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. 2019 Jan 24;14(1):e0211159.
doi: 10.1371/journal.pone.0211159. eCollection 2019.

Genetic and genomic analyses of testicular hypoplasia in Nellore cattle

Haroldo H R Neves  1 , Giovana Vargas  2 , Luiz F Brito  3 , Flavio S Schenkel  4 , Lucia G Albuquerque  2   5 , Roberto Carvalheiro  1   5
Affiliations

Genetic and genomic analyses of testicular hypoplasia in Nellore cattle

Haroldo H R Neves et al. PLoS One. .

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.

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Conflict of interest statement

We have the following interests. Haroldo H.R. Neves and Roberto Carvalheiro are employed by GenSys Associated Consultants. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

Figures

Fig 1
Fig 1. Estimates of genetic correlations between testicular hypoplasia and the traits/indexes used as selection criteria in the studied population.
BWG: birth-to-weaning weight gain; WYG: weaning-to-yearling weight gain; WC, WP and WM: conformation, finishing precocity and muscling score at weaning, respectively; YC, YP and YM: conformation, finishing precocity and muscling score at yearling, respectively; BW: birth weight; YH: height at yearling; WD: adult weight of cow; TEMP: temperament; SC: scrotal circumference; LPREG: length of pregnancy; IW: selection index at weaning; IFINAL: selection index combining traits at weaning and yearling; AFC: age at first calving.
Fig 2
Fig 2. Manhattan plot for testicular hypoplasia in Nellore cattle.
Fig 3
Fig 3. Results distribution after implementation of InterProScan results.
GOs before merge: total number of added GO terms after Blast2GO annotation; GOs after: total number of GO annotations after implementation of InterProScan results; Confirmed IPS GOs: number of initial GO annotations confirmed by InterProScan result; Too general IPS GOs: number of GO annotations removed after InterProScan because of a lack of specificity.
Fig 4
Fig 4. Protein network of candidate genes for testicular hypoplasia in Nellore cattle, according to STRING action view.
Nodes represent proteins; edges and arrows indicate interaction.
See this image and copyright information in PMC

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