Contents lists available at ScienceDirect Livestock Science journal homepage: www.elsevier.com/locate/livsci Genome-wide associations and detection of candidate genes for direct and maternal genetic effects influencing growth traits in the Montana Tropical® Composite population Laís Grigoletto a,b, ⁎ , Luiz Fernando Brito b , Elisângela C. Mattos a , Joanir Pereira Eler a , Fernando Oliveira Bussiman a , Barbara da Conceição Abreu Silva a , Rosiane Pereira da Silva a , Felipe Eguti Carvalho a , Mariana Piatto Berton c , Fernando Baldi c , José Bento Sterman Ferraz a a Department of Veterinary Medicine, Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Avenue Duque de Caxias Norte, 225, Pirassununga, São Paulo 13635-900, Brazil b Department of Animal Sciences, Purdue University, West Lafayette, IN, USA c Department of Animal Sciences, Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University, Jaboticabal, São Paulo, Brazil ARTICLE INFO Keywords: Biological pathways Composite Crossbreeding Growth Genome-wide association Tropical beef cattle ABSTRACT The Montana Tropical® Composite beef cattle have been developed in Brazil to serve as a genetic resource to meet the consumers’ needs for higher-quality meat while animals are raised in extensive production systems under tropical conditions. In order to optimize the selection process for economically important traits in this population, various genetic and genomic studies are still lacking. In this regard, the aim of this study was to assess genetic parameters and identify genomic regions and potential candidate genes associated with various growth traits, using the single-step Genomic Best Linear Unbiased Predictor (ssGBLUP) method. Approximately 400,000 cows, bulls and progeny had measurements for birth weight (BW), weaning weight (WW), yearling weight (YW) and post-weaning weight gain (WG). A total of 1394 animals were genotyped for 27,199 SNPs (after the quality control) to enable implementation of weighted single-step genome-wide association studies. The traits included in this study were shown to be moderately heritable (i.e. heritability estimates ranging from 0.16 ± 0.01 to 0.33 ± 0.04) and the genetic correlations ranged from 0.60 ± 0.067 (between WW and WG) to 0.88 ± 0.08 (between BW and WW). Single-trait weighted genome-wide association studies enabled the identification of 83 genomic regions for direct genetic effects (all traits) and 29 genomic regions associated with maternal genetic effects on BW and WW traits. Furthermore, biological processes and pathways associated with survival to adult age, calf behavior, fatty acid metabolism, muscle development, fertility, and immune system were identified. The findings of this study greatly contribute to a better understanding of the genetic architecture of growth traits in the Montana Tropical® Composite population. Furthermore, the genomic regions identified can be given more importance (weight) when implementing genomic selection for these traits, by using weighted ssGBLUP or Bayesian approaches. 1. Introduction Composite populations are formed by crossing individuals from two or more breeds with the purpose of exploiting heterosis and com- plementarity between them (Gregory et al., 1999). This has been done in various species, including sheep (e.g., Brito et al., 2017), dairy cattle (e.g., Cole and Silva, 2016), and beef cattle (e.g., Dodenhoff et al., 1999; Gregory et al., 1994; Lund et al., 2014; Hay and Roberts, 2018). In this regard, the Montana Tropical® Composite (Fig. 1) was developed by crossing animals from four different biological types (i.e., breed groups) termed NABC (Ferraz et al., 1999). The genetic variability obtained by combining these four complementary biological types re- sults in animals with better carcass yield and meat quality while still retaining important adaptation and robustness characteristics. These traits are paramount to obtain high performance in challenging en- vironments, particularly in tropical regions with harsh environmental conditions (Ferraz et al., 1999; Hansen, 2004; Porto-Neto et al., 2014). Growth traits are key variables associated with the profitability of beef https://doi.org/10.1016/j.livsci.2019.09.013 Received 19 March 2019; Received in revised form 25 July 2019; Accepted 12 September 2019 ⁎ Corresponding author at: Department of Veterinary Medicine, Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Avenue Duque de Caxias Norte, 225, Pirassununga, São Paulo 13635-900, Brazil. E-mail address: lgrigoletto@usp.br (L. Grigoletto). Livestock Science 229 (2019) 64–76 Available online 13 September 2019 1871-1413/ © 2019 Elsevier B.V. All rights reserved. T