future. While these tests will be benefi-
cial to individual flocks, they will have only limited
beneficial effect to the national sheep sector as the
mutations are typically at a low frequency.
In the late 1990s, it became apparent that DNA
parentage testing was on the verge of becoming
economically viable. A Technology New Zealand
grant from the Foundation for Research, Science and
Technology brought together the then DIBO stud
with Massey University and AgResearch scientists to
undertake a feasibility study. Over the ensuing years,
this work resulted in the now commercial testing
system offered by Catapult Genetics™. There are
several advantages of DNA parentage testing, but
the one of primary interest in this discussion is the
potential to increase the accuracy of selection by
accurately assigning offspring to parents to ensure
the inclusion of the correct pedigree information.
A number of studies reported in Kilgour & Dalton
(1984) suggested that between 6 and 18% of lambs
can be stolen from their dam by another ewe; clearly
this would result in the wrong dam being recorded,
and therefore most likely the wrong sire. It is likely
that this level of inaccuracy is higher in flocks with
higher reproductive rates. DNA parentage testing
can assign offspring to parents with accuracy near
to 1.0, but this requires the use of many informative
genetic markers which in turn increases the cost of
the test. By using a lesser number of markers, a sub-
stantial proportion of the offspring can be accurately
93
assigned to one sire and one dam, with the remaining
lambs being assigned to multiple parents (Dodds
et al. 2005). This will still result in an increase in
accuracy because by using DNA parentage testing,
the lambs with multiple possible parents are known
accurately, whereas, when a shepherd assigns a
lamb to a mother, it is known there will be errors,
but the erroneous assignations are not known and it
is simply assumed that they are accurate.
The first DNA tests for performance traits in sheep
have been associated with litter size (Davis 2005),
with a marker test for the Booroola gene offered in
1993. However, there has been limited uptake of
these tests as there are sufficient ram breeders with
flocks already in the market with high genetic merit
for litter size.
In summary, the New Zealand sheep breeding
sector has a good track record in adopting suitable,
cost-effective, new technologies. Not surprisingly,
the cost of the new technology can slow the rate of
adoption, especially when the financial return to the
ram breeder may be some years in the future. As in
any industry, sheep farming has a sector that are
early adopters of new ideas and concepts, and it is
well recognised that these people act as mentors for
others in the industry.
NEW TECHNOLOGIES
Breeding goal
The breeding goal consists of two components,
estimates of genetic merit for the traits to be im-
proved (BV) and their economic values (EV). The
impact of new technologies on BV estimation will
be discussed below. Selection modifies the future
performance of animals and it is therefore the future
EV that are critical to assess. It has long been known
that the rate of genetic gain is tolerant to modest
inaccuracies of EV in most cases, but with some
important exceptions (Smith 1983). Nevertheless,
estimation of EV are compromised by many factors,
including fashion and market failure. Poor informa-
tion or market signals are characteristic across the
value chain due to prices and returns being held by
privately owned companies. The sharing of informa-
tion would enable breeders to better predict the EV
for (especially) product quality traits such as meat
tenderness and taste. Currently, most EV for the
New Zealand sheep industry have been estimated
by the application of farm models to determine the
value of a unit change in a trait. Such models are
94 New Zealand Journal of Agricultural Research, 2007, Vol. 50
typically simplistic, and the application of more
comprehensive bio-economic models to predict EV
would allow greater rigour to be applied. This will
result in more accurate selection of animals with the
best aggregate genotype, thereby improving the rate
of genetic improvement towards the breeding goal.
However, the improvement in genetic gain is likely
to be only modest.
Within-breed genetic improvement
Selection differential
In large nucleus flocks and/or group breeding opera-
tions there is an opportunity to increase the selec-
tion differential by selecting more intensely among
candidate male and female replacements. This can
be achieved by increasing the number of available
candidates or reducing the number of selected can-
didates. The latter corresponds to using fewer rams
and/or ewes. With the upper limit of natural mating
being 500 or so ewes per ram, significant gains in
the ram selection differential will only be achieved
through the application of artificial insemination
(AI) (Baker et al. 1990). However, the use of AI
in situations where the female is not regularly ob-
served to detect oestrus will require the develop-
ment or refinement of additional technologies such
as oestrus synchronisation, fresh semen AI and/or
long-life semen. Decreasing the number of females
used requires the reproductive rate of each ewe to
be significantly increased. While naturally achieved
litter sizes of four to five are already feasible, signifi-
cant gains in female reproductive rate will only be
achieved by some artificial means such as multiple
ovulation followed by embryo transfer (MOET).
Baker et al. (1990) showed that caution was needed
when using MOET due to improved rates of genetic
gain being offset by losses via inbreeding depres-
sion. Adult cloning (Wilmut et al. 2002) could be
used to produce more copies of high genetic merit
rams, obviating the need for AI (although embryo
transfer and other female reproductive technologies
will be required). A cost/benefit analysis is required
to assess the value of the additional genetic gain
against the cost of cloning. Other potential uses of
cloning are discussed below.
In a flock of constant size, a change in the sex
ratio of offspring can modify the selection differen-
tial. Current reproductive technologies provide for
intense selection on the male, and moderate selection
on the female pathways. Altering the sex ratio in
favour of more ewe lambs at the expense of fewer
ram lambs would provide for a greater increase in
female selection intensity than would be foregone on
male intensity. However, once again, semen sexing
technologies (see review by Evans et al. 2004) are
currently expensive, meaning the cost to benefit ratio
is unfavourable.
The selection differential can also be increased
by increasing survival to selection and then repro-
ductive age, and also by increasing the age at which
animals are culled from the nucleus (longevity). It is
unlikely that any technology will provide quantum
impact on these aspects of selection differential,
although they can be improved through management
and selection.
There is some potential to increase the annual rate
of genetic gain by increasing the selection differen-
tial from the current values of between 1.3 and 1.7 to
about 1.8 by selecting the top 1% of rams and 46%
of ewes assuming 130% of lambs are reared to time
of selection. If this percentage can be lifted to 200%,
the average selection differential can be increased
to 1.9. These figures do not assume the use of new
reproductive technologies, just the wider adoption
of existing technologies. The selection differential
could be increased even further if rams could be used
to the limit of their natural mating ratio (say 1 ram
to 500 ewes), however caution is needed to ensure
that rates of inbreeding are not unduly increased.
Predicting genetic merit
A first step in improving the accuracy with which
an animal's genetic merit is predicted is to ensure
that comprehensive, relevant and accurate industry
databases are available to record phenotypes and
pedigrees. New Zealand is fortunate in having a re-
cently built, web-based, data recording system in the
custodial care of Sheep Improvement Ltd (Geenty
2000). While New Zealand is currently in a strong
position relative to the sheep industries of other
countries, it should be remembered that the previous
sheep industry databases had been many years old.
It is not always economically feasible to introduce
the latest technology, and sometimes the transition
from the current technology to the new technology
can require substantial investment.
Once data have been recorded, statistical tech-
niques are used to manipulate the data to generate
predictions of genetic merit. These statistical tech-
niques are typically incorporated into computer
packages, and for the last decade it has been possible
to access free-ware off the web. Recent advances
in statistical theory have made little difference to
within-flock, within-breed genetic evaluations.
However, techniques such as BLUP have enabled
Blair & Garrick—New technologies in sheep breeding
across-breed and across-flock genetic comparisons,
which allows for greater selection intensity (but
probably requires the use of AI to increase the se-
lection differential), and a more efficient transfer of
genetic merit from nucleus to commercial flocks. It
is unlikely that improved statistical techniques will
have any great impact on the accuracy with which
BVs are predicted.
Reproductive technologies can be used to improve
the accuracy with which genetic merit is predicted.
While AI is used in the dairy industry to prove young
bulls by progeny testing before their genetic material
is widely spread throughout the industry, this is not
necessary in the sheep industry as a ram can generate
sufficient progeny by natural mating for an accurate
evaluation if required. Also, many traits of interest
in the sheep industry are measurable in both sexes,
whereas the dairy sector is heavily dependent on a
sex-limited trait. However, as mentioned earlier,
Rae (1976, 1984) showed that progeny testing for
meat-related traits could significantly increase the
annual rate of genetic gain.
Blair et al. (1990) and Baker et al. (1990) sug-
gested that metabolic or physiological phenotypes
could be used as indirect predictors of genetic mer-
it to significantly improve rates of genetic gain.
However, despite significant research effort (see
for example, Blair & Lee 1997; Xing et al. 1993;
Blair et al. 2002), none of these types of measures
have been applied in any livestock industry in New
Zealand. Recently, Primegro™ have begun offer-
ing a test for plasma levels of insulin-like growth
factor-1 (IGF-1) to Australian beef cattle and pig
breeders (www.primegro.com.au/html/fr_primeg-
ro_igf.htm). Analysis of several large datasets have
suggested that low plasma levels of IGF-1 several
weeks after weaning are genetically associated with
improved feed efficiency and improved leanness
(e.g., Bunter et al. 2005). However, data from the
Massey University IGF-1 flock (Blair, Kenyon and
Jenkinson unpubl. data) show that after some 15
years of selection for low plasma levels of IGF-1,
there is a significant decline in female reproductive
capacity. This provides a good example of the cau-
tion needed when using metabolic or physiological
indicator traits (and indeed DNA-related measures)
for selection when their functions are not completely
understood. It seems likely that the search for meta-
bolic/physiological indicators of genetic merit will
be superseded by measures of epigenetic marking
in the future, see below.
After more than two decades of intensive research,
technologies associated with DNA and RNA are now
95
beginning to show promise for application to assist
with genetic improvement (see review by Crawford
(2003), and earlier comments). DNA-related tech-
nologies are now offering a small number of tests for
specific sequences of DNA (e.g., microsatellites or
single nucleotide polymorphisms (SNPs)) associated
with desirable phenotypes. The use of tests associ-
ated with prolificacy genes was discussed earlier;
additionally DNA tests are now being offered for
muscling and disease traits by Catapult Genetics™
and Lincoln University, respectively (Hickford &
Zhou 2003; Johnson et al. 2005); it is not known
how many tests are being undertaken on an annual
basis.
DNA tests can improve the accuracy with which
the genetic merit of the animal is predicted. How-
ever, studies to date have only succeeded in finding
DNA sequences that control 3-15% of the genetic
variation of the trait in question, and consequently
it is still necessary to collect phenotypic information
on the animals and/or its relatives to provide a suf-
ficiently accurate BV for final selection decisions.
In addition, caution should be shown in applying
these tests widely in commercial populations before
the biological function of the (often unknown) gene
is determined. Applying positive selection pressure
to the "favoured" section of DNA will result in a
region of DNA (maybe a haplotype) moving to-
wards homozygosity in the population. The poten-
tial loss of the apparently less desirable haplotype
under negative selection pressure and indeed linked
alleles of unknown function must be considered.
This may be especially so when the alleles in ques-
tion lie in the major histocompatability complex
(MHC), in which it is typically considered that
greater heterozygosity is more favourable (Penn et
al. 2002).
It is worth reflecting where DNA tests will lead to
in the future. If it is accepted that most economically
important traits are controlled by a large number of
genes and that scientists will eventually identify all
these genes and the variants that cause differences
in performance, how will this information be ap-
plied to assist with selection? Blair (1997) pointed
out that even with a simple set of assumptions, it
appeared that there will be more possible genotypes
for the animals in a stud flock than could possibly be
observed and understood by a ram breeder. In fact
with current knowledge, it will be an impossible
task to identify which is the best genotype by direct
observation as there will be insufficient phenotypes
or even computer power to examine all possible
genotypes (Sherriff, Morel, and Blair unpubl. data).
96 New Zealand Journal of Agricultural Research, 2007, Vol. 50
Thus, new techniques for utilising this information
will be needed.
One approach to using the large amounts of data
that will be generated by DNA-related technologies
is that of genomic selection as suggested by Meuwis-
sen et al. (2001). Genomic selection requires a dense
marker map (probably SNPs), and a phenotypic ef-
fect to be assigned to each haplotype in every inter-
marker region. It is important to note that genomic
selection still requires phenotypes to be measured
on the animal or its relatives, although several cy-
cles of selection may be able to occur without the
need for re-estimating the association between the
chromosomal region and phenotype providing there
is an absence of epistasis. Genomic selection will
likely be applied to livestock industries before any
technique that selects solely on the known functional
genetic value for each allele affecting performance
(Blair 1997), because functional genetic values are
known for very few loci.
The sheep industry continues to be dominated
by phenotypes involving counting, weighing and
subjective scores, for the simple reason that the costs
associated with these measures are in keeping with
the value of the animal products. A variety of new
phenotypes have been available to sheep breeders in
New Zealand for some time, but their uptake is at
best variable. Some examples include GGT levels
for facial eczema tolerance, ELIS A tests for levels of
parasite burden, CT scanning for body composition,
ultrasonic measurement of backfat and muscle di-
mensions, video imaging of carcasses and chromium
oxide or alkane measures of feed intake. There will
be new opportunities for measuring new phenotypes
in the future (also see below), and it would be ben-
eficial for scientists with a genetics and breeding
focus to actively collaborate with scientists who have
nanotechnology and/or engineering interests. While
there will be serendipitous inventions that will offer
the opportunity to measure new phenotypes, active
collaboration should improve the odds of solving a
problem in a shorter timeframe.
In addition to the tools that are used to measure
phenotypes, a variety of new technologies are avail-
able to assist with more efficiently doing the same
historical tasks associated with performance record-
ing and selection. Most ram breeders will by now
be using electronic scales to measure animal and/or
fleece weights so that data can be downloaded into a
computer for transfer (possibly through the internet)
to the site of data analysis. Some breeders are using
electronic eartags to automate animal identification.
However, these tools do not change the accuracy of
predicting genetic merit (except perhaps by mini-
mising recording errors); they are more often used
from a labour efficiency perspective, which in turn
impacts on the cost efficiency of the entire breeding
programme.
There is only limited potential to increase the an-
nual rate of genetic gain by increasing the accuracy
of selection from the current values of between 0.2
and 0.4. The most obvious way to increase accuracy
is to undertake progeny testing, and this is certainly
feasible for meat-related traits as the generation in-
terval is only increased to 2 years for rams, providing
that rams are first used at 6 months of age. However,
the organisation and cost of progeny testing is not
attractive to many ram breeders. It may be more
desirable to hold the accuracy of selection at the cur-
rent levels by using DNA-related measurements and
metabolic/physiological phenotypes and decrease
the generation interval (see below).
Variability
Wide variation was previously seen as undesirable
by pedigree breeders when uniformity in a line of
animals was desired for aesthetic purposes. In more
recent times, uniformity has also been desired by
supermarkets to enable portion size to be consistent.
However, for nucleus breeders, increased genetic
variation increases the rate of gain. Within a breed,
there is little that individual nucleus breeders can do
to increase variation. However, they can minimise
the rate at which variation is lost by minimising the
degree of inbreeding. If several nucleus breeders
combine their resources, say through group breeding
schemes, variation can be maintained due to a larger
effective population size.
When considering the New Zealand sheep indus-
try in its entirety, variation can be increased through
the introduction of new breeds. New Zealand has
been fortunate in having a relatively wide range of
breeds introduced at various times throughout the
last 150 years. However, with the risks of disease
introduction, any further large-scale introductions
seem unlikely.
Subsequent to the release of the new breeds into
New Zealand in the early 1990s, a number of ram
breeders have formed a variety of new compos-
ite breeds. Composite breeds have the potential to
have increased genetic variation, however this is
dependent on adequately sampling the genetic vari-
ation from the foundation breeds contributing to the
composite. Tervit et al. (1986) reported the number
of ewes and rams sampled for the Finnish Landrace
(47 and 17) and Texel (70 and 16) imports in the mid
Blair & Garrick—New technologies in sheep breeding
1980s; these numbers do not include those imported
separately by Lamb XL. The founding numbers of
East Friesian sheep were 11 ewes and 4 rams (Al-
lison 1995). To the authors' knowledge, the impact
of the above sample sizes on levels of genetic vari-
ation in new composite breeds in New Zealand has
not been evaluated.
Reproductive techniques that increase the selec-
tion differential by decreasing the number of males or
females needed to produce the next generation will all
decrease the level of variation in a population. Thus,
procedures such as artificial insemination, embryo
transfer, and cloning must all be utilised with care
by balancing the gains in selection differential and
possibly reduced generation interval (see below),
with any loss of variation in the population.
While not typically considered to be of major
importance in the lifetime of most nucleus breed-
ers, mutations nevertheless play a role in providing
new genetic variation to any population of animals.
Some of the more obvious beneficial mutations are
those associated with fecundity, but also muscling
and polledness. Currently, there is no satisfactory
laboratory technique for increasing the rate of ben-
eficial mutations, although manipulation of DNA
at the base level (so-called genetic engineering),
should be considered a type of mutation. A flock
of sheep genetically modified to express human
alpha-1-antitrypsin (AAT) (Carver et al. 1993) were
briefly farmed in New Zealand. Low levels of AAT
in humans may lead to emphysema and liver disease;
it was intended to recover the protein from the milk
of transgenic sheep for human replacement therapy.
Unfortunately, little economic benefit accrued to
New Zealand as the sheep were destroyed before any
product was sold. In the future it may be possible to
use genome sequencing to identify new mutations
in order to characterise any effect on performance.
Molecular genetic tools can also be used to as-
sist with maintaining genetic diversity. By ensuring
genetic markers spread throughout the genome
are maintained in a heterozygous state, genetic
diversity can be maintained (Simianer et al. 2003).
However, while genetic improvement in the New
Zealand sheep industry remains under the control
of many ram breeders, loss of genetic diversity in
sheep is unlikely to be of major concern. This is
because, firstly, the many breeders bring to bear
multiple breeding goals thereby avoiding uniform-
ity, and secondly, there is a minor dependence on
reproductive technologies such as AI and embryo
transfer which might otherwise reduce the effective
population size.
97
The opportunities to increase the rate of genetic
gain by increasing the level of variation in a popu-
lation are limited. It is more important to ensure
that the selection practices do not reduce levels of
variation as a consequence of poor genetic sampling
when selection is very intense.
Generation interval
With natural mating, it is feasible to use only ram
lambs at mating, resulting in the male contribution
to the generation interval being 1 year. However,
while ewe lambs may also be used, the low litter
size requires the use of ewes for at least 2 years and
typically more. This results in a minimum contri-
bution of about 2½-3 years from the female side,
and an overall generation interval of about 2 years,
somewhat less than the current industry average.
However, there is often insufficient phenotypic
information recorded on the young animals to pro-
duce a sufficiently accurate BV for selection pur-
poses. Consequently, breeders are often prepared
to wait for an additional year before they choose
their breeding stock. For meat production systems,
it is feasible to select both rams and ewes prior to
6 months of age, and there is some evidence in the
New Zealand ram breeding sector of an increased
use of ram lambs (Garrick unpubl. data). There is
some evidence that offspring of ewe lambs perform
less satisfactorily than offspring from two-tooth
and older ewes (Morris and Kenyon unpubl. data).
Where the main purpose of a flock is to generate
genetic gain for the commercial sector, it could be
argued that superior phenotypic performance of
the stud stock is of little importance. However, the
reality is that ram breeders must compete with oth-
ers to sell their rams. If their stock are seen to be
in poorer condition, their genetic superiority may
be overlooked in favour of better grown animals.
This situation will only be resolved when ram buy-
ers truly understand the value of high genetic merit
rams (Garrick et al. 1992).
The generation interval may be further reduced
by the use of artificial reproductive techniques. For
example, ewe lambs may be superovulated to allow
the female contribution to the generation interval to
also drop to just 1 year, giving an overall generation
interval of 1 year. To obtain some selection pres-
sure on the female side, it will be necessary for the
ewe lamb to produce several offspring, which in
turn will require the use of embryo transfer. Other
reproductive tools offer the possibility of obtain-
ing gametes from pre-pubertal animals and even
foetuses (see below).
98 New Zealand Journal of Agricultural Research, 2007, Vol. 50
If ram breeders do reduce the age at which ani-
mals become parents, it will be necessary to find
new ways of measuring relevant phenotypes and/or
genotypes to maintain an acceptable level of accu-
racy of selection (see earlier comments).
Using natural mating of rams and ewes at
18 months and current phenotypes, the generation
interval could be reduced from the current 3-4 years
to about 2.7 years. If accuracy of selection could be
maintained through the use of DNA-related meas-
urements or the use of metabolic/physiological phe-
notypes, and rams and ewes first mated at 6 months
of age, the generation interval could be reduced to
about 1.6 years.
By combining the improvements in selection dif-
ferential and generation interval, while maintaining
accuracy of selection and variation at current levels,
the predicted rate of annual genetic gain could be
raised from the current 0.1-0.2 genetic standard
deviations to about 0.3 if rams and ewes are first
used at 18 months of age. However, if both sexes
are first used at 6 months of age this figure is lifted
to near 0.5 genetic standard deviations. This figure is
just 15% of the theoretical maximum of 3.4 genetic
standard deviations if the selection differential is
increased to 3.4, the accuracy of selection to 1.0,
and the generation interval reduced to 1 year.
Industry structure
Sheep farm business structures are going through a
period of rapid change. The traditional stud flock of
50 years ago has largely disappeared. The current
generation of ram breeders that has come to domi-
nate ram sales is less interested in pedigree informa-
tion, animal appearance and performing well at show
days. They have a greater focus on the increases in
productivity and profit that result from the use of
their sires. However, these performance-focused
breeders are being challenged by breeding con-
glomerates that are operating franchises throughout
New Zealand. These changes in business structures
may allow for improvements in genetic gain in the
ram breeding sector. For example, by spreading the
costs of some technologies over a larger number of
animals, it may become cost effective to use new
technology. However, ram buyers must not equate
large animal numbers to increased genetic gain. Un-
less at least one of the four components of genetic
change is modified, an increase in numbers per se
does not change the rate of progress. These larger
breeding organisations may also be able to improve
the way in which market signals are transferred from
the consumer to the breeder because the retailer has
more interest in talking to a significant supplier,
rather than trying to engage with hundreds of farm-
ers. If the economic values needed for the breeding
goal can be better specified, this will in turn improve
genetic change towards that goal.
The reproductive technologies described earlier
have the potential to reduce genetic lag between
nucleus and commercial breeders in the sheep in-
dustry. Because the nucleus breeders must retain the
genetically best animals in their flock to generate
genetic improvement, these animals are not available
to the commercial sector; they get to choose from
amongst the remainder. AI, embryo transfer and
adult cloning all have the potential to allow com-
mercial farmers access to the genetically elite stock
at the same time it is being used in the nucleus flock.
However, as has been mentioned before, while the
value of breeding stock remains of the order of
$ 1,000 the cost benefit ratio is not in favour of using
these technologies. In contrast, the international
dairy sector has used cloning to produce bulls. This
is feasible because of the high value of dairy bulls,
with the cost of cloning being recovered by the
widespread sale of semen.
Mating plans
The different mating plans of straightbreeding, in-
breeding and the various types of crossbreeding
have already received significant consideration and,
where useful, application in the New Zealand sheep
industry. Any new uses of mating plans will largely
be refinements of existing options. An example that
utilises the substantial computing power now avail-
able is the design of matings of individual animals
available today after consideration of the genetic
outcomes of future matings. Look-ahead mating
schemes such as Total Genetic Resource Manage-
ment (TGRM™) provides a portfolio of options to
livestock breeders to assist with constructing their
mating plans (Kinghorn 2000). As more is learned
about more complex genetic interactions such as
epistasis and genotype by environment interactions,
these effects may be included in look-ahead mating
schemes to provide genetically more desirable stock
in the future.
THE FUTURE
New technologies are preceded by a period of
innovative scientific discoveries that do not always
have obvious applications in farming and in animal
breeding in particular. However, there are a number
Blair & Garrick—New technologies in sheep breeding
of threads in science that may have application to
animal breeding within the next decade.
New phenotypes and communication systems
Advances in knowledge in biology, nanotechnology,
electronic engineering and communications will
probably lead to as yet unthought of opportunities
for remote measurement and communication of
phenotypes to a central point from which the ram
breeder can make selection decisions. Biosensors
have had a chequered history to date, with expec-
tations exceeding our biological and engineering
knowledge. This will change, and there seems little
doubt that it will be possible to detect in vivo events
in an animal at a remote location and communicate
those events to a place were the information can be
stored and interpreted as needed. While the emphasis
of this discourse is on animal breeding and genetic
applications, it is likely that these new systems will
find wider application as farm management tools
on commercial farms. This will be advantageous,
as it will mean more systems will be sold thereby
bringing down the per unit cost.
Epigenetic marking
The term epigenetics covers a variety of mechanisms
that enable heritable changes in gene expression
not caused by changes in the DNA sequence (e.g.,
Morgan et al. 1999). In the last decade the science of
epigenetics has grown rapidly to the point of being
mainstream, such that information on the human
epigenome is now appearing in the literature (e.g.,
Eckhardt et al. 2006); undoubtedly, farm animal
epigenomes will shortly follow. It is accepted that
epigenetic marking of the DNA is an integral compo-
nent of how cells will utilise the genetic instructions
provided by the DNA. More importantly, knowledge
is now accumulating about environmental factors
that can influence epigenetic marking (Gluckman &
Hanson 2004). Arguably the best known of these is
the long-term effects of being born small in human
populations, leading to the field of Developmental
Origins of Health and Disease (DOHaD). What is
more important in the current context is, firstly, is it
possible to identify animals with different epigenetic
markings, secondly, are some markings associated
with better/poorer health and/or productivity, and
thirdly, can epigenetic marking be modified through
management intervention? The application of knowl-
edge about epigenetic marking to benefit animal
improvement may only be a tool to better describe
permanent environmental effects, and hence to make
genetic evaluations more accurate. As yet, we do not
99
understand epigenetic marking well enough to know
whether it may also help with a better description
of genetic events such as heterosis and genotype by
environment interactions, but it would seem likely
that it will. However, knowledge about epigenetic
marking has tremendous potential in the commercial
tier of any animal industry, whereby farmers will be
able to better discriminate amongst potential replace-
ment stock regarding their lifetime profitability.
Nanotechnology
Drexler (1986) used nanotechnology to refer to
self-assembling nano-scale machines. However, the
term is now understood to have a wider meaning,
this being the manipulation of objects less than 1 μm
in size. This field of endeavour has rapidly shifted
from a new scientific discipline to mainstream sci-
ence. It is difficult to predict how nanotechnology
will ultimately impact on the genetic improvement
of livestock. However, it is quite conceivable that at
least new tools for measuring phenotypes and novel
means of communication will occur. Undoubtedly,
the early applications will likely be orientated to-
wards human medicine and military purposes rather
than in animal science, so the new generation of
animal scientists must keep abreast of developments
in nanotechnology in disparate fields to ensure that
new opportunities are identified and utilised for the
benefit of animal improvement.
Tissue culture
It has long been possible to grow some cell types
in tissue culture and more recently to grow rudi-
mentary organs (Lanza et al. 2002). It has already
been demonstrated that it is possible to grow muscle
tissue, but there are many hurdles to clear before
routine production of desirable, affordable meat is
achieved (Edelman et al. 2005). In the immediate
future, it is likely that the primary research drive
will be provided by scientists searching for solutions
for humans with muscle loss and/or dysfunction
rather than as a means of growing food. The impact
of tissue culture on the ram breeding sector will be
as an additional competitor in the marketplace, a
competitor that is likely to have strong attraction
to those with animal rights and/or sustainability
interests. The most likely impact will be to reduce
the need for meat animals and hence to reduce the
need for rams and ram breeding flocks. However,
the science required to achieve the in vitro growth
of muscle tissue that accurately mimics the qualities
of muscle tissue grown in vivo will probably lead
to other opportunities for novel ways of measuring
100 New Zealand Journal of Agricultural Research, 2007, Vol. 50
a wide variety of meat quality traits, giving rise to
a new suite of phenotypes that can be assessed to
assist the prediction of genetic merit.
Reproductive technologies
The term velogenetics was suggested by Georges &
Massey (1991) to describe what might be possible
in the future if oocytes could be harvested from
female foetuses and fertilised in an in vitro system.
Betteridge et al. (1989, cited by Georges & Massey
1991) suggested that such a system could double the
rate of genetic gain for dairy cattle milk yield rela-
tive to progeny testing. In vitro meiosis would en-
able the velogenetics system suggested by Georges
& Massey (1991) to achieve an even faster rate of
generation turnover and hence more rapid genetic
gain (Haley & Visscher 1998). Forsberg (2005) has
proposed that by using a combination of technolo-
gies, cloned transgenic males that produce mono-sex
sperm could be generated; this would obviate the
need for semen sexing.
CONCLUDING REMARKS
Innovative ram breeders in New Zealand have a
good track record of adopting appropriate tech-
nologies to assist with improving the rate at which
genetic progress is made. However, while the New
Zealand sheep industry continues to be dominated by
lambs returning $50-$ 100 to commercial farmers, it
seems likely that several new available technologies
will not be widely implemented in the near future.
This is because the economic benefits do not justify
the financial outlay required to implement the po-
tentially useful technologies. However, the cost of
new technologies typically decline with time and at
some point they may become beneficial to the sheep
improvement sector. Adoption of these new technol-
ogies is dependent on a close relationship between
influential ram breeders and the research community.
Adoption of available, cost-acceptable, technologies
could increase the annual rate of genetic gain from
the current 0.1-0.2 genetic standard deviations to as
much as 0.5 genetic standard deviations; this would
seem worthwhile.
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