Identification of molecular markers for oocyte competence in bovine cumulus cells E. O. Melo*, D. M. Cordeiro † , R. Pellegrino ‡ , Z. Wei § , Z. J. Daye ¶ , R. C. Nishimura † and M. A. N. Dode* *Embrapa- Genetic Resources and Biotechnology, Bras  ılia, DF 70770-917, Brazil. † School of Agriculture and Veterinary Medicine, University of Brasilia, Bras  ılia, DF 70910-900, Brazil. ‡ Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA. § Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA. ¶ Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85721, USA. Summary Cumulus cells (CCs) have an important role during oocyte growth, competence acquisition, maturation, ovulation and fertilization. In an attempt to isolate potential biomarkers for bovine in vitro fertilization, we identified genes differentially expressed in bovine CCs from oocytes with different competence statuses, through microarray analysis. The model of follicle size, in which competent cumulus–oocyte complexes (COCs) were recovered from bigger follicles (≥8.0 mm in diameter) and less competent ones from smaller follicles (1–3 mm), was used. We identified 4178 genes that were differentially expressed (P < 0.05) in the two categories of CCs. The list was further enriched, through the use of a 2.5-fold change in gene expression as a cutoff value, to include 143 up-regulated and 80 down- regulated genes in CCs of competent COCs compared to incompetent COCs. These genes were screened according to their cellular roles, most of which were related to cell cycle, DNA repair, energy metabolism, metabolism of amino acids, cell signaling, meiosis, ovulation and inflammation. Three candidate genes up-regulated (FGF11, IGFBP4, SPRY1) and three down-regulated (ARHGAP22, COL18A1 and GPC4) in CCs from COCs of big follicles (≥8.1 mm) were selected for qPCR analysis. The selected genes showed the same expression patterns by qPCR and microarray analysis. These genes may be potential genetic markers that predict oocyte competence in in vitro fertilization routines. Keywords cattle, gene expression, microarray, oocyte quality Introduction Despite great improvements in assisted reproductive tech- nology (ART), the success of in vitro embryo production remains relatively low. Most of the oocytes used to produce in vitro embryos are recovered from small follicles (<6 mm in diameter), forming a heterogeneous population that must be matured in vitro. Since the original in vitro maturation (IVM) experiments (Heilbrunn et al. 1939), the process by which the most competent oocytes are selected to produce blastocysts remains similar and is still based on morpho- logical aspects of the oocyte cytoplasm and the number of layers and compaction of cumulus cells (CCs) attached to the oocyte surface (Armstrong 2001; Krisher 2003; Lon- ergan et al. 2003; Coticchio et al. 2004). However, there is increasing evidence that these morphological criteria are insufficient to precisely distinguish oocytes of high and low competence (Krisher 2003; Lonergan et al. 2003; Coticchio et al. 2004). Therefore, lack of full competence is a major factor responsible for the lower blastocyst rate when in vitro matured oocytes are used for ARTS as compared to the in vivo matured oocytes (Dieleman et al. 2001; Humblot et al. 2005; Assidi et al. 2008). Therefore, to improve IVM results and ART outcomes, a means to select the most competent oocytes is of great importance. Despite the accumulation of a great deal of knowledge obtained through IVM research, it is necessary to find more precise parameters to select the best quality oocytes to produce an elevated number of high quality blastocysts. The competence of the oocyte to produce high-quality blastocysts is acquired gradually during folliculogenesis by cellular and molecular events that provide the oocyte with the capacity to complete meiotic divisions, to be fertilized and to develop into a viable embryo (Fair 2003; Coticchio et al. 2004). The information about the molecular events needed for the acquisition of competence that takes place Address for correspondence E. O. Melo, Embrapa- Genetic Resources and Biotechnology, Bras  ılia, DF, 70770-917, Brazil. E-mail: eduardo.melo@embrapa.br Accepted for publication 18 July 2016 doi: 10.1111/age.12496 19 © 2016 Stichting International Foundation for Animal Genetics, 48, 19–29