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DNA fingerprints lift wool clip quality doption of genetic fingerprinting in the Merino industry is set to herald a dramatic improvement in the quality of the nation’s woolclip. The fingerprinting technology, developed by CSIRO Animal Production, will accelerate the genetic improvement of the industry by identifying rams and ewes with desirable traits and eliminating those with undesirable characteristics such as black or coloured wool. Some wool growers are already using the technology successfully and new developments have reduced the cost of the procedure, making it a viable option for more producers. The fingerprinting technology is based on a simple blood test carried out to isolate and characterise the animal’s deoxyribonucleic acid (DNA) and allows sheep breeders to identify the likely parents of a lamb. It is known as fingerprinting technology because, like fingerprints, DNA does not change and it is possible to determine the identity of a person or animal from a tiny blood sample. The technology is also based on methods used to help resolve disputes of human parentage. Accurate pedigree information can allow Merino breeders to achieve better estimates of their animals’ genetic value and quickly discard inferior animals from breeding flocks. Commercial wool producers will have the opportunity to buy rams that have been bred selectively for highly desirable qualities such as fine wool, no black wool and more efficient fleece growth. The technology will also help producers compare the merit of rams bought recently and those bought in the past as well as A • DNA fingerprinting technology is being used in the Merino industry to eliminate wool faults and improve fleece quality by determining the pedigrees of sheep with desirable and undesirable traits. • Farmers can prepare tests for DNA analysis by pricking the sheep’s ear, soaking the blood onto special filter paper and sending the sample to be analysed. inbrief • Results are sent to the farmer within a few weeks to help select ewes and rams. • Researchers are developing genetic markers for traits such as fleece weight and fibre diameter. 72 by Jane Rogers, KONDININ GROUP Science and Macquarie University aim to have the kit widely used in the Merino industry during the next 12 months. Traditional breeding methods CSIRO LIVESTOCK Breeding Sheep Merino breeders across Australia have the opportunity to adopt new technology which promises to eliminate undesirable characteristics from flocks. DNA fingerprinting technology is allowing breeders to identify the likely parents of a lamb. providing a clearer picture of the genetic trends in their flocks. Another benefit of DNA fingerprinting is that it provides commercial wool producers with detailed information about the value of sheep before they are bought and this should allow more flexibility when sourcing animals in the future. The ultimate aim of the work is to produce a genetic fingerprinting kit which will help speed the selection of breeding animals and lift the rate of genetic improvement in the national flock so wool can compete favourably with alternatives such as cotton. Project collaborators CSIRO Animal Production, Victorian Institute of Animal At present, Merino breeders who want pedigree information rely on a labour intensive system of running ewes in single sire mobs so they can track and record the parentage lines. But this method relies on tagging newborn lambs according to their apparent mothers and fencing an area into small paddocks to accommodate different sire groups. The CSIRO has estimated the cost in labour, watering and fencing to be as much as $15 per lamb. The accuracy of assessing flock pedigrees using this method also can be reduced by sheep breaking through fences and, more commonly, natural cross-fostering of lambs. In some cases researchers have found crossfostering errors of lambs to be 10% or more. DNA testing has shown cross-fostering levels of 10-20%. Other problems include reduced lambing percentages if a ram in a single sire paddock has a low fertility level. Due to these constraints only a proportion of Merino studs use some kind of pedigree information. Most only identify the sire with very few collecting a full pedigree. Researchers hope DNA fingerprinting technology will provide sheep breeders with a more precise and economical tool to identify the parents of lambs. The benefits of establishing accurate pedigrees for Merino sheep include: Quick results from DNA tests estern Australian Merino breeder John Dunne is using DNA fingerprinting in his stud breeding enterprise. W During the 1980s the Beacon-based farmer recorded the full pedigrees of his flock and progeny-tested several rams each year in order to make better breeding decisions. This exercise gave John a clear understanding of the costs associated with such an intensive operation in terms of the labour required to install and maintain fences and watering points, as well as for the collection and recording of data. To ensure that his replacement sires did not carry the recessive black gene, Mr Dunne maintained a flock of about 80 black ewes for a number of years and joined up to 15 at a time to his best performing rams each year. While a black or coloured lamb is now a rarity in the stud flock, they are still causing some embarrassment for Mr Dunne among some of his clients’ flocks. After hearing about the CSIRO’s DNA pedigree technology during 1997, Mr Dunne realised its enormous potential for identifying carriers of the black gene. With the co-operation of the CSIRO, a local veterinarian and his clients, Mr Dunne has tested about 75 sheep belonging to his clients, to specifically identify a number of black lambs and all their possible sires. There has been a significant reduction in the incidence of black lambs in all but one flock, and further testing this year using the technology is expected to eradicate all black sheep from their FARMING AHEAD No. 83 - November 1998 • More precise progeny testing of rams to improve estimates of their genetic value. • Tighter control of genetic improvement. For example, it is possible to eliminate sires or dams that carry genes for black wool, metabolic disorders or conformation faults. • Being able to plot genetic trends in the flock over time to obtain an average genetic value of the flock. Currently there is little objective knowledge about the rate of genetic improvement in the Merino industry. • Reduced inbreeding because breeders can monitor the relationships between rams and the ewes to which they are mated. Inbreeding can reduce fertility and wool production. DNA pedigree technology is also used widely in the racehorse and greyhound industries. Owners currently pay about $80 per head for a DNA test but the different structure of the Merino sheep industry makes such costs prohibitive. The CSIRO research team is fine-tuning a simple, inexpensive and accurate test kit ready for commercial release during late 1999. DNA testing is particularly suited to the Merino industry because of its hierarchical stud structure. This means the benefits of pedigree testing on a ram breeder’s flocks will spread throughout the industry without the need to test animals on an industry-wide scale. FIGURE 1 Sheep DNA The genetic make-up of a lamb is determined by the fusion of genetic material from its sire and dam. The unique combination of genes is established at fertilisation and provides a ‘blueprint’ for the lamb’s physical appearance. A gene is a tiny unit of DNA carried on ribbon-like structures called chromosomes. Each chromosome contains thousands of genes attached in single file along its length (see Figure 1). Chromosomes are made of two chains of DNA, arranged together to form a spiralling structure. Scientists use a process called polymerase chain reaction (PCR) to magnify areas of the DNA so they can isolate sections of genetic material that vary greatly between individual animals. These sections may vary in length or the DNA code may read differently. The PCR process involves heating and cooling a sample of DNA, which can be as small as one molecule, so that a specific fragment of the DNA can be copied many times, making it easier to identify and read. The highly variable DNA sequences are known as markers and scientists worldwide Parakeelya 9P681 which, apart from the black spot on his nose, gave all appearances of being a pure white ram. The black ewes were joined with Parakeelya 9P681. Black ewes by definition must carry two copies of the recessive black gene. DNA typing flocks. Mr Dunne considered the cost of $25 per DNA sample commercially viable in his situation, believing there was no other way he could have achieved such definitive pedigree information so quickly. FARMING AHEAD No. 83 - November 1998 While Mr Dunne has been using the technology to remove unwanted traits. He said the greatest benefit was likely to be in identifying animals with desirable characteristics and so increasing the rate of genetic improvement in the Merino industry. have identified 500 markers in sheep. The markers are used to identify a location on a chromosome that may be associated with a particular trait (see Figure 2, page 74). To determine parentage in Merinos, scientists have sifted through all the markers available and chosen to use 15 variable length DNA markers (also known as microsatellites). These microsatellites consist of different repeats of the DNA code. For example one animal may have a code with three repeats such as ABABAB while another will have six repeats such as ABABABABABAB. The number of times the code is repeated varies between animals but a parent will pass its motif to the next generation in exactly the same form. By studying enough of the microsatellites on different chromosomes it is possible to match a lamb’s DNA pattern to its parents’. To make the system commercially viable the CSIRO has chosen 15 markers so they can be tested simultaneously using one or two tests for each lamb rather than testing for each marker individually. Collection method In an effort to cut costs the CSIRO has devised a method where farmers can collect blood samples for DNA analysis rather than employing a veterinarian. The farmer needs to prick the lamb’s ear and soak the bloodspot onto special filter paper, taking care to record each sample accurately. The samples are sent to the CSIRO laboratory and the DNA extracted from the blood sample using a simple and inexpensive method. Robotics are used in the laboratory to handle the samples for optimum accuracy and to minimise labour costs. Pictured are Parakeelya 9P681’s progeny from the black ewes. The two black lambs are proof that 9P681 is a black ‘carrier’. Because the ‘white’ lambs are known to be progeny of 9P681 out of the black ewes, they too must be black carriers (heterozygous) and are destined for slaughter if females and castration if males. 73 LIVESTOCK Sheep... LIVESTOCK Sheep... The CSIRO is currently holding a trial with some Merino breeders to test for sire-only and full pedigree information. The aim of the trial is to streamline and enhance the system to ensure sheep breeders find it profitable to use DNA testing. Economic analyses carried out by the CSIRO have shown the cost of the test needs to be reduced to about $10-$15. At present each test costs about $25. FIGURE 2 Comparing DNA markers Mark Casey The first step The market demands wool growers produce consistent, high quality, clean wool free of black fibres.. The only labour-intensive stage of the testing is loading each DNA sample onto a special gel to enable analysis. After individual lamb samples are loaded, automated software is used to read the gel and the information is transferred to a computer program which analyses the results and generates a report to be sent to the farmer. The system has been developed to minimise labour costs and maximise efficiency at every stage, from blood collection, transmission of samples to the laboratory, genetic marker analysis to the final report to the farmer. DNA pedigree testing is the first step in molecular genetic technology and breeders who start recording the parentage of their sheep can take advantage of new genetic markers as they become available. The research team is using its parentage trials to measure important commercial traits such as fleece weight and fibre diameter, and subjective measurements such as colour and style of wool, in the hope that they will identify more markers for genes that contribute to variations in wool quality. As scientists are able to alter an expanding range of traits, farmers who are pedigreeing their flocks can immediately screen for the new markers at a relatively minor cost. It will then be possible to select sheep that have the highest chance of transmitting desirable traits to the next generation. Sheep breeders who want to take advantage of DNA fingerprinting Make your hay and Lamb 2 has inherited the upper marker band from its mother (ewe) and the lower band from its father (ram), indicating that these are the correct parents. Neither of the bands in Lamb 1 have been inherited from the ewe or ram. now have access to a new consultancy service developed by the CSIRO, known as Select Breeding Services. For further information contact Select Breeding Services or Ian Franklin at CSIRO Animal Production on phone (02) 9840 2700 or fax (02) 9840 2940. Cut and Dried Covers every aspect of fodder management from production and machinery maintenance to storage and feeding out. With 420 pages, Cut and Dried has practical ideas on making hay and silage, reliability and service tips on common machinery, and the best advice from leading Australian beef, dairy and sheep farmers. $ 40 Growing Oat Hay silage work harder. An essential addition to your office shelves whether you want to improve your profits from hay production or produce hay for the export market. With 120 pages, Growing Oat Hay has information on fertiliser rates, crop nutrition, disease management, oat varieties and specifications for export quality hay. $ 25 Phone 1800 677 761 to order these books 74 FARMING AHEAD No. 83 - November 1998