BMC Genomics 2006, 7:42 http://www.biomedcentral.com/1471-2164/7/42 tFDhiiegff uelorregenr1caetidoNooftrhmeamlQea-Qn plot for the modified T value of Differenced Normal Q-Q plot for the modified T value of the log ratio of the mean. The expected normal deviate (normal score) is plotted against the difference between the observed order statistic and the expected nor- mal order statistic (95% confidence limits shown in red). Data is combined from all 16 slides of the experiment. ESTs more highly expressed in resistant animals are shown on the right while ESTs more highly expressed in susceptible animals are shown on the left. Background Grazing ruminants are constantly exposed to natural chal- lenge by gastrointestinal nematodes. Infection by such parasites leads to clinical disease and production losses and is a serious problem in animal husbandry. The eco- nomically important gastrointestinal parasites of sheep belong to the Order Strongylida and the family Trichos- trongyloidea and include Teladorsagia (Ostertagia), Tri- chostrongylus, Nematodirus and Haemonchus spp. The host response to parasite challenge is complex and poorly understood due to its polygenic nature. The response var- ies from sheep breed to sheep breed and from animal to animal [1]. The response can result in rapid or delayed expulsion of parasites and the host response is critical for determining subsequent parasite status [2]. Resistance to nematodes is primarily due to acquired immunity and is largely a Th2 type response [3-8] although innate immu- nity is also thought to play a role [9]. Sheep lines which have been selected to be resistant to one particular nema- tode species have been shown to have increased resistance to other nematode species [10-13] primarily due to a non- specific mechanism of parasite expulsion [2]. Historically anthelmintic drenching has been used to control nema- tode infection, however, the efficacy of this treatment is decreasing as parasite resistance to anthelmintics increases and nematodes resistant to multiple classes of anthlemintics are now found worldwide [14]. The use of chemicals in food production is also increasingly encoun- tering public hostility [15]. An alternative method of helminth control is vaccination of host animals. This strategy has successfully combated many bacterial and viral diseases, however, despite exten- sive research there is currently no vaccine available against the major gastrointestinal parasitic nematode species [15- 17]. This is most likely due to the number of nematode species infecting the host and the complex parasite life cycle which expresses different antigens at each stage. A natural method of parasite control is breeding for host resistance. Resistance to internal parasites, as measured by faecal egg count (FEC), has moderate heritability (h2 = 0.23–0.41, [1]) and this method has been shown to make significant genetic gains in a variety of sheep breeds [18- 24] due to the combination of reduced FEC and reduced pasture contamination. The current method of animal selection is cumbersome and inefficient, however, as ani- mals are selected based on their phenotype. Genetic gain could be accelerated if animals were selected on genotype rather than phenotype. Lines of Perendale sheep have been divergently selected for parasite resistance and susceptibility at AgResearch, New Zealand since 1986 and differ in FEC by 4.9 fold [24]. The number of adult nematodes in the gastrointesti- nal tract of animals from the resistant line is also lower than that from the susceptible line [25]. Resistant animals therefore have an increased genetic capability to respond to and subsequently reject parasites when challenged. The identification of genes involved in this process would allow the development of genetic markers, which could be used in marker assisted selection breeding programs. A previous study identified genes differentially expressed between the selection lines in response to parasite chal- lenge, but the use of challenged animals confounded the resistance status of the animals with level of infection. This study also did not distinguish innate from acquired immunity [25]. We therefore chose to look at those genes that were differentially expressed between the selection lines regardless of the level of infection by using naïve ani- mals that had never been exposed to gastrointestinal nem- atodes. We did this using high-throughput DNA microarray technology. This allowed us to examine the relative expression of thousands of genes in a single exper- iment and to group genes into expression classes, provid- ing insight into their biological function. Page 2 of 12 (page number not for citation purposes)