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Application of Integrative Genomics and Systems Biology to Conventional and in Vitro Reproductive Traits in Cattle

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Application of Integrative Genomics and Systems Biology to Conventional and in Vitro Reproductive Traits in Cattle DOI: 10.21451/1984-3143-AR993 Proceedings of the 31st Annual Meeting of the Brazilian Embryo Technology Society (SBTE); Cabo de Santo Agostinho, PE, Brazil, August 17th to 19th, 2017. Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle Gianluca Mazzoni1,6, Hanne S. Pedersen2, Gerson A. de Oliveira Junior3, Pamela Alexandre3, Eduardo M. Razza4, Henrik Callesen2, Poul Hyttel1, Marcelo F.G. Nogueira5, Jose Bento S. Ferraz3, Haja N. Kadarmideen6, 7 1Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark. 2Department of Animal Science, Aarhus University, 8830 Tjele, Denmark. 3Research Center on Animal Breeding, Biotechnology and Transgenesis, FZEA, University of São Paulo, Pirassununga, SP, Brazil. 4Department of Pharmacology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil. 5Department of Biological Sciences, School of Sciences and Languages, São Paulo State University (UNESP), Assis, SP, Brazil. 6Section of Systems Genomics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark. Abstract The combined GS-IVP-ET procedures are not routinely implemented yet. While it is possible to Assisted reproductive technologies (ARTs) collect embryo biopsies for DNA genotyping without have a strong impact on breeding especially when affecting the pregnancy rate of the embryos (Saadi et coupled with genomic selection (GS). The routine al., 2014), the IVP-ET efficiency is still relatively low implementation of in vitro production (IVP) and GS of and remains the bottleneck in this process. A possible embryos before embryo transfer (ET) in breeding way to increase the efficiency of IVP-ET procedures is companies is not yet possible. Improvement of oocyte identification and selection of high-quality oocyte donor and embryo recipient quality is needed to make donors and embryo recipients. In order to successfully realistic a commercialization of these procedures in the predict donor and recipient cow quality in IVP near future. A better understanding of both biological procedures, a better understanding of the molecular mechanisms and molecular markers associated to IVP- mechanisms responsible for these traits is needed ET related traits is necessary to improve the prediction (Salilew-Wondim et al., 2010). of donor and recipient cow quality for IVP procedures. The literature provides a complex picture of the The huge amount of data generated from high molecules associated with oocyte competence at throughput technologies has a tremendous impact in the different molecular level: proteomics, transcriptomics search for biomarkers of complex traits. This paper (Jiang et al., 2010; Gilbert et al., 2012; Nivet et al., reviews integrative genomics and systems biology 2013) and metabolomics (Matoba et al., 2014). approaches as applied to both Bos indicus and Bos Furthermore, numerous studies focused on the taurus cattle reproduction by both conventional and characterization of the expression profiles of granulosa ARTs such as OPU-IVP. The integration of systems cells from follicles at different developmental stages biology information across different biological layers (Hatzirodos et al., 2014b; Girard et al., 2015) and generates a complete view of the different molecular physiological condition (Hatzirodos et al., 2014a). networks that control complex traits and can provide a Research in recipient cows on transcriptomic profiles strong contribution to the understanding of traits related has usually been applied to the endometrial tissue, and to ARTs. this has increased the knowledge about molecular mechanisms responsible for good or inadequate uterine Keywords: systems biology, IVP, reproduction, cattle, environment for pregnancy recognition and biomarkers, data integration. implantation (Salilew-Wondim et al., 2010; Forde and Lonergan, 2012; Ponsuksili et al., 2012; Minten et al., Introduction 2013; Killeen et al., 2014). In the same way endometrial gene expressions have been characterized both during Breeding for more efficient animals is the estrous cycle and early pregnancy before implantation becoming of increasing importance, and new and faster (Bauersachs et al., 2005; Mitko et al., 2008; Bauersachs breeding methods are needed. Assisted reproductive et al., 2009; Mansouri-Attia et al., 2009; Ponsuksili et al., technologies (artificial insemination (AI), ovum pick-up 2012) as well as after implantation (Bauersachs et al., (OPU), IVP and ET) have significantly contributed to 2006; Binelli et al., 2015). animal breeding programs. Similarly, genomics has Considering the huge amount of data generated significantly increased both speed of genetic gain and by use of modern high-throughput technologies at all selection accuracy (Kadarmideen et al., 2015). levels of biological systems (e.g. genome-wide, However, the greatest benefits of those tools can only be transcriptome-wide, metabolome-wide or proteome-wide expected when they are combined, allowing animals to measurements), systems biology analysis is the most be selected accurately early in life and with a more promising approach to provide a holistic view of precise estimation of their breeding value. important biological mechanisms and of molecular _________________________________________ 7Corresponding author: [email protected] Received: May 22, 2017 Accepted: June 21, 2017 Mazzoni et al. Systems biology of reproductive traits in cattle. markers associated with complex traits, such as those (www.gift.ku.dk) aimed to identify biomarkers for the related to IVP-ET procedures. Systems biology is a selection of superior oocyte donor and embryo recipient holistic approach to analyze and decipher complex cows, and (iii) a GWAS for the identification of biological systems through computational and candidate genes and metabolic pathways for early mathematical modeling of the whole set of molecular puberty and reproductive traits in Nellore heifers. networks within an organism. Systems biology aims to decipher systems structures (the network of gene Integrative systems biology analyses and application interactions and biochemical pathways), but also the to IVP related traits in cattle dynamic changes of these network under different conditions (Kitano, 2002; Chuang et al., 2010; To correctly predict donor and recipient quality Kadarmideen et al., 2011; Kadarmideen, 2014). A huge we need a list of biomarkers and biological processes to part of the computational methods in systems biology is be included in the prediction methods for the selection based on network approaches that identify group of of the best donor or recipient cows. This implies genes or molecules with common behavior assuming gathering enough information about specific molecules that clustered molecules are functionally related and biological processes associated to the IVP-ET (Brazhnik et al., 2002). As reviewed in (Mazzoni et al., performance of the animals. 2015), several approaches are available to build gene The definition of a biomarker is strictly interaction or association networks: Co- dependent on the field of study. The features of a expression/regulatory patterns (Horvath, 2011), biomarker are described by Austin Bradford Hill's Bayesian networks (Friedman et al., 2000), Random guidelines (Aronson, 2005) and here adapted to the Forest Tree approaches (Breiman, 2001) or Artificial context of IVP related traits: strength (a strong Neural Networks (ANN) (McCulloch and Pitts, 1943; association between marker and IVP-ET outcome), Cookson et al., 2009). consistency (the association identified in the cow Integrative systems biology is based on reference set should persist in cow populations from analyses of networks of different types of molecules different farms and different physiological status of the trying to integrate information at different biological cows), specificity (the biomarker should be associated levels (Dixon et al., 2007; Mazzoni et al., 2015; with the specific IVP-ET related trait), plausibility (the Suravajhala et al., 2016; Wang and Michoel, 2016). The biomarker should be part of meaningful biological analyses of a specific outcome (blastocyst rate and mechanisms), coherence (the biomarker and the quality or endometrial receptive competence) with biological functions performed should be consistent systems biology methods together with the integration with previous knowledge), analogy (previous findings of systems biology approaches at different biological for the same association make the biomarkers more levels is of vital importance for identification of valuable). Furthermore, in order to be routinely applied biomarkers for incredibly complex traits like IVP and in IVP-ET procedures, the biomarker should be easily ET outcome. accessible and the costs of its measurement affordable. While above we discussed about ARTs, it is According to the guidelines the search for a biomarker very important to apply integrative systems biology is not an easy task. Until now, the search of biomarkers approaches also to conventional cattle reproduction via for IVP related traits have been based mainly on GS and genomic breeding. Fundamental to this are transcriptomic data for two reasons: first, it allows Genome Wide Association Studies (GWAS). A very amplification of small samples (Orozco-Lucero and important proportion of the world beef production trade Sirard, 2014) and second, it provides information about comes from tropical and subtropical regions.
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