Genome-wide association study (GWAS) for reproductive traits in Nellore heifers

Author(s)

Gerson Antônio de Oliveira Júnior

• Document type: Doctoral Thesis
• Press: Pirassununga.
• Institution: Universidade de São Paulo (USP). Faculdade de Zootecnica e Engenharia de Alimentos (FZE/BT)
• Defense date: 2017-03-24

Examining board members

José Bento Sterman Ferraz; Roberto Carvalheiro; Aline Silva Mello Cesar; Daniel Jordan de Abreu Santos; Adam Taiti Harth Utsunomiya

• Advisor: José Bento Sterman Ferraz; Marcos Vinícius Gualberto Barbosa da Silva

Abstract

Considering the economic importance of sexual precocity in beef cattle production system, the objective of this study was to explore genomic regions associated with heifer pregnancy (HP) and total number of antral follicle (NF) in a population of Nellore (Bos indicus) heifers. The dataset was composed by 2,283 animals, which were daughters of 78 sires, coming from three different commercial farms in Brazil. From these, 1,267 were genotyped with around 74 K SNP markers. After quality control analyses, the remained dataset was formed by 1,255 animals and 64,800 markers. Genotypic information of 42 sires was also available, and non-genotyped sires with more than five genotyped progenies in the dataset were imputed for the same marker density of the heifers. A Genome-wide Association Study (GWAS) was performed under a BayesB method to identify potential genomic windows (~1 Mb) that explained at least 1% of the total additive genetic variance of the traits. The pointed genomic regions were used in MeSH enrichment analyses as well as for genes searching. Haplotype blocks that span these potential genomic regions were fitted as classificatory effects in the BayesB model, aiming to estimate the effect of each allele of the heterozygous sires for these regions. The estimated heritabilities coefficients were 0.28 ± 0.07 and 0.49 ± 0.09 for HP and NF, respectively, with genomic correlation of -0.21 ± 0.29. The GWAS results pointed to significant genomic windows on chromosomes 5, 14 and 18 for HP and 2, 8, 11, 14, 15, 16 and 22 for NF. The MeSH enrichment analyses revealed significant (p < 0.05) terms associated with HP: Munc-18 Proteins, Fucose and Hemoglobins, and with NF: Cathepsin B, Receptors-Neuropeptide and Palmitic Acid. The pointed regions by GWAS harbored important genes that can help explain the genetic basis of the considered traits. A total of 15 haplotype alleles obtained better results (p < 0,10) than their alternative copy for HP and 16 for NF. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and can be useful to selection strategies in improving reproductive indices in Nellore cattle. (AU)

• FAPESP's process: 13/12097-9 - Genome-wide association studies (GWAS) applied to reproductive traits in Nellore heifers
• Grantee: Gerson Antônio de Oliveira Júnior
• Support Opportunities: Scholarships in Brazil - Doctorate