Genetic Testing

Genomics & Terminals

A Breeders Perspective

Steve Milne, Chair – Hypotrichosis Action Committee

As ‘seed stock’ producers we are increasingly being made aware of the research and development of genomic technologies in the Australian sheep industry. It is clear from the literature, and from the many presentations I have heard on the subject, that the greatest value in the use of genomic information will be in three areas. Firstly, through increasing accuracy of selection, because genomic information will enhance the accuracy of Australian Sheep Breeding Values (ASBV’s). Secondly, because genomic information will allow selection decisions for a number of traits to be made at an earlier age than is now possible, thus potentially shortening generation interval, and thirdly due to the ability to select for traits which we as breeders find difficult, expensive, or even impossible to measure on the live animal - the traits that have become known collectively as the ‘hard to measure’ (HTM) traits.

The current situation

When considering the role that genomics may have within the terminal sire industry, I chose to look at its potential role in selection for what I call ‘core’ and ‘non-core’ traits. The ‘core’ traits are those that have been traditionally selected for within this sector of the sheep industry, namely weight, fat, and muscle. There is also an argument to say that selection for parasite resistance through the measurement of worm egg counts (WEC) would also be considered a ‘core’ trait by a number of breeders.
In the case of many terminal sire breeding operations, by the time potential replacement animals are six months of age, breeders have already collected upwards of ten pieces of information relating to phenotype and pedigree. This allows the use of Australian Sheep Breeding Values (ASBVs) with accuracies in the range of 65 – 75 % in selecting both rams and ewes to use within a breeding program at 7 months of age. It follows therefore that we are practising early selection with reasonable accuracy, and so although genomic information will enhance the accuracy of selection for these core traits slightly, the gains over the current situation will be minimal.
The story for ‘non-core’ traits is quite different. As mentioned previously these traits include many which may not be possible to measure on live animals. Of particular interest to us are those traits directly linked to eating quality, such as shear force and intra muscular fat, although there are many others for which genomic information will possibly be the only information available, or at least the major information source, when estimating breeding values. It is here that genomic information will be of the greatest use in terminal sire breeding operations. It is also here that we have the greatest need for a reference population to both discover and validate genomic information.

Future challenges

There are many challenges for the sheep industry in relation to genomics, but three are of particular importance. The first is the uptake and use of genomic information by breeders, and the industry as a whole. History clearly shows us that there are different categories of users of new technologies within the sheep industry, ranging from the early adopters through to those that will never use the technology, no matter what the demonstrated advantage. The early adopters will embrace this technology, and they will be followed by the ‘second tier’ adopters, but only if a financial advantage or reward can be demonstrated. So here we come to the real crux of the problem – the early adopters will use the technology, in many cases regardless of the economics, because that is their nature. The second tier may dabble, but there will need to be a clearly demonstrated reward for them to adopt this technology in the long term – in short, a reward for effort. This is then the first challenge for industry – to reward those who use this technology through increased market share and financial returns.
The second challenge is how this genomic information is reported to breeders. Stand alone ‘molecular’ breeding values are of little use to me. What will be of greatest use, is the incorporation of genomic information into existing genetic evaluation programs, such as LAMBPLAN, with the inclusion of that information reflecting an increase in accuracy of breeding values. This will then mean that we as breeders, along with our commercial clients, are only dealing with one source of information. The challenge for industry here will be to forge cooperation between a number of commercial and research agencies to facilitate the sharing of information, as opposed to the duplication of testing and research.
The third challenge for industry is the maintenance of a reference population beyond the timeframe of the current Sheep CRC Information Nucleus. In the case of the ‘core traits’ mentioned earlier, there are a number of breeders, or breeding groups, that could be used in both the discovery and validation roles required of a reference population. It is in the ‘non-core’ situation that the real challenge exists, and it is here that the entire industry, from seed stock producers through to the consumer, must be engaged to allow the work already done on traits linked to eating quality and nutrition to continue. Putting it bluntly, that engagement must be financial, and it must be enduring – there will have to be greater returns for the higher quality product produced through the use of genomic information to allow industry to support relevant reference populations, and that support must be long term.


While genomic information will marginally improve the accuracy of selection for the ‘core traits’ of weight, fat and muscle in the terminal sire industry, it will have minimal effect on increasing genetic gain through the reduction of generation interval because terminal breeders already have the ability to select early with reasonable accuracy. It is clear, however, that there may be significant value to the terminal sire sector of the sheep industry in the area of HTM traits, which I have designated as the ‘non-core’ traits. The challenge for the industry is to develop a cheap reliable test, which may be incorporated into existing genetic evaluation programs, and to engage the entire industry in its uptake and use. Additionally, the sheep industry must work towards the maintenance of viable reference populations to allow genomic information to remain relevant to the industry population. Genomic information does have the ability to enhance what the lamb industry is producing, but only if the whole of industry is engaged in this ‘genomics revolution’.



What is Hypotrichosis?

The hairless condition, Hypotrichosis, is present in many mammalian species. From the literature relating to this condition, the indication is that in most cases it is a simple autosomal recessive trait, meaning that both parents must carry the recessive gene before there is any chance of it being expressed, and then the odds are one in four.
In sheep the condition has not been widely reported, however there is published evidence dating back to Popova-Wassina’s (1931) description of a ‘naked’ ram.
In the Australian sheep population the condition was first identified in the Poll Dorset breed by Dolling and Brooker (1966) and again by Mackie and McIntyre in 1992. In White Suffolks, the presence of the condition has recently been identified by a small number of stud breeder members. The gene was most likely introduced into the breed through appendix infusions of outside genetics in its development and improvement programs.
The ‘classical’ hypotrichosis phenotype in sheep exhibits a lack of fibres on the head and legs (and possibly the brisket and breech region)(Bawden, 2007). This mirrors the wool patterning phenotype, with the bareness being restricted to areas normally covered by shorter thicker hair fibres.
Observation of the skin from the bare areas shows a thickening of the epidermal layer, probably associated with an increased exposure to the elements. Microscopic examination of skin tissue by both Mackie and McIntyre (1992) and Bawden (2007) indicate an absence of fibres in the follicles, the degeneration of primary follicles into cyst-like structures, and the presence of cyst like structures associated with sebaceous glands.
In a terminal sire situation within commercial flocks Hypotrichosis is of little or no consequence, but in a breeding flock it requires some awareness and action. In addition, the AWSA Federal Council recognises that more White Suffolk cross lambs are being retained for breeding as prime lamb dams, so rather than ignore the problem, the White Suffolk breed has taken a proactive role.
The AWSA, through its Federal Council, is working closely with SARDI who have developed a DNA test which will identify sheep that carry this recessive gene. This means that AWSA members are able to test for the gene within their flocks, identifying its prevalence, and then move towards eliminating it from the breed.

Bawden, C.S. (2007) Milestone report : AWI/MLA Sheep Genomics Project SG306
Dolling, C.H.S.,and Brooker, M.G. (1966) A viable hypotrichosis in Poll Dorset sheep J Hered 57 : 87 – 89
Mackie, J.T., and McIntyre,B., ( 1992) Congenital hypotrichosis in Poll Dorset sheep. Australian Veterinary Journal, Vol 69, No 6.
Popova-Wassina, E.T., (1931) A Naked Lamb. J Hered 22 : 91 - 92