NEW OPPORTUNITIES IN GENETICS AND GENOMICS

Practical information for the Sheep Industry The following pages include practical information that the Sheep CRC has developed from the scientific research carried out during 2007–2014. It is intended as a source of information to help the Sheep Industry put into practice some of these new ideas.

Contents PRACTICAL WISDOM................................................................. 3 Genomics and DNA testing: new tools for ram breeders to accelerate genetic gain.............................................................................3 Breeding towards a poll flock with the Sheep CRC Poll test.......................... 10 Sheep CRC genomic test for Merinos—what are the benefits?...................... 15 Sheep CRC genomic test for maternal breeds—what are the benefits?.......... 19 Sheep CRC genomic test for terminal breeds—what are the benefits?......................................................................................... 24 Using Australian Sheep Breeding Values................................................... 28

CASE STUDY............................................................................ 32 New Opportunities for Merinos................................................................ 32 New Opportunities for Terminals.............................................................. 34 JIVET—Juvenile In Vitro Embryo Transfer.................................................. 36

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PRACTICAL WISDOM Genomics and DNA testing: new tools for ram

breeders to accelerate genetic gain

By Julius van der Werf, University of New England; Stephen Lee, University of Adelaide; and Lu Hogan, Sheep CRC

Key points ●● Genomics refers to the use of information from DNA samples. ●● DNA samples can be generated by collecting blood from an animal on a specific bar-coded card and sending this to a service provider (currently Sheep Genetics and Sheep CRC). ●● DNA tests are now available to determine parentage, poll status and to estimate breeding values for many economically important traits. ●● The Parentage test is accurate and compatible with other SNP-based tests. It requires a DNA sample from an animal and its probable parents and provides an alternative, labour saving method for determining sire only or full pedigree. ●● The Poll test identifies carriers of the horn gene and can assist in eradicating horns from a poll flock. ●● The Sheep Genomic test provides information about breeding value and this information is combined with pedigree and performance data in the Sheep Genetics database to increase the accuracy of Australian Sheep Breeding Values.

Introduction DNA technology has developed rapidly over the past decades and we can now relatively cheaply generate information from the DNA of individuals. Information from a DNA test can be used to predict traits or determine parentage. Taking a DNA test from an animal is sometimes referred to as ‘genotyping’ the animal. The Sheep CRC has developed a number of DNA tests useful for sheep enterprises. These are the Parentage test, the Poll test and the Sheep Genomic test.

How is a DNA test sample collected? A DNA test requires the collection of a small blood sample on a blood card. This can be done, for example, by making a small cut on the ear. Blood cards are provided when ordering tests, they are specially designed for collecting blood for the purpose of DNA testing. The cards are bar-coded and the identification number of the animal that the sample belongs to must be provided on the card.

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What tests are available? Parentage Test The Parentage test uses about 180 genetic markers (SNPs) to test whether animals are the likely parents of a particular animal. The test requires a DNA sample from the animal and its likely parents. The Parentage test is suitable for all breeds of sheep. The Parentage test based on DNA has a number of advantages:

Figure 1. SNP chip.

●● The test is expected to be more accurate than existing parentage tests for sheep. ●● The test is compatible with the other Sheep CRC SNPbased tests. This means that animals tested using the Sheep Genomic test will not need to be re-sampled by the breeder for parentage, as the genotyping has already been recorded. ●● It is a labour saving alternative to manually allocating lambs to their dams at lambing time. ●● It can be used to determine sire pedigree in syndicate matings.

Figure 2. Blood cards being used at lamb marking.

The Parentage test can be used for ‘full pedigree’, that is, linking a lamb to its dam and sire, or ‘sire pedigree’, linking lambs only to their sire. Alternatively, breeders may choose to only link ram lambs with the sires. It is very important to collect blood samples from all of the animals that need to be matched up. For example, failing to sample a sire makes it difficult to assign lambs to their sires. The same applies to sampling all ewes if full pedigrees are required.

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Potential parents may have been tested before, either in a Parentage test or via an Sheep Genomic test. In that case, these do not need to be tested again, but they need to be listed as potential parents using their Sheep Genetics ID (16 digit code). The Parentage test can determine DNA mismatches between progeny and sires or dams, in which case we can be confident that those are not the parents. There could, in some cases, be a match with more than one sire (or dam), for example, when the potential sires (or dams) are closely related. In most cases, it is then still possible to determine that one is more likely the parent than the other. However, in a small number of cases the test may have difficulty to assign parentage with full confidence. This can occur if there is only one potential parent or potential parents are highly related. In general, better results will be achieved if: ●● larger numbers of progeny are tested in the batch ●● at least two sires are nominated ●● both sire and dam are DNA sampled

Poll Test The Poll test has been developed by the Sheep CRC using measurements and DNA tests on animals in the Information Nucleus Flocks. The test is based on two genetic markers that are very close to the Poll gene. The test is normally used on Merinos. Identification of polledness only requires individuals of interest to be sampled. In most situations this involves sampling only the rams and possibly some ewes being selected for a breeding program. The information on poll status of both parents provides a prediction of the progeny’s poll status. The test provides an important opportunity for breeders to identify sires and dams that carry the Poll gene, and is therefore an effective tool to breed towards a purely poll flock. Another paper provides more detail and describes strategies on using the Poll test to eradicate the horned gene.

Sheep Genomic Test The Sheep Genomic test provides information on 12,000 genetic markers. These markers are SNPs (Single Nucleotide Polymorphisms) and refer to a single letter variation in the DNA alphabet. SNPs are usually neutral markers that are close to a gene (rather than within the gene), but they can predict differences in performance or phenotype due to genetic differences.

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The whole package of DNA, including the genes and the gene markers, is referred to as the genome, and selection based on the information obtained from many SNP markers is termed ‘genomic selection’. Genomic selection allows ram breeders to select animals for breeding using a DNA test in conjunction with phenotypic data and pedigree to increase the accuracy of Australian Sheep Breeding Values (ASBVs). Genomic selection is now revolutionizing animal breeding around the world. For example, most of the dairy bulls used for artificial insemination are now selected based on a genomic test; this has replaced a lengthy and costly process of progeny testing. Also, in sheep, we can predict the breeding value based on the genomic testing with some accuracy. This is especially useful for traits that we cannot measure easily on an animal before we make selection decisions. Genomic selection is therefore particularly useful for traits that are measured later in life, for example adult wool weight or mature weight, or reproduction, and for traits that are difficult to measure on breeding animals such as meat traits. Genomic selection works by DNA testing an animal and comparing its DNA profile with that of thousands of other animals that have been measured for traits used for selection. Based on this DNA comparison we can predict the breeding value of an animal. In Australia, we use information from the Sheep CRC Information Nucleus flock and the Sheep Genomics flock, which comprise close to 20,000 animals that have been DNA tested and measured for most important traits, including many meat quality traits. The MLA resource flocks continue to measure and genotype animals every year to maintain an ongoing data resource that can be used for predicting genomic breeding values. When an animal is tested, the DNA information is merged with other information in the Sheep Genetics database, such as pedigree, the breeding value of its parents and its own performance information; this is used to predict the animal’s breeding value. Ram breeders and ram buyers can use ASBVs to select animals based on genetic merit as they are the best prediction of breeding value, combining all the available information. The Sheep Genomic test is available for four breeds: Merino, White Suffolk, Poll Dorset and Border Leicester. To use the Sheep Genomic test the breeder must be a member of Sheep Genetics with the individual animals to be tested entered into the database with at least sire pedigree recorded. The test will provide information for almost all of the major traits reported by Sheep Genetics and is also used to provide ASBVs for some new traits that are generally not measured by breeders, such as carcase and meat quality traits.

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What is the benefit of using an Sheep Genomic test? Genomic information is most useful if the information about an animal is otherwise limited. Genomic information increases the accuracy of ASBVs, particularly early in the life of an animal when only few performance records are available. Increased accuracy has a positive impact on the rate of genetic gain. Table 1, below, shows how the value of genomic information changes as the animal gets older and information is gathered on its parents, the animal itself and siblings and progeny. Table 1. Accuracies of ASBVs change depending on the sources of information used.

Information used DNA test only Parents records (PR) PR + 20 half sibs (20H) PR + 20H + own info (OI) PR + 20H + OI + 20 progeny PR + 20H + OI + 100 progeny

Trait with heritability of 10% Without With genomics genomics 0 0.22 0.22 0.31 0.35 0.40 0.45 0.48 0.66 0.67 0.86

0.86

Trait with heritability of 30% Without With genomics genomics 0 0.39 0.39 0.51 0.49 0.58 0.66 0.69 0.84 0.85 0.95

0.95

The Sheep Genomic test is expected to significantly increase the ASBV accuracy for young rams. The accuracy increase can vary from 0.02 to 0.24 accuracy points. This means that breeders can select and use rams, especially at young ages when little phenotypic information is available, with more confidence than without this DNA information. Selecting rams more accurately and earlier is beneficial for breeding programs as higher rates of genetic gain can be achieved in a ram breeders flock with a high accuracy of selection of breeding animals combined with a short generation interval. For older rams with many progeny recorded, the ASBV accuracy will already be high (as shown in Table 1) and the additional gain in accuracy from the Sheep Genomic test is relatively small. The largest increases in accuracy will be for rams prior to first use when ASBV accuracy is low. Sheep Genomic testing will bring the accuracies of young rams closer to those of older rams, therefore making it more likely that they can be competitive for use in the breeding program.

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Using genomic selection will improve the rates of genetic improvement especially for traits that: ●● can only be measured late in an animal’s life, such as mature weight and mature wool production ●● have a low heritability and that can only be measured on females, such as reproductive rate ●● are not measured at all, such as carcase traits and eating quality traits The net outcome of DNA testing based on the Sheep Genomic test is faster genetic gain within the stud, which is then passed onto commercial flocks using rams from that stud. Refer to the other Practical Wisdom notes that quantify the likely benefits of genomic testing specifically for Merino, maternal and terminal ram breeding flocks and describe which and how many animals should ideally be tested in order to be cost-effective.

How do I get a DNA test? The blood cards needed for DNA testing will be provided when the genetic test is ordered via a designated website (via Sheep Genetics or another provider, currently the Sheep CRC). The card must clearly identify the animal being tested using its 16 digit Sheep Genetics identification code. Once the blood cards are returned to Sheep Genetics, they are forwarded on to a laboratory for analysis. The test results are returned to Sheep CRC and Sheep Genetics. Parentage and Poll results are returned directly to the breeder, whilst Sheep Genomic tests results are incorporated into the ASBVs provided by Sheep Genetics.

Take home messages ●● The Sheep Genomic test increases breeder confidence to use animals at a young age. ●● The Sheep Genomic test increases the rate of genetic gain in ram breeding flocks by increasing the accuracy of selection and reducing the generation interval. ●● Testing older animals is still beneficial due to the increased accuracy of ASBVs, but the quantum of benefit is reduced. ●● Commercial flocks benefit from the increased rate of genetic gain that ram breeders can achieve with genomic testing.

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Further information and to order tests Sheep CRC website: www.sheepcrc.org.au, then choose Genotyping tests. Sheep CRC Practical Wisdom notes: ●● Sheep CRC genomic test for Merinos—what are the benefits? ●● Sheep CRC genomic test for maternal breeds—what are the benefits? ●● Sheep CRC genomic test for terminal breeds—what are the benefits? ●● Breeding towards a poll flock with the Sheep CRC Poll test.

Acknowledgements The various DNA tests developed by the Sheep CRC are the result of the inputs of many collaborators including researchers from the CRC partners and the staff at the INF sites at Cowra and Trangie (NSW DPI) Armidale (UNE), Rutherglen and Hamilton (Victoria DEPI), Struan and Turretfield (SARDI) and Katanning (DAFWA) and the many breeders that contributed to the INF program. Data was also provided by Meat & Livestock Australia and Australian Wool Innovation Ltd via Sheep Genetics and the Sheep Genomics Program. The input of the Animal Genetics and Breeding Unit (AGBU) has been critical in the enhancement of the ASBVs with genomic information and Sheep Genetics have provided invaluable support during the pilot testing and the final delivery of the test information. We also acknowledge the input of the International Sheep Genomic Consortium (ISGC) in their work to develop the 50k SNP-chip and initiating the DNA parentage SNP panels.

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Breeding towards a poll flock with the Sheep CRC Poll test By Stephen Lee, University of Adelaide and Julius van der Werf, University of New England

Key points ●● Poll status is completely controlled by genetics; environmental factors have no impact. ●● Development of horns in sheep appears to be mostly controlled by a single gene. ●● The Poll test identifies carriers of the horn gene and can assist in eradicating horns. ●● Producers should consider horned status as only one trait in a breeding program. ●● The use of Poll test can reduce the chance of breeding horned Merino rams by 75% in just one year.

The genetics of horns and the development of the Sheep CRC poll gene test Observations of 2300 Merino progeny in the Sheep CRC Information Nucleus Flock has identified three possible gene combinations that determine whether a sheep is horned (H) or polled (P): HH, PH or PP. Because the horned gene is recessive, horned animals must carry the trait from both parents. By using DNA testing to identify whether an animal is PP, PH or HH, breeders can predict whether the progeny of a ram are more or less likely to have horns when mated to ewes with different genotypes. The Poll test is predictive of the horn status of tested animals. HH rams are almost always horned, whereas PH rams are rarely horned and PP rams are always polled. The poll test is based on a genetic marker and not on the gene itself. The accuracy of predicting poll status is about 95%. Prior to development of the Poll test, breeders relied on a visual assessment of the horn site and/or progeny testing, which takes many years to confirm whether a phenotypically polled ram is PP or PH. Overall, the Poll test will allow ram breeders to increase the number of PP rams and potentially capture the rewards given the commercial preference for polled Merinos.

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Which breeders can benefit? This test benefits ram breeders who want to produce more polled and fewer horned rams. Even though you may not see horns very often, the frequency of the horn gene can be quite high. In fact, even if only 1% of males appear with horns, the horn gene is still present in around 10% of the flock. This means that in 10% of matings a sire or dam could pass on a horn gene to its offspring and 18% of polled rams being used will be carriers of the horn gene. The new genomic test for the Poll gene Figure 1. Variety of horn phenotypes. means that, in poll flocks, breeding from rams that are carriers can be avoided. The terminology of polledness ●● Homozygous polled (PP) will only pass polled genes on to their progeny, and will mostly produce polled lambs. ●● Heterozygous polled (PH) can pass on either polled or horned genes to their progeny and are capable of producing lambs that are horned, polled or have scurs or half-sized horns (depending on the genetics of the other parent). ●● Homozygous horned (HH) will only pass horned genes on to their progeny and are capable of producing horned or polled lambs (depending on the genetics of the other parent).

How fast can the number of horned rams be reduced? Producers wanting to transition to a polled flock can achieve the desired outcome in a variety of ways. The pathway chosen will affect the time taken to achieve a polled flock and will also affect the cost. The Sheep CRC has researched the impact of various DNA testing regimes for breeding out the presence of the genes responsible for horns on Merinos based on a model flock to help inform breeders about the options available.

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The Sheep CRC has modelled the impact of DNA testing a poll flock with 1000 ewes, using 25 rams each year. Each year 10 of the rams are replaced by young rams and 410 new ewe replacements are needed. Based on a flock with a horn gene frequency of 10% (1% rams horned) the use of the Poll test only on rams to be used can reduce the chance of breeding horned Merino rams by 75% in just one year, where not selecting for horns or polls would generally result in six or seven horned rams born each year, but less than two annually if rams were tested and only full polls (PP) were used (Figure 2). It would take a little over 20 years to completely remove the horn gene from the flock. If ewes were tested as well, the response was even greater, with the chance of breeding horned Merino rams reduced by 80% in just one year (Figure 3), and the horn gene completely removed from the flock in just seven years.

Figure 2. Predicted number of horn rams born each year for three approaches to testing over a 20-year period where initial horn gene frequency was 10%.

In the transition to a poll flock there will also be rams with the PH genotype. These rams will show a variety of phenotypes from small bony knobs at the horn site hidden by the wool, through larger knobs obvious above the wool, to scurs that may curl back toward the skull, and finally to horns that can reach about half the size of the true horned genotype.

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While testing rams as well as replacement ewes reduces the frequency of the horn gene more quickly than just testing rams, the cost of testing is much higher and this should be carefully factored into breeding budgets. There is also potential for ram breeders to transition quickly from flocks where many more animals carry the horn gene. Based on the same model flock as above, but with a horn gene frequency of 50% the number of ram lambs born that will be horned can be reduced by over 90% in just one year by testing all new rams. This equates to a change from over 100 rams with horns born per year to fewer than 10 just by testing and using only homozygous poll (PP) sires. It is predicted that there would be less than three horned rams born per year after 10 years of using PP sires.

Figure 3. Predicted number of horn rams born each year for three approaches to testing over a 20-year period where initial horn gene frequency was 50%.

Take home messages ●● The Poll test allows breeders to accurately identify which animals are PP versus PH. ●● Rapid reductions in the number of horned animals can be achieved simply through testing sires and using only PP sires. ●● Even greater reduction in horn genes can be achieved by testing ewes as well, but this comes at a substantial cost.

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Further information Sheep CRC website: www.sheepcrc.org.au, then choose Genotyping tests. Sheep CRC Practical Wisdom notes: ●● Genomics and DNA testing: new tools for ram breeders to accelerate genetic gain. ●● Sheep CRC genomic test for Merinos—what are the benefits? ●● Sheep CRC genomic test for maternal breeds—what are the benefits? ●● Sheep CRC genomic test for terminal breeds—what are the benefits?

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Sheep CRC genomic test for Merinos—what are the benefits? By Stephen Lee, University of Adelaide and Julius van der Werf, University of New England

Key points ●● Genomic tests increase ASBV accuracy and, therefore, rate of genetic gain. ●● Genomic tests can increase overall genetic gain in Merinos by approximately 10–15%. ●● The accuracy increase is highest when there are limited Figure 1. Collecting blood measurements available, for example in young animals. samples onto a ‘blood card’ ●● The most cost effective use is to test mainly rams.

for genomics testing.

●● Test more rams than you need as replacements. ●● Test about 20% of the ram drop to achieve most of the extra genetic gain.

Introduction Genetic gain in sheep breeding programs can be made by identifying and selecting the best animals. Greater genetic gain is achieved when those animals can be more accurately selected and mated at younger ages. Australian Sheep Breeding Values (ASBVs) are based on performance and pedigree information, but can now also include DNA marker information from the Sheep Genomic test. This genomic test increases the accuracy of selection of young animals, especially for traits that are generally measured later in life, or not measured at all.

What increase in genetic gain can genomic tests offer? For all three Merino selection indexes reported by Sheep Genetics, genomic testing would add accuracy to ASBVs. This would increase the rate of genetic gain by approximately 10% where rams are first mated at 18 months and would be even higher (15%) if the best rams were first mated at 6 months. Note that in the latter scenario only the better rams are used at 6 months, typically around 70% of all rams used.

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Table 1. Predicted rates of gain ($/ewe/year) for various indexes with and without use of genomic testing on rams prior to selection.

MERINOSELECT Index

Merino Production Fibre Production Dual Purpose

Ram first use at 6 months Without Genomics $2.05

With Genomics

$2.06 $1.91

Ram first use at 18 months With Genomics

$2.34

Without Genomics $1.87

$2.36 $2.20

$1.91 $1.74

$2.10 $1.91

$2.05

Which animals should be tested and when? Test the best 20% of rams For many ram breeders who are already recording considerable performance and pedigree information, much of the potential gain from genomic tests can be obtained from testing a relatively small percentage of the ram drop. Rams that have poor ASBV and index values when identifying candidates for genomic testing are unlikely to be selected in the sire team and therefore breeders can focus on the top 20% of rams. Testing 20% of the ram drop is expected to give approximately 80% of the potential additional genetic gain from genomics compared with testing the entire ram drop for rams first selected at 6 months and over 90% of the gain when selection is done at 18 months. There is little benefit to be gained from testing more than 30% of the drop, as shown in Table 2. Table 2. Percentage of possible additional genetic gain achieved compared with testing 100% of the ram drop for first use of rams at 6 or 18 months old.

Proportion of ram drop tested 5% 10% 15% 20% 30%

Proportion of possible extra genetic gain First use at 6 months 27% 61% 79% 87% 94%

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First use at 18 months 29% 72% 88% 94% 98%

Test more rams than you will need Test more rams than you need as replacement sires so that the test results can be used to narrow your selection. Testing only the number of replacements that you need means you have already made your selection and the genomic tests will add no more gain than what you could achieve without them.

Test from a number of progeny bloodlines Sample animals from a number of progeny bloodlines or family groups to widen your pool of future sires, to maintain sufficient genetic diversity and avoid future inbreeding.

How are ASBV accuracies increased with the genomic test? The value of the genomic information depends on the increase in ASBV accuracy compared with conventional performance recording at the time of selection. The increase in ASBV accuracy is highest for traits that are measured later in life; increases tend to be smaller for traits where animals have had performance recorded prior to genomic testing. Traits that increase more in accuracy will have a relatively higher boost in genetic gain when using genomic selection. Table 3 shows the increase in ASBV accuracy for several important traits when first use of rams is at either 6 or 18 months. Table 3. Accuracy of some ASBV and indexes for rams at 6 and 18 months of age.

Trait

Post weaning WEC Yearling clean fleece weight Yearling mean fibre diameter Yearling CV fibre diameter Yearling staple strength Merino Production Index

6 months Without With genomics genomics 0.28 0.36 0.43 0.63 0.54 0.71 0.44 0.57 0.29 0.48 0.28 0.40

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18 months Without With genomics genomics 0.47 0.50 0.67 0.75 0.80 0.84 0.70 0.74 0.46 0.56 0.38 0.45

Take home messages ●● The Sheep CRC Sheep Genomic test increases ASBV accuracy, especially for young rams and for traits that are measured later in life. ●● More accurate selection will increase genetic gain. ●● Young rams can be used with more confidence, and using more young rams in the stud reduces generation interval. ●● General testing recommendations for the ram breeder: ○○ Test animals prior to selection. ○○ Test more animals than you need, about 20% of the ram drop. ○○ Consult with an advisor to optimize your testing strategy.

Further information Sheep CRC website: www.sheepcrc.org.au, then choose Genotyping tests. Sheep CRC Practical Wisdom notes: ●● Genomics and DNA testing: new tools for ram breeders to accelerate genetic gain. ●● Sheep CRC genomic test for maternal breeds—what are the benefits? ●● Sheep CRC genomic test for terminal breeds—what are the benefits? ●● Breeding towards a poll flock with the Sheep CRC Poll test.

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Sheep CRC genomic test for maternal breeds— what are the benefits? By Stephen Lee, University of Adelaide and Julius van der Werf, University of New England

Key points ●● Genomic tests increase ASBV accuracy and, therefore, rate of genetic gain. Figure 1. Border Leicester ●● Currently, there are modest potential increases in rate of genetic progress available through genomic tests for maternal ram breeders who already conduct extensive performance recording.

●● The accuracy increase is highest when there are limited measurements available, for example in young animals. ●● Maternal ram breeders can also benefit from the ability to include hard-tomeasure carcase traits such as eating quality.

Introduction Genetic gain in sheep breeding programs can be made by identifying and selecting the best animals. Greater genetic gain is achieved when those animals can be more accurately selected and mated at younger ages. Australian Sheep Breeding Values (ASBV) are based on performance and pedigree information, but can now also include DNA marker information from the Sheep Genomic test. This genomic test increases the accuracy of selection of young animals, especially for traits that are generally measured later in life, or not measured at all.

What increase in genetic gain can genomic tests offer? Genomics has the potential to deliver increases in the rate of genetic gain for the maternal breeds that can use genomics (currently Border Leicester).

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Although increases for standard traits are modest, more importantly, the Sheep Genomic test generates breeding values for three new and important carcase traits: Lean Meat Yield (LMY), intramuscular fat (IMF) and shear force (ShearF5), the latter two are associated with eating quality. Breeders who use an Sheep Genomic test are receiving Research Breeding Values from Sheep Genetics for these traits with accuracies typically between 40% and 50%. This is sufficient accuracy to make selection decisions. If initial selection is based on traits such as post weaning weight, post weaning eye muscle depth and post weaning fat, which can be readily recorded, but may have unfavourable genetic correlations with hard-to-measure traits such as eating quality, then there is a risk that genetic merit for eating quality may decline. Breeders are already adopting the use of genomics as a tool to screen young rams, so they can improve both traits. Testing approximately 20% of the ram drop and incorporating carcase trait ASBVs into selection will allow producers to simultaneously improve eating quality (through higher intramuscular fat) and lean meat yield. Also, as the genomic tests continue to improve, a greater amount of variation in hardto-measure, but economically important traits, such as number of lambs weaned, will improve. This is expected to result in substantial increases in genetic gain for maternal breeders that use genomics in the future.

Which animals should be tested and when? Test the best 20% of rams For many ram breeders who are already recording considerable performance and pedigree information, much of the potential gain from genomic tests can be obtained from testing a relatively small percentage of the ram drop. Rams that have poor ASBV and index values when identifying candidates for genomic testing are unlikely to be selected in the sire team and therefore breeders can focus on the top 20% of rams. Testing 20% of the ram drop is expected to give approximately 80% of the potential genetic gain compared with testing the entire ram drop for rams first selected at 6 months.

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Table 1. Proportion of possible additional genetic gain achieved compared with testing 100% of the ram drop for first use of rams at 6 months old.

Proportion of ram drop tested Proportion of possible genetic gain 5% 27% 10% 61% 15% 79% 20% 87% 30% 94%

Test more rams than you will need Test more rams than you need as replacement sires so that the test results can be used to narrow your selection. Testing only the number of replacements that you need means you have already made your selection and the genomic tests will add no more gain than what you could achieve without them.

Test from a number of progeny bloodlines Sample animals from a number of progeny bloodlines or family groups to widen your pool of future sires, to maintain sufficient genetic diversity and avoid future inbreeding.

How are ASBV accuracies increased with the genomic test? The value of the genomic information depends on the increase in ASBV accuracy compared with conventional performance recording at the time of selection. The increase in ASBV accuracy is highest for traits that are measured later in life; increases tend to be smaller for traits where animals have had performance recorded prior to genomic testing. Traits that increase more in accuracy will have a relatively higher boost in genetic gain when using genomic selection. Table 2 shows the increase in ASBV accuracy when genomics is used for several important traits when first use of rams is at 6 months old.

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Table 2. Accuracy of some ASBVs for rams selected for use at 6 months old.

Trait Birth weight Weaning weight Post weaning weight Post weaning eye muscle depth (C) Post weaning fat depth (C) Post weaning WEC Yearling greasy fleece weight Number of lambs weaned Maternal $ Index

Without genomics 0.52 0.63 0.64 0.64

With genomics 0.62 0.71 0.71 0.67

0.68 0.60 0.15 0.14 0.39

0.69 0.61 0.27 0.16 0.43

Take home messages ●● The Sheep CRC Sheep Genomic test increases ASBV accuracy, especially for young rams and for traits that are measured later in life. ●● More accurate selection will increase genetic gain. ●● Young rams can be used with more confidence, and using more young rams in the stud reduces generation interval. ●● General testing recommendations for the ram breeder: ○○ Test animals prior to selection. ○○ Test more animals than you need, about 20% of the ram drop. ○○ Consult with an advisor to optimize your testing strategy.

Further information Sheep CRC website: www.sheepcrc.org.au, then choose Genotyping tests Sheep CRC Practical Wisdom notes: ●● Genomics and DNA testing: new tools for ram breeders to accelerate genetic gain. ●● Sheep CRC genomic test for Merinos—what are the benefits? ●● Sheep CRC genomic test for terminal breeds—what are the benefits? ●● Breeding towards a poll flock with the Sheep CRC Poll test.

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Acknowledgements The various DNA tests developed by the Sheep CRC are the result of the inputs of many collaborators including researchers from the CRC partners and the staff at the INF sites at Cowra and Trangie (NSW DPI) Armidale (UNE), Rutherglen and Hamilton (Victoria DEPI), Struan and Turretfield (SARDI) and Katanning (DAFWA) and the many breeders that contributed to the INF program. Data was also provided by Meat & Livestock Australia and Australian Wool Innovation Ltd via Sheep Genetics and the Sheep Genomics Program. The input of the Animal Genetics and Breeding Unit (AGBU) has been critical in the enhancement of the ASBVs with genomic information and Sheep Genetics have provided invaluable support during the pilot testing and the final delivery of the test information. We also acknowledge the input of the International Sheep Genomic Consortium (ISGC) in their work to develop the 50k SNP-chip and initiating the DNA parentage SNP panels.

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Sheep CRC genomic test for terminal breeds— what are the benefits? By Stephen Lee, University of Adelaide and Julius van der Werf, University of New England

Key points ●● Genomic tests increase ASBV accuracy and, therefore, rate of genetic gain. ●● Genomics provides valuable information on hard-to-measure meat traits, including lean meat yield and intramuscular fat. ●● Genomics will allow terminal ram breeders to simultaneously select for improved eating quality and lean meat yield. ●● Using current selection indexes, there are modest potential increases in the rate of genetic progress for standard traits through use of genomic tests.

Introduction Genomic testing offers terminal ram breeders substantial potential opportunity to identify and select rams that are superior for lean meat yield (LMY) and eating quality traits. To date, terminal ram breeders have successfully used current selection indexes and measurements for growth, muscle and fat depth to achieve substantial genetic gain. It is expected that clearer price signals will develop for LMY and eating quality in the medium term. The Sheep Genomic test developed by the Sheep CRC provides information on many traits including LMY and eating quality traits. The Sheep Genomic test will allow breeders to incorporate selection for LMY and eating quality, for which there was previously limited information.

What increase in genetic gain can genomic tests offer? The likely largest benefit of genomic tests for terminal ram breeders lies in the ability to make selection decisions based on information for hard-to-measure traits. For example, genomics increases the accuracy of selection for traits that could not be routinely measured before including eating quality. With the use of genomic testing, it is possible for these traits to now be considered in the selection process, since genomic breeding values can be predicted with some accuracy for these traits.

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The Sheep Genomic test generates breeding values for three new and important carcase traits: lean meat yield (LMY), intramuscular fat (IMF) and shear force (ShearF5), the latter two are associated with eating quality. Breeders who use a Sheep Genomic test are receiving Research Breeding Values from Sheep Genetics for these traits with accuracies typically between 40% and 50%. This is sufficient accuracy to make selection decisions. If initial selection is based on traits such as post weaning weight, post weaning eye muscle depth and post weaning fat, which can be readily recorded, but may have unfavourable genetic correlations with hard-to-measure traits such as eating quality, then there is a risk that genetic merit for eating quality may decline. Breeders are already adopting the use of genomics as a tool to screen young rams, so they can improve both traits. Testing approximately 20% of the ram drop and incorporating carcase trait ASBVs into selection will allow producers to simultaneously improve eating quality (through higher intramuscular fat) and lean meat yield. For terminal ram breeders already conducting extensive performance recording there are currently modest increases in accuracy for most ASBV at time of selection when using genomic testing. For example, increases in accuracy for weight and carcase traits were between 5 and 7% percentage points, however, post weaning worm egg count had a substantial increase, going from 30% to 40% accuracy. Overall, the use of genomics was predicted to increase rate of gain by 3% for the Lamb 2020 selection index. These small predicted increases are because many of the traits in the Lamb 2020 selection index can be recorded on the animal prior to selection at 6 months. This results in a relatively high ASBV accuracy at time of selection even without the use of genomics.

Which animals should be tested and when? Test the best 20% of rams In flocks that already do extensive performance recording, testing the best 20% of the ram drop is expected to give approximately 80% of the potential additional genetic gain compared with testing the entire ram drop when rams are first selected at 6 months.

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Test more rams than you will need Test more rams than you need as replacement sires so that the test results can be used to narrow your selection. Testing only the number of replacements that you need means you have already made your selection and the genomic tests will add no more gain than what you could achieve without them.

Test from a number of progeny bloodlines Sample animals from a number of progeny bloodlines or family groups to widen your pool of future sires, to maintain sufficient genetic diversity and avoid future inbreeding.

Take home messages ●● The Sheep CRC Sheep Genomic test gives information on many traits. ●● There are now lean meat yield and eating quality breeding values that are informed by the Sheep Genomic test. ●● The Sheep Genomic test increases ASBV accuracy for young rams and for traits that are measured later in life. ●● General testing recommendations for the ram breeder ○○ Test animals prior to selection. ○○ Test more animals than you need, about 20% of the ram drop. ○○ Consult with an advisor to optimize your testing strategy.

Further information Sheep CRC website: www.sheepcrc.org.au, then choose Genotyping tests Sheep CRC Practical Wisdom notes: ●● Genomics and DNA testing: new tools for ram breeders to accelerate genetic gain. ●● Sheep CRC genomic test for Merinos—what are the benefits? ●● Sheep CRC genomic test for maternal breeds—what are the benefits? ●● Breeding towards a poll flock with the Sheep CRC Poll test. ●● New Breeding Values for Yield and Eating Quality technical note.

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Acknowledgements The various DNA tests developed by the Sheep CRC are the result of the inputs of many collaborators including researchers from the CRC partners and the staff at the INF sites at Cowra and Trangie (NSW DPI) Armidale (UNE), Rutherglen and Hamilton (Victoria DEPI), Struan and Turretfield (SARDI) and Katanning (DAFWA) and the many breeders that contributed to the INF program. Data was also provided by Meat & Livestock Australia and Australian Wool Innovation Ltd via Sheep Genetics and the Sheep Genomics Program. The input of the Animal Genetics and Breeding Unit (AGBU) has been critical in the enhancement of the ASBVs with genomic information and Sheep Genetics have provided invaluable support during the pilot testing and the final delivery of the test information. We also acknowledge the input of the International Sheep Genomic Consortium (ISGC) in their work to develop the 50k SNP-chip and initiating the DNA parentage SNP panels.

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Using Australian Sheep Breeding Values What is an ASBV? ASBV stands for Australian Sheep Breeding Values. They are the national language for benchmarking sheep based on their genetic merit and are produced by Sheep Genetics. ASBVs describe a sheep’s breeding value for a trait, e.g. fleece weight or body weight, and express the relative breeding value of sheep across different breeding flocks of that breed (or across breeds in the case of Terminal breeds). They are equivalent to estimated breeding values (EBVs) used in other livestock industries e.g. BREEDPLAN in the beef cattle industry.

Why are ASBVs more effective than raw measurements when selecting sheep? ASBVs incorporate all of the available pedigree and performance data of the sheep and its relatives, making the genetic estimate far more accurate than raw measurements alone. The calculation of ASBVs also removes environmental effects that can obscure a sheep’s breeding value. Environmental effects removed include birth type, rear type, dam age and differences between management groups. Because management differences between drops of progeny and flocks are removed, ASBVs can be directly compared across age groups and flocks, which is not possible if using raw measurements.

Which traits should I use? As a ram breeder or a ram buyer there are a large number of traits that can be reported as ASBVs. However it is up to the individual to use the traits relevant to them. Particularly when starting, choose just a few ASBVs to use. These should be the traits you consider most important in your breeding program. More can be incorporated in the future if they are important to you. In the past, ASBVs were only reported for measured traits, however visually assessed traits are now being scored to an Australian standard allowing body structure and conformation traits and wool quality traits to be reported as ASBVs in the near future.

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Is a high or low ASBV better? ASBVs are reported as above and below an industry base of zero. The optimum value for any ASBV depends on the particular trait and your breeding objective. If you consider a high raw measurement better, e.g. higher fleece weight, then a higher ASBV is better. If you consider a lower raw measurement better, e.g. a low worm egg count, then likewise a lower ASBV is better. For some traits you will prefer a value in between, e.g. a fine-medium fibre diameter or a moderate amount of carcase fat, likewise the ASBV should be neither high nor low.

What raw measurement is the average ASBV for a trait? ASBVs cannot be expressed as a raw measurement because the raw measurement will depend on the age of the sheep and the environment they are experiencing. For instance, if one ram and 50 ewes, all with a body weight ASBV right on average were mated, then the average raw body weight of the lamb progeny, could be very different if they were raised under different management at Cowra or Bendigo or Narrogin. The genetics are the same, but the environmental conditions differ. If another ram was joined to the same average ewes and he had a body weight ASBV of 2 (2 kg heavier than the average) then the progeny will be about 1 kg heavier (as they only get half of) than those from the first ram at the same age, whether raised at Cowra, Bendigo or Narrogin. The progeny of ram 2 are only 1 kg heavier than ram 1 because only half of their genes come from the ram. As you start to use ASBV you will quickly gain an understanding of how a trait’s ASBV values relate to raw performance in your environment and at a particular age.

What does the accuracy of an ASBV show? The accuracy indicates how reliable the ASBV is at predicting the genetic merit of the sheep’s progeny. An ASBV with an accuracy of 95% is highly accurate, whereas one that is 55% is moderately accurate. The accuracy of an ASBV increases as a sheep has more data for that trait from itself or its relatives. Sheep Genetics have threshold accuracy levels that vary for each trait and are the level considered accurate enough to report the ASBV. Only ASBVs above the accuracy thresholds are published.

Figure 1. Pen cards with ASBVs

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Table 1. Example of ASBVs reported for an animal (Trait Leader values are highlighted) Animal ID

YWT

AWT

YEMD

YCFW

YFD

YDCV

YSL

YSS

YWEC

NLW

7%DP

7%

10%ss

14%ss

505045-2005-

0.5

-0.1

-0.1

-3.0

-3.3

-0.6

-3.5

-0.5

-17

-3%

123

133

148

146

050134

87%

86%

59%

88%

93%

89%

88%

86%

72%

35%

Why do ASBVs change over time? The initial published ASBV for a sheep may be based on limited data, such as the ASBVs of its parents. As more data is provided for the sheep, from itself and its siblings and later its progeny, then a trait’s ASBV may change to reflect that extra data, and will also become more accurate.

In what units are ASBVs shown? For most ASBVs the unit is the same as the raw value of the underlying trait, such as kilograms for body weight (WT), where a body weight ASBV of 7 indicates a sheep is 2 kg heavier genetically than a sheep with an ASBV of 5. The exceptions are fleece weight, worm egg count and number of lambs weaned, which are shown as a percentage, e.g. an ASBV of 5 for clean fleece weight (CFW) indicates the sheep has a 5% heavier fleece weight than a sheep with a clean fleece weight ASBV of zero.

What is a selection index and how can it be used? A selection index combines the ASBV performance for a number of traits into one value. There are many different indexes, each reflecting different breeding objectives or different emphasis on different traits. The higher the index value a sheep has, the more suitable it is for the objective defined by the index. Index values are very easy to use and are a good starting point. They provide a summary of the sheep’s performance for the traits in the index—they are like a headline in a newspaper. But just like a headline you need to look at the detail—in this case the ASBVs, before finalising selection. It is critical you use an index that matches your breeding objective and you also account for traits that are not in the index when making selections.

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How do I use a percentile chart? Percentile charts show the range of each ASBV value for the drop that is approximately 1 year old. The table allows you to benchmark ASBV and index performance to the current range in industry standards. The left column in the table shows the percentile band. The 50% band is average performance for the drop. The 10% band shows “trait leaders” and is the performance of the 10% most extreme performers in the drop for that trait or index.

Table 2. ASBV and Percentile band table (MERINOSELECT)

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CaseStudy

CASE STUDY

New Opportunities for Merinos Mark Murphy, Karbullah Poll Merinos, Qld There is enormous potential for producers of the Merino breed to bolster productivity and grow their markets by embracing the genomic technology developed by the Sheep CRC, but current industry attitudes need to change to encourage more producers to adopt.

About Mark Murphy Mark Murphy is the principal of Karbullah Poll Merinos, located 70 km north of Goondiwindi on the Queensland-NSW border. Showing the adaptability of the Merino breed, the 3200-hectare operation takes in Brigalow and Belah country, ironbark ridges, and a mixture of red and grey soils and native and introduced pastures. Although located in a 600 mm mostly summer rainfall area, the variability in climate means management strategies include sowing more than 150 ha to Old Man Saltbush to assist with drought proofing. “Unlike a lot of studs servicing the Merino industry, we operate at the geographical periphery of the industry,” Mr Murphy said. “This means we are extra conscious of the production challenges faced by commercial producers, and it is also why we’ve been involved in the Sheep CRC’s genomics projects because they allow us to more accurately target the traits that we need to be profitable.” Mr Murphy said that in order to capture the full potential on offer from genomic technology, industry should be united in encouraging the uptake of research advances. “We’ve used genomic data in selecting for shear force and intramuscular fat and I’m busting at the seams to apply the technology to other traits as well, but we have been held back by drought and seasonal conditions,” he said. “Depending on their individual circumstances, producers will travel at their own speed in adopting new technology, but we should ensure that the leading producers can lead without being burdened by industry structures that hold them back from trying new things.

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“Genomic technology and ASBVs will allow producers to increase the speed of genetic gain in their flock by targeting traits that are either difficult to assess visually or can only be measured after slaughter.” Mr Murphy said genomic research offered the industry the opportunity to make significant advances in the areas of animal welfare and lamb survival, where progress by producers has been limited despite research having shown more than 10 years ago that selecting for positive fat was a major influence on fertility and constitution. “In our conditions survivability is vital and industry needs to ensure producers are more in touch with research breeding values so that we can get the most out of them,” he said.

Take home messages ●● Genomics offers Merino producers the ability to accurately target specific traits not easily identified visually, which are important to their business and farming environment. ●● Opportunities include improving on-farm animal welfare and lamb survival rates. ●● Industry should encourage producers to engage with new research, even if it challenges conventional wisdoms.

Further information ●● www.sheepcrc.org.au ●● www.karbullahpollmerinos.com.au

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CaseStudy New Opportunities for Terminals Murray Long, Pendarra White Suffolks, NSW By placing meat quality traits at the forefront of genetic selection, Murray Long and the Australian White Suffolk Association are positioning themselves as key suppliers of rams to help the industry continue to meet consumer demands for tender and flavoursome lamb.

About Murray Long Murray Long is the principal of the Pendarra White Suffolk Stud at Ardlethan, NSW, and immediate past president of the Australian White Suffolk Association and committee member of the Superwhites Group. The Superwhites group of 20 White Suffolk breeders was an early participant in the Sheep CRC’s genomics program, and Mr Long has been leading the charge in redesigning his breeding program to maximise the gains on offer from DNA testing for hard to measure traits such as meat eating quality. “People used to worry about how to fit genomics into their flock management, but it’s actually a question of building your management around the benefits DNA testing offers,” Mr Long said. In particular, he says the additional accurate information on offer from DNA testing will allow him to manage for antagonistic traits such as intramuscular fat and lean meat yield, as well as traits that are hard to measure in his arid environment such as worm resistance. “Meat eating quality is too important to ignore. As consumer choice increases you can’t have your genetics years behind market demand,” he said. “Genomics is not only a way of getting a better product for my commercial producers and ultimately consumers, but I can also use genomics to make my management a lot easier and a lot more streamlined.” Mr Long DNA tests 25–30 per cent of his ram lambs each year using the Sheep CRC’s Sheep Genomic test.

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“The ultimate thing that genomics will give you is that consistency of product because genes are not affected by feed or the climate so once you have analysed the genes for these meat eating quality traits it is not going to change.”

Take home messages ●● DNA testing can accurately identify breeding stock with hard to measure traits including meat eating quality. ●● Set clear breeding objectives and select stock according to a consistent genetic profile. ●● Adoption will lead to more consistent product for consumers and labour savings on-farm.

Further information ●● www.sheepcrc.org.au ●● www.pendarra.com

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CaseStudy JIVET—Juvenile In Vitro Embryo Transfer Andrew Michael, Leahcim Poll Merinos, SA The JIVET program is super-charging the speed of genetic gain in Andrew Michael’s flock. It has already delivered stud lambs years in advance of those from his conventionally joined flock, thanks to a combination of visual appraisal, traditional measurement techniques, and the latest DNA testing and embryo collection methods.

About Andrew Michael Andrew Michael is the principal of the Leahcim Poll Merino Stud based at Snowtown, SA, but with sheep spread across three properties encompassing vastly different environmental conditions. Mr Michael says the key to breeding sheep that can perform in these different environments and deliver against the profit drivers for his business, is to understand their genetic make-up. He has done this through over 30 years of data collection for ASBVs and more recently through the Sheep CRC’s DNA testing programs. “Understanding fat and muscle traits are important because I want to transform the Merino to being an animal that can perform in every environment, as well as being more productive in terms of fleece weight, wool production and number of lambs weaned,” Mr Michael said. “The major benefit that genomics has delivered for us is that we can make breeding decisions much earlier and with a lot of confidence. Before we even scan the rams, we have an idea of what genetic groups they should go into and what these rams can offer in terms of hard to measure traits.” In the JIVET program, Mr Michael is using genomic technology to make those selection decisions even earlier, with superior breeding stock now being identified within weeks of birth; advanced embryo technology is then used to collect eggs from ewe lambs at approximately six to eight weeks of age; with joining occurring in a test tube before the lambs are carried to term in surrogate mothers.

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“For the first time we can do rapid genetic evaluation and do it very accurately, and this dramatically shortens the generation interval,” Mr Michael said. “The dollar returns are staggering—we estimate the superior genetics will deliver an $8 increase in returns from every ewe lamb every year compared to a figure of just over $2/ewe per year for our conventional program.”

Take home messages ●● Embryos are harvested from ewe lambs at 6–10 weeks of age—there are no long term impacts on natural reproductive performance. ●● Eggs and semen from top ram lambs are fertilised in vitro then carried to term by recipient commercial ewes. ●● In the space of six months a new drop of high performance lambs are on the ground—traditional breeding methods would have taken up to 2 years.

Further information The JIVET program was implemented with assistance from the Sheep CRC and SHEEP GENETICS, with design support from Greg Popplewell, Total Genetic Resource Management, and Stephen Lee, University of Adelaide. ●● www.leahcim.com.au ●● www.sheepcrc.org.au

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CJ Hawkins Homestead, University of New England, Armidale NSW 2351 Phone: 02 6773 1317 Facsimile: 02 6773 1400 Email: [email protected] www.sheepcrc.org.au