Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results1

Abstract

Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of

Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle

“…Thus, the discovery of genetic markers related to male fertility through GWAS can contribute to the evaluation of fertility traits, such as SC and SM, and their implications on male fertility. Spermatic related traits, including SM are commonly measured in dairy cattle where semen is widely used for artificial insemination and measuring semen parameters is a standard practice 15 , 21 , 24 – 27 . However, SM measurements are much less common in the beef industry where natural breeding is often used, which can be seen in our sample size.…”

“…However, SM measurements are much less common in the beef industry where natural breeding is often used, which can be seen in our sample size. Testicular related traits, including SC have higher heritability values and correlations with fertility traits, although the majority of studies on SC have been on purebred bulls 18 , 21 , 28 – 32 . Few SC GWAS have been conducted in crossbred beef cattle 26 , 33 , which represents a significant proportion of the beef industry 20 .…”

“…Functional candidate gene prioritization was conducted using the Topp-Gene Suite 85 . A trained list of genes associated with keywords outlined by Fonseca et al 21 using the GUILDify 86 software and a species-specific (Homo sapiens) interaction network, including, "scrotal circumference, " "scrotal, " "testicular, " "testis, " "testes, " "sperm, " "semen, " "spermatozoa, " "spermatogenesis, " and "fertility, " made up the "trained list" of genes. From this analysis, the top 100 genes ranked using an algorithm based on network topology on GUILDify were used to create the "trained" gene list.…”

“…Relatively fewer GWAS for bull fertility traits have focused on crossbred beef cattle, which represent a significant proportion of the beef cattle population, compared to purebred cattle 20,21 . This is in part due to multiple beef breeds with each breed association carrying out a separate genetic evaluation using different methods to calculate expected progeny deviation and the correspondence of SNP effects 22 .…”

Differential gene expression in dairy cows under negative energy balance and ketosis: A systematic review and meta-analysis

“…A systematic review of NEB and subclinical and clinical ketosis in dairy cattle was carried out as described by Fonseca et al (2018) to identify significant SNPs located within genomic regions overlapping with candidate genes that are differentially expressed under these metabolic conditions. Different transcriptomic techniques for gene expression studies were considered, including microarray, quantitative PCR (qPCR), and RNA-Sequencing (RNA-Seq).…”