Reproduction in Domestic Animals

Reprod Dom Anim 43 (Suppl. 2), 359–367 (2008); doi: 10.1111/j.1439-0531.2008.01185.xISSN 0936-6768Use of Microarray Technology to Profile Gene Expression Patterns Important forReproduction in CattleACO Evans 1 , N Forde 1 , GM O’Gorman 1 , AE Zielak 2 , P Lonergan 1 and T Fair 11 School of Agriculture, Food Science and Veterinary Medicine, and the Conway Institute, University College Dublin, Dublin, Ireland; 2 Institute ofAnimal Breeding, Faculty of Biology and Animal Science, Wroclaw University of Environmental and Life Sciences, Wroclaw, PolandContentsFertility in cattle is a major component of many agriculturalenterprises and there is pressure to devise methods to improvethis. A number of approaches are ongoing, one of which is tobetter understand the cellular and molecular events of thedevelopment of reproductive tissues and to use these as targetsfor developing new strategies. Microarray technologies nowallow us the potential to determine the transcriptional profileof expressed genes in a given tissue. This review focuses on thetypes of microarrays available for studies in cattle andconcludes that genes associated with one or more of thecellular processes of cell survival ⁄ death, intracellular signalling,transcription and translation, cell division and proliferationand cellular metabolism are the main transcriptionalpathways that control the development of ovarian follicles,oocytes, early embryos and the uterine endometrium about thetime of the establishment of pregnancy.IntroductionFertility rates in cattle (pregnancies per insemination)are depending on the types of animals being bred andthe production system that they are in; however, ratesof more than 50% in multiparous animals (i.e. notheifers) are not often achieved (Diskin et al. 2006).Strategies that aim to improve fertility rates depend onimproving our understanding of organ, cellular andmolecular events that control reproduction and it is forthis reason that there is a great interest in determiningthe relationship between the expression of genes intissues and their consequences for fertility. A numberof recent publications have reviewed the potential formicroarrays and bovine reproduction (Niemann et al.2007; Smith and Rosa 2007; Wrenzycki et al. 2007;Bonnet et al. 2008; Mitko et al. 2008). In this review,we focus on the different microarray approaches andtechnologies that are in use and then go on to reviewthe genomics of ovarian follicle development, oocytedevelopment, embryo development and uterine functionabout the time of the establishment of pregnancyin cattle.Microarrays and Functional GenomicsThe term genomics was proposed in 1987 as thebringing together of molecular biology, cell biology andgenetics (McKusick and Ruddle 1987) and refers to thestudy of whole sets of genes and their interactions. Thestudy of the expression of particular genes at specifictimes in cells, that leads to a description of theirfunction, is termed functional genomics. Advances inthe scale and sophistication of DNA microarrays haveheralded a new era away from the traditional gene-bygeneapproach and towards the study of complexinterrelated processes that frequently occur in biologicalsystems. Although many different microarraysystems have been developed, the most commonly usedsystems are complementary DNA (cDNA) microarrays,oligonucleotide microarrays and high-density(Affymetrix-style) fabricated short oligonucleotidemicroarrays.Complementary DNA (cDNA) microarraysThe earliest and still most widely used form of geneexpression arrays are DNA microarrays where a presynthesizedprobe (cDNA or oligonucleotide) is spottedonto a support (Hager 2006). The first generation ofmicroarrays used cDNA as probes on glass slides(Schena et al. 1995). These early microarrays weregenerally available for human, rodent and other majormodel organisms, while those for cattle were developedlater and continue to be developed. Many of thesebovine cDNA microarrays are customized or specificfor particular research areas of interest, which has anadvantage of producing ‘bespoke’ in-house microarrays.Probes for cDNA microarrays are usuallyproducts of the polymerase chain reaction (PCR)generated from cDNA libraries or clone collections,using either vector-specific or gene-specific primers, andare printed onto glass slides or nylon membranes asspots at defined locations (Schulze and Downward2001). On most slides, genes are spotted in duplicate ortriplicate, where the cDNA in each spot is usually awhole gene or expressed sequence tag (EST) and isoptimally approximately 300–800 nucleotides long(Bryant et al. 2004). The availability of cDNA clonesets for arraying has depended on large-scale ESTsequencing projects that have resulted in millions ofEST sequences being deposited in GenBank; subsequentlythe complexity of these collections is reducedby the assembly of related sequences into clusters(Lyons 2003). Overall, cDNA microarrays have beenvital for the initial development and dissemination ofmicroarray technology. However, a range of technicalissues arise during their production; these include phagecontamination, incorrect annotation and errors in highthroughputproduction of probe sets generated fromtens of thousands of bacterial clones. These problemshave prompted a search for an alternative type of probeand spotted oligonucleotide microarrays have been onepopular alternative.Ó 2008 The Authors. Journal compilation Ó 2008 Blackwell Verlag