Imputação de sequência completa do cromossomo x e associação genômica ampla para características da reprodução na raça holandês

Abstract

Reproductive efficiency is an essential factor for the sustainability of dairy cattle production. However, improving reproductive traits is a challenging for breeding programs due to the low heritability of selection criteria, female-limited traits, and relatively later traits measurements. The primary objectives of this thesis were: 1) to evaluate the imputation accuracy of variants on the X chromosome, and 2) to identify genomic regions associated with reproductive traits in Holstein cows, using whole- genome sequence (WGS) data. In the first objective, different imputation strategies were assessed based on scenarios varying in the composition of reference and validation populations. The scenarios were tested in two imputation software tools. The inclusion of both males and females in the populations, as well as the choice of imputation software, directly influenced the imputation accuracy. Overall, high levels of imputation accuracy were observed, highlighting the potential of genotype imputation for more precise bovine genome analyses. In the second objective, a genome-wide association study (GWAS) was conducted for age to first service (AFS), calving at first service (PFS), and days open (DO) based on WGS-imputed data. Genomic regions significantly associated with these traits were identified, which harbor potential candidate genes. Functional analyses revealed relevant biological pathways involved in fertility regulation. The results reinforce the importance of using high-density genomic data and carefully selected methodological strategies to improve imputation accuracy, while contributing to a better understanding of the genetic mechanisms affecting fertility in dairy cattle.