Abstract
Reproductive performance is a key indicator of the long-term sustainability of any livestock production system. Testicular hypoplasia (TH) is a morphological and functional reproductive disorder that affects bulls around the world and consequently causes major economic losses due to reduced fertility rates. Despite the improvements in management practices to enhance performance of affected animals, the use of hypoplastic animals for reproduction might contribute to expand the prevalence of this disorder. The aim of this study was to identify genomic regions that are associated with TH in Nellore cattle by performing a genome-wide association study (GWAS) and functional analyses. Phenotypic and pedigree data from 47,563 animals and genotypes (500,689 Single Nucleotide Polymorphism, SNPs) from 265 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. The estimated breeding values (EBVs) were calculated by fitting a single-trait threshold animal model using a Bayesian approach. The SNP effects were estimated using the Bayes C method and de-regressed EBVs for TH as the response variable (pseudo-phenotype). The top-15 ranking windows (5-adjacent SNPs) that explained the highest proportion of variance were identified for further functional and biological network analyses. The posterior mean (95% highest posterior density) of the heritability for TH was 0.16 (0.08; 0.23). The most important genomic windows were located on BTA1, BTA3, BTA4, BTA5, BTA9, BTA22, BTA23, and BTA25. These windows explained together 22.69% of the total additive genetic variance for TH. Strong candidate genes associated with metabolism and synthesis of steroids, cell survival, spermatogenesis process and sperm motility were identified, which might play an important role in the expression of TH. Our findings contribute to a better biological understanding of TH and future characterization of causal variants might enable improved genomic prediction of this trait in beef cattle.
Highlights
Beef production is a large component of the Brazilian economy and over time various investments have been made by producers, breeding companies and research institutions to increase the industry production efficiency and profitability
The main objectives of this study were: 1) to perform a genome-wide association study (GWAS) to detect genomic regions associated with testicular hypoplasia (TH) in Nellore cattle; and, 2) to perform comprehensive functional analyses of TH to identify and better understand the candidate genes and metabolic pathways associated with the expression of this disorder
Considerable negative genetic correlation was obtained between TH and scrotal circumference (-0.53), since this latter is an indirect measurement of the sperm-producing capacity of the testicles and it is highly correlated with testis weight [34]
Summary
Beef production is a large component of the Brazilian economy and over time various investments have been made by producers, breeding companies and research institutions to increase the industry production efficiency and profitability. After the traditional genetic evaluation, these animals are evaluated for morphological and functional defects or disorders to confirm their eligibility to receive the CEIP. These phenotypes include feet and leg problems, prognathism and agnathism, nasal deviation, depigmentation and testicular hypoplasia (TH). Despite of having a high genetic merit, animals with these defects or disorders will have reduced reproductive and productive performance as well as welfare issues. These undesirable phenotypes could be transmitted to their progeny, which could increase the problem and, the economic losses
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