An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population

Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.

A systematic review with meta-analysis of heritability estimates for temperament-related traits in beef and dairy cattle populations

Temperament (docility) is a key breeding goal in the cattle industry due to its direct relationship with animal welfare, cattle handler's safety and animal productivity. Over the past six decades, numerous studies have reported heritability estimates for temperament-related traits in cattle populations ranging from low to high values. Therefore, the primary objective of this study was to perform a comprehensive systematic review with meta-analysis to obtain weighted estimates of heritability for temperament-related traits in worldwide cattle populations. After data editing and quality control, 106 studies were included in the systematic review, of which 29.2% and 70.8% reported estimates of heritability for temperament-related traits in dairy and beef cattle populations, respectively. Meta-analyses were performed for 95 heritability estimates using a random model approach. The weighted heritability estimates were as follow: (a) flight score at weaning = 0.23 (95% CI: 0.15-0.32); (b) flight speed at weaning = 0.30 (95% CI: 0.26-0.33); (c) joint analysis of flight speed and flight score at weaning = 0.27 (95% CI: 0.22-0.31); (d) flight speed at yearling = 0.26 (95% CI: 0.21-0.30); (e) joint analysis of flight speed at weaning and yearling = 0.27 (95% CI: 0.24-0.30); (f) movement score = 0.12 (95% CI: 0.08-0.15); (g) crush score at weaning = 0.21 (95% CI: 0.17-0.25); (h) pen score at weaning = 0.27 (95% CI: 0.19-0.34); (i) pen score at yearling = 0.20 (95% CI: 0.17-0.23); (j) joint analysis of pen score at weaning and yearling = 0.22 (95% CI: 0.18-0.26); (k) cow's aggressiveness at calving = 0.10 (95% CI: 0.01-0.19); (l) general temperament = 0.13 (95% CI: 0.06-0.19); (m) milking temperament = 0.16 (95% CI: 0.11-0.21); and (n) joint analysis of general and milking temperament = 0.14 (95% CI: 0.11-0.18). The heterogeneity index ranged from 0% to 77%, and the Q-test was significant (p < 0.05) for four single-trait meta-analyses. In conclusion, temperament is moderately heritable in beef cattle populations, and flight speed at weaning had the highest weighted heritability estimate. Moreover, between-study heterogeneity was low or moderate in beef cattle traits, suggesting reasonable standardization across studies. On the other hand, low-weighted heritability and high between-study heterogeneity were estimated for temperament-related traits in dairy cattle, suggesting that more studies are needed to better understand the genetic inheritance of temperament in dairy cattle populations.

Genetic parameters for yearling male reproduction traits in tropical composite cattle population

Fertility is economically important but is hard to quantify and measure in breeding programs which has led extensive breeding programs to ignore fertility in their selection criteria. While female fertility traits have been extensively researched, male fertility traits have been largely ignored. It is estimated that 20% to 40% of bulls have sub-fertility, reducing the number of calves born and profits, highlighting the importance of investigating bull fertility. The most practical measure of male fertility is a bull breeding soundness evaluation (BBSE) which assesses structure as well as semen quality and quantity. Generally, traits recorded in a BBSE are neither genetically evaluated nor used for selection in breeding programs. All traits recorded during a BBSE were analyzed through a series of univariate and bivariate linear mixed models using a genomic relationship matrix to estimate genetic parameters. All genotype and phenotype data were obtained from a tropical composite commercial cattle population and imputed to 27,638 single-nucleotide polymorphisms (SNPs) with a total of 2,613 genotyped animals with BBSE records ranging from 616 to 826 animals depending on the trait. The heritabilities of the 27 traits recorded during a BBSE ranged from 0.02 to 0.49. Seven of the male fertility traits were recommended to be included in a breeding program based on their heritability and their phenotypic and genetic correlations. These traits are scrotal circumference, percent normal sperm, proximal droplets, distal midpiece reflex, knobbed acrosomes, vacuoles/teratoids, and sheath score. Using these seven traits in a breeding program would result in higher calving rates, increasing production and profitability.

Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle

BACKGROUND

Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models.

RESULTS

Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability's of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation.

CONCLUSIONS

This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed.

Sequence level genome-wide associations for bull production and fertility traits in tropically adapted bulls

BACKGROUND

The genetics of male fertility is complex and not fully understood. Male subfertility can adversely affect the economics of livestock production. For example, inadvertently mating bulls with poor fertility can result in reduced annual liveweight production and suboptimal husbandry management. Fertility traits, such as scrotal circumference and semen quality are commonly used to select bulls before mating and can be targeted in genomic studies. In this study, we conducted genome-wide association analyses using sequence-level data targeting seven bull production and fertility traits measured in a multi-breed population of 6,422 tropically adapted bulls. The beef bull production and fertility traits included body weight (Weight), body condition score (CS), scrotal circumference (SC), sheath score (Sheath), percentage of normal spermatozoa (PNS), percentage of spermatozoa with mid-piece abnormalities (MP) and percentage of spermatozoa with proximal droplets (PD).

RESULTS

After quality control, 13,398,171 polymorphisms were tested for their associations with each trait in a mixed-model approach, fitting a multi-breed genomic relationship matrix. A Bonferroni genome-wide significance threshold of 5 × 10^- 8 was imposed. This effort led to identifying genetic variants and candidate genes underpinning bull fertility and production traits. Genetic variants in Bos taurus autosome (BTA) 5 were associated with SC, Sheath, PNS, PD and MP. Whereas chromosome X was significant for SC, PNS, and PD. The traits we studied are highly polygenic and had significant results across the genome (BTA 1, 2, 4, 6, 7, 8, 11, 12, 14, 16, 18, 19, 23, 28, and 29). We also highlighted potential high-impact variants and candidate genes associated with Scrotal Circumference (SC) and Sheath Score (Sheath), which warrants further investigation in future studies.

CONCLUSION

The work presented here is a step closer to identifying molecular mechanisms that underpin bull fertility and production. Our work also emphasises the importance of including the X chromosome in genomic analyses. Future research aims to investigate potential causative variants and genes in downstream analyses.

Estimating genetic parameters of reproductive, carcass, and meat quality traits in Polled Nellore cattle

Considering the economic and commercial efficiency of the beef production chain, the yield and quality of the meat produced must also be included in breeding programs. For the Nellore breed, including the polled herd, these aspects have not been much studied. The aim of this study was to estimate genetic parameters for scrotal circumference adjusted to 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), accumulated productivity (AP), stayability (STAY), longissimus muscle area (LMA), thickness of subcutaneous fat over the 12th-13th ribs (BF), thickness of subcutaneous fat over the rump (RF), and shear force measured by Warner-Bratzler shear force (WBSF) of polled Nellore cattle. Bayesian analyses were performed by adopting a linear animal model, whereas STAY analyses used the linear threshold model. Heritability estimates were 0.31 (SC365), 0.37 (SC450), 0.16 (AFC), 0.25 (AP), 0.16 (STAY), 0.30 (LMA), 0.13 (BF), 0.24 (RF), and 0.15 (WBSF), indicating moderate response to selection. Genetic and residual correlations between SC365 and SC450 were high (0.91 and 0.74, respectively), as well as the genetic correlations of AP with SC365, SC450, AFC, and STAY (0.61, 0.62, - 0.69, and 0.83, respectively). Genetic and residual correlations of WBSF with reproductive and carcass characteristics exhibited high standard deviations, however favorable. Based on the results, it is expected that in the medium term, animals with greater sexual precocity will also have greater accumulated productivity and longer permanence of females in the herd, along with superior carcass traits. However, due to the low heritabilities and small genetic associations with reproductive traits, fat thickness characteristics (BF and RF) will still require direct selection.

Multi-breed genomic predictions and functional variants for fertility of tropical bulls

Worldwide, most beef breeding herds are naturally mated. As such, the ability to identify and select fertile bulls is critically important for both productivity and genetic improvement. Here, we collected ten fertility-related phenotypes for 6,063 bulls from six tropically adapted breeds. Phenotypes were comprised of four bull conformation traits and six traits directly related to the quality of the bull's semen. We also generated high-density DNA genotypes for all the animals. In total, 680,758 single nucleotide polymorphism (SNP) genotypes were analyzed. The genomic correlation of the same trait observed in different breeds was positive for scrotal circumference and sheath score on most breed comparisons, but close to zero for the percentage of normal sperm, suggesting a divergent genetic background for this trait. We confirmed the importance of a breed being present in the reference population to the generation of accurate genomic estimated breeding values (GEBV) in an across-breed validation scenario. Average GEBV accuracies varied from 0.19 to 0.44 when the breed was not included in the reference population. The range improved to 0.28 to 0.59 when the breed was in the reference population. Variants associated with the gene HDAC4, six genes from the spermatogenesis-associated (SPATA) family of proteins, and 29 transcription factors were identified as candidate genes. Collectively these results enable very early in-life selection for bull fertility traits, supporting genetic improvement strategies currently taking place within tropical beef production systems. This study also improves our understanding of the molecular basis of male fertility in mammals.

Identification of genomic regions associated with total and progressive sperm motility in Italian Holstein bulls

Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.

Weak genotype x environment interaction suggests that measuring scrotal circumference at 12 and 18 months of age is helpful to select precocious Brahman cattle

The aim of this study was to evaluate the genotype x environment interaction (GxE) for scrotal circumference (SC) measured at different ages using pedigree-based (A -1) and pedigree and genomic-based (H -1) relationship matrices. Data from 1,515 Brahman bulls, from the Cooperative Research Centre for Beef Genetic Technologies (Beef CRC) experimental dataset were used in this study. SC was adjusted to age and body weight measured at 6 months (SC6), 12 months (SC12), 18 months (SC18) and 24 months of age (SC24). Body weight (BW) measured at 6 months (BW6), 12 months (BW12), 18 months (BW18) and 24 months of age (BW24) were used as criteria to describe the environment for SC in each age. All the animals measured were genotyped using medium-density SNP chips ("50k" or "70k" SNP) and their genotype were imputed using a reference panel with 729,068 SNP. The environment gradient (EG) was obtained by standardizing the solutions of the contemporary groups obtained by Animal Model with BW as the dependent variable. Then, the reaction norms (RN) were determined through a Random Regression Model. The breeding values (EBV) were estimated using either A -1 or H -1. The rank correlation was obtained using Spearman's correlation among the EBV estimated for the traits in analysis. For SC6 and SC24, higher estimates of heritability (h²) were obtained using A -1, when compared to those observed with H -1. In those ages, the improvement of the environment decreases the h² coefficient. On the other hand, the h² for SC12 and SC18 increased as the environment became more favorable, regardless of the matrix used. The RN for SC6 and SC24 estimated using A -1 and H -1 showed a decrease of variance from the worst to the best environment, an indication of existence of GxE. On the other hand, for SC12 and SC18, there were no significant differences between the EBV estimated in the lower and in the higher environments, regardless of the kinship matrix used, suggesting absence of GxE on those ages. Spearman's correlation among EBV estimated using A -1 and H -1 in different EG were practically equal to unity for all traits evaluated. In our study, there was weak evidence of GxE effect on SC in ages suitable for selection for sexual precocity. So, the absence of GxE at 12 and 18 months means these ages are advantageous for measuring SC to selection for sexual precocity. The advantage is that no changes in classification were observed when the sires were evaluated in different environments.

Genome-wide association study of beef bull semen attributes

Background

Cattle production is dependent upon fertility because it results in producing offspring to offset production costs. A number of semen attributes are believed to affect fertility and are frequently measured as part of routine breeding soundness exams or semen collection procedures. The objective of this study was to perform a single-step genome-wide association study (ssGWAS) for beef bull semen attributes. Beef bull fertility phenotypes including volume (VOL), concentration (CONC), number of spermatozoa (NSP), initial motility (IMot), post-thaw motility (PTMot), three-hour post-thaw motility (3HRPTMot), percentage of normal spermatozoa (%NORM), primary abnormalities (PRIM), and secondary abnormalities (SEC) were obtained from two artificial insemination (AI) centers. A total of 1819 Angus bulls with 50,624 collection records were used for ssGWAS. A five-generation pedigree was obtained from the American Angus Association and consisted of 6521 sires and 17,136 dams. Genotypes on 1163 bulls were also obtained from the American Angus Association and utilized in ssGWAS.

Results

A multi-trait animal model was used for the estimation of single nucleotide polymorphism (SNP) effects. Significant SNP were those with a -log10P-value threshold greater than 4.0. Volume, CONC, NSP, IMot, PTMot, 3HRPTMot, %NORM, PRIM, and SEC have five, three, six, seven, two, six, six, and two genome-wide significant SNP, respectively.

Conclusions

Several significant SNP were determined to be near or within quantitative trait loci (QTL) associated with beef bull semen attributes. In addition, genes associated with fertility were found to contain or be near the significant SNP found in the study. The results indicate there are regions of the genome that impact fertility, proving inclusion of genomic information into genetic evaluation should be advantageous for genetic improvement of male fertility traits.

Genome-wide association and genomic prediction for scrotal circumference in Hereford and Braford bulls

Scrotal circumference (SC) is widely used as a selection criterion for bulls in breeding programs, since it is easily assessed and correlated with several desirable reproductive traits. The objectives of this study were: to perform a genome-wide association study (GWAS) to identify genomic regions associated with SC adjusted for age (SCa) and for both age and weight (SCaw); to select Tag SNPs from GWAS to construct low-density panel for genomic prediction; and to compare the prediction accuracy of the SC through different methods for Braford and Hereford bulls from the same genetic breeding program. Data of SC from 18,172 bulls (30.4 ± 3.7 cm) and of genotypes from 131 sires and 3,545 animals were used. From GWAS, the top 1% of 1-Mb windows were observed on chromosome (BTA) 2, 20, 7, 8, 15, 3, 16, 27, 6 and 8 for SCa and on BTA 8, 15, 16, 21, 19, 2, 6, 5 and 10 for SCaw, representing 17.4% and 18.8% of the additive genetic variance of SCa and SCaw, respectively. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene functions related to the SCa and SCaw. The genomic enhancement methods, especially single step GBLUP, that combined phenotype and pedigree data with direct genomic values generated gains in accuracy in relation to pedigree BLUP, suggesting that genomic predictions should be applied to improve genetic gain and to narrow the generation interval compared to traditional methods. The proposed Tag-SNP panels may be useful for lower-cost commercial genomic prediction applications in the future, when the number of bulls in the reference population increases for SC in Hereford and Braford breeds.

Development of a RAPD marker-based classification criterion for quality semen production in Holstein crossbred bulls

In cattle production systems, an intense selection pressure for production traits has resulted in the decline of fertility traits. To optimize an efficient reproduction system, the inclusion of both male and female fertility traits in the selection process is very much essential. RAPD (Random Amplified Polymorphic DNA) was developed as a molecular biology tool and has been extensively used, to study intra- and interspecific genetic diversity. The present study was undertaken to utilize RAPD primers to investigate the association between DNA markers and semen quality traits viz. Sperm concentration, total sperm count ejaculate and initial sperm motility and thereby to identify good/poor semen producers. DNA isolated from the blood samples of healthy bulls was subjected to RAPD-PCR. The multiple regression analysis followed by independent t test was carried out to identify suitable markers. Based on the results, only 12 bands were identified as marker suitable for any of the quality trait. This includes, OPA2 ~ 760, OPA2 ~ 700, OPA6 ~ 1,200, OPA9 ~ 400, OPA9 ~ 380, OPA12 ~ 970, OPA14 ~ 715, OPA14 ~ 605, OPA16 ~ 485, OPA17 ~ 860 and OPA18 ~ 480. Multiple regression analysis selected, OPA2 ~ 760 and OPA2 ~ 1,750 for sperm concentration and OPA2 ~ 760, OPA2 ~ 700, OPA9 ~ 620, OPA4 ~ 670 and OPA18 ~ 1,015 for total sperm count/ejaculate. But the t test revealed a significant association between OPA2 ~ 760 and total sperm count. Further, discriminant function analysis also identified this marker in the first step itself. The results of the present study can be exploited as a low-cost alternative strategy for identification of good /poor semen producers in crossbred bulls at an early age.

Genetic parameter estimation for beef bull semen attributes

Improvements in bull reproductive performance are necessary to optimize the efficiency of cattle production. Female fertility has been enhanced through assisted reproductive technologies as well as genetic selection; however, improving beef bull fertility has been largely ignored. Phenotypes routinely collected at bull semen collection facilities are believed to affect fertility and provide the phenotypes necessary for a genetic evaluation. The first objective of this study was to determine the significant fixed effects for modeling beef bull fertility using data from bull semen collection facilities. The second objective was to estimate variance components, heritabilities, repeatabilities, and correlations between beef bull semen attributes. Beef bull fertility phenotypes including volume (VOL), concentration (CONC), number of spermatozoa (NSP), initial motility (IMot), post-thaw motility (PTMot), 3-h post-thaw motility (3HRPTMot), percentage of normal spermatozoa (%NORM), primary abnormalities (PRIM), and secondary abnormalities (SEC) were obtained from two bull semen collection facilities. A total of 1,819 Angus bulls with 50,624 collection records were analyzed. Of the fixed class and covariate effects tested, the significant class effects were collection location and collection day within year and the significant covariate effects included age at collection, days since previous collection, and cumulative comprehensive climate index (CCI). For this study, the CCI was calculated for a 75-d period including the 61-d spermatogenesis cycle and 14-d epididymal transit time. The 75 d prior to collection accounted for the environmental stress a bull may have experienced over the course of development of the spermatozoa, which was more significant than the CCI calculated for collection day or spermatogenesis start date. Pre-thaw beef bull semen traits had low heritability estimates of 0.11 ± 0.02 (VOL), 0.09 ± 0.02 (CONC), 0.08 ± 0.02 (NSP), and 0.12 ± 0.03 (IMot). Heritabilities of post-thaw beef bull semen attributes were more variable at 0.10 ± 0.02 (PTMot), 0.05 ± 0.04 (3HRPTMot), 0.10 ± 0.04 (%NORM), 0.03 ± 0.03 (PRIM), and 0.18 ± 0.04 (SEC). Correlations of breeding values for these traits with scrotal circumference (SC) expected progeny difference (EPD) are low. The low to moderate heritability estimates indicate that genetic improvement can be made in beef bull semen quality traits if new tools are developed to augment the scrotal circumference EPD that are currently available within the industry.

Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle

Context Studies have shown that favourable genetic correlations exist between female and male fertility traits. However, investigations regarding these correlations in Australian tropical beef cattle are limited to either pedigree or single-breed analysis. Aim The study aims to use genomic information to estimate genetic parameters of six female and seven male fertility traits measured during the first 2 years of life, in two tropical breeds. Methods Single-, bivariate and multi-trait models were used to analyse fertility data from Brahman (BB; 996 cows and 1022 bulls); and Tropical Composite (TC; 1091 cows and 998 bulls) cattle genotyped with high-density single-nucleotide polymorphism chip assay. Key results Heritability estimates in BB cows ranged from low (0.07 ± 0.04) for days to calving at the first calving opportunity (DC1, days) to high (0.57 ± 0.08) for age at first corpus luteum (AGECL, days). In BB bulls, estimates varied from low (0.09 ± 0.05) for sperm motility (score 1–5) to high (0.64 ± 0.06) for scrotal circumference (SC) measured at 24 months (SC24, cm). Similarly, heritability estimates in TC cows were low (0.04 ± 0.03) for DC1 and high (0.69 ± 0.02) for AGECL. In TC bulls, the heritability was low (0.09 ± 0.05) for sperm motility and high (0.69 ± 0.07) for SC24. Within-sex for both breeds, blood concentrations of insulin growth-factor 1 (IGF1) measured in cows at 18 months (IGF1c) were negatively correlated with female fertility phenotypes. In BB, across-sex, bulls’ blood concentration of IGF1 measured at 6 months (IGF1b) was a good indicator trait for the following four female traits: AGECL, the first postpartum anoestrus interval, age at first calving and DC1. In TC, IGF1b and percentage normal sperm were good predictors of female fertility phenotypes. Conclusions The heritability estimates and genomic correlations from the present study generally support and confirmed the earlier estimates from pedigree analyses. The findings suggest that selection for female fertility traits will benefit male fertility, and vice versa. Implications Heritability estimates and genomic correlations suggest that we can select for fertility traits measured early in life, with benefits within and across sex. Using traits available through veterinary assessment of bull fertility as selection indicators will enhance bull and cow fertility, which can lead to better breeding rates in tropical herds.

X chromosome variants are associated with male fertility traits in two bovine populations

BACKGROUND

Twenty-five phenotypes were measured as indicators of bull fertility (1099 Brahman and 1719 Tropical Composite bulls). Measurements included sperm morphology, scrotal circumference, and sperm chromatin phenotypes such as DNA fragmentation and protamine deficiency. We estimated the heritability of these phenotypes and carried out genome-wide association studies (GWAS) within breed, using the bovine high-density chip, to detect quantitative trait loci (QTL).

RESULTS

Our analyses suggested that both sperm DNA fragmentation and sperm protamine deficiency are heritable (h2 from 0.10 to 0.22). To confirm these first estimates of heritability, further studies on sperm chromatin traits, with larger datasets are necessary. Our GWAS identified 12 QTL for bull fertility traits, based on at least five polymorphisms (P < 10-8) for each QTL. Five QTL were identified in Brahman and another seven in Tropical Composite bulls. Most of the significant polymorphisms detected in both breeds and nine of the 12 QTL were on chromosome X. The QTL were breed-specific, but for some traits, a closer inspection of the GWAS results revealed suggestive single nucleotide polymorphism (SNP) associations (P < 10-7) in both breeds. For example, the QTL for inhibin level in Braham could be relevant to Tropical Composites too (many polymorphisms reached P < 10-7 in the same region). The QTL for sperm midpiece morphological abnormalities on chromosome X (QTL peak at 4.92 Mb, P < 10-17) is an example of a breed-specific QTL, supported by 143 significant SNPs (P < 10-8) in Brahman, but absent in Tropical Composites. Our GWAS results add evidence to the mammalian specialization of the X chromosome, which during evolution has accumulated genes linked to spermatogenesis. Some of the polymorphisms on chromosome X were associated to more than one genetically correlated trait (correlations ranged from 0.33 to 0.51). Correlations and shared polymorphism associations support the hypothesis that these phenotypes share the same underlying cause, i.e. defective spermatogenesis.

CONCLUSIONS

Genetic improvement for bull fertility is possible through genomic selection, which is likely more accurate if the QTL on chromosome X are considered in the predictions. Polymorphisms associated with male fertility accumulate on this chromosome in cattle, as in humans and mice, suggesting its specialization.

Supplementation of rangeland primiparous Bos indicus x Bos taurus beef heifers during lactation. 2. Effects upon the reproductive development of bull calf progeny

This experiment evaluated the effect of pre-weaning plane of nutrition of dams upon reproductive development in Bos indicus x Bos taurus bull offspring reared under extensively managed conditions in the northern Australia rangelands. Following artificial insemination (AI cohort; n = 26), or natural mating (NM cohort; n = 36), grazing primiparous heifers received either nil supplement (Control; CON), thereby experiencing a moderate nutritional restriction, or were provided a protein supplement (SUPP) between parturition and weaning at mean age 199 ± (SD) 26 d. Bull progeny grazed rangeland pastures without supplementation from weaning until the experiment concluded at 675 d. At 120 ± 3 d and 140 d ± 10 d age, within the AI and NM cohort, respectively, bull calves were subjected to a GnRH challenge (1.5 μg/kg of body weight i.m.). Jugular blood samples collected immediately before and at 60 min after administration of GnRH were analysed for LH, FSH, testosterone and inhibin concentrations. Overall mean concentrations of testosterone in SUPP bulls were greater in both the AI cohort (P = 0.05) and the NM cohort (P = 0.06). At 60 d intervals during the post-weaning period, scrotal circumference (SC) was measured and semen collected to assess concentration, progressive motility and morphology of sperm. Bulls reared by SUPP heifers had greater (P = 0.05) SC at 375 d and tended to have greater (P = 0.09) mean percentage of morphologically normal sperm (PNS). Within the NM cohort, NMSUPP bulls had greater (P = 0.04) overall mean SC and tended (P = 0.07) to demonstrate both greater progressive motility and PNS. A greater incidence of sperm morphological abnormalities, associated with sexual immaturity, were observed in CON bulls. Consequently, NMCON bulls demonstrated delayed (P = 0.03) age of sexual maturity as compared to NMSUPP bulls. In summary, improving the plane of nutrition supplied to Bos indicus x Bos taurus bulls between parturition and weaning via moderate supplementation of grazing dams reduces age at sexual maturity with consequent economic advantages to the producer.

Selection for bull fertility: a review

Fertility is a critically important factor in cattle production because it directly relates to the ability to produce the offspring necessary to offset costs in production systems. Female fertility has received much attention and has been enhanced through assisted reproductive technologies, as well as genetic selection; however, improving bull fertility has been largely ignored. Improvements in bull reproductive performance are necessary to optimize the efficiency of cattle production. Selection and management to improve bull fertility not only have the potential to increase conception rates but also have the capacity to improve other economically relevant production traits. Bull fertility has reportedly been genetically correlated with traits such as average daily gain, heifer pregnancy, and calving interval. Published studies show that bull fertility traits are low to moderately heritable, indicating that improvements in bull fertility can be realized through selection. Although female fertility has continued to progress according to increasing conception rates, the reported correlation between male and female fertility is low, indicating that male fertility cannot be improved by selection for female fertility. Correlations between several bull fertility traits, such as concentration, number of spermatozoa, motility, and number of spermatozoa abnormalities, vary among studies. Using male fertility traits in selection indices would provide producers with more advanced selection tools. The objective of this review was to discuss current beef bull fertility measurements and to discuss the future of genetic evaluation of beef bull fertility and potential genetic improvement strategies.

Genetic parameters for fertility traits in Nellore bulls

Nellore is the main cattle breed used in Brazil, being the largest commercial herd in the world. Beyond the importance of male reproductive efficiency for farm profit, the use of reproductive techniques, mainly artificial insemination, turns the evaluation of male reproductive traits even more important. Estimation of genetic parameters increases the knowledge on traits variances and allows envisaging the possibility of the inclusion of new traits as selection criterion. Genetic parameters for fifteen traits that can be classified as testicular biometry or physical and morphological semen traits were estimated for a Nellore bull population ranging from 18 to 36 months. Single-trait and bi-trait animal models were used for (co)variance components estimation. The contemporary group was considered as fixed effect and age at measurement as covariable. Scrotal circumference presented heritability of 0.47 ± 0.12. This value is similar to the heritabilities found for all testicular biometry traits (0.34-0.48). Sperm progressive motility, which has a direct effect on bull fertility, presented low heritability (0.07 ± 0.08). Major and total sperm defects presented moderate to high heritabilities (0.49 ± 0.18 and 0.39 ± 0.15, respectively), indicating that great genetic gain can be obtained through selection against sperm defects. High and positive genetic correlations were observed among testicular biometry traits, which also presented favourable genetic correlations with physical and morphological traits of the semen with magnitude ranging from high to low. Scrotal circumference presented moderate to high and favourable genetic correlations with sperm progressive motility, sperm turbulence, major sperm defects and total sperm defects. Thus, the selection for scrotal circumference results in favourable correlated genetic response for semen quality. The results show that the use of scrotal circumference as reference trait for bull fertility is appropriate, since it presents high heritability and favourable genetic correlation with semen quality.

Genetic analysis of semen characteristic traits in young Norwegian Red bulls

The aim of this study was to estimate genetic parameters and genetic trends for male fertility in Norwegian Red bulls. We analyzed data on semen characteristics traits collected at the performance test station of young bulls from 1994 to 2016, in an andrology test used to ensure acceptable semen quality before being selected as an artificial insemination bull. Traits included were volume, concentration, and motility (percentage of moving sperm cells) in fresh samples and after storing for 24 and 48 h, and sperm defects. The data consisted of 14,972 ejaculates from 3,927 young (11-15 mo) Norwegian Red bulls. Genetic parameters were estimated using bivariate linear animal models that included age in months, group-year, and collection-group (main effect of the interaction between ejaculate number and interval between collections) as fixed effects, and test-day and additive genetic and permanent environment effect of the bull as random effects. Considerable genetic coefficients of variation were found for concentration and volume, with lower values for motility. Estimated heritabilities ranged from 0.02 and 0.03 (for sperm defects and motility in fresh samples) to 0.14 (volume and concentration measured on a continuous scale). All estimated genetic correlations were favorable, but the genetic correlations between volume and concentration and volume and sperm defects were not significantly different from zero. The genetic correlations between concentration and motility traits ranged from 0.53 to 0.83, and those between volume and the motility traits were between 0.24 and 0.57. All traits showed a slightly unfavorable genetic trend. Our results indicate that selection of bulls with better sperm quality is possible.

Across-breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle

The aim of this study was to identify candidate regions associated with sexual precocity in Bos indicus. Nellore and Brahman were set as validation and discovery populations, respectively. SNP selected in Brahman to validate in Nellore were from gene regions affecting reproductive traits (G1) and significant SNP (p ≤ 10^-3 ) from a meta-analysis (G2). In the validation population, early pregnancy (EP) and scrotal circumference (SC) were evaluated. To perform GWAS in validation population, we used regression and Bayes C. SNP with p ≤ 10^-3 in regression and Bayes factor ≥3 in Bayes C were deemed significant. Significant SNP (for EP or SC) or SNP in their ±250 Kb vicinity region, which were in at least one discovery set (G1 or G2), were considered validated. SNP identified in both G1 and G2 were considered candidate. For EP, 145 SNP were validated in G1 and 41 in G2, and for SC, these numbers were 14 and 2. For EP, 21 candidate SNP were detected (G1 and G2). For SC, no candidate SNP were identified. Validated SNP and their vicinity region were located close to quantitative trait loci or genes related to reproductive traits and were enriched in gene ontology terms related to reproductive success. These are therefore strong candidate regions for sexual precocity in Nellore and Brahman.

Evaluation and prediction of scrotal circumference in beef bulls

Scrotal circumference (SC) is considered a useful tool for predicting age at puberty and is performed to improve the reproductive performance in beef cattle industry. We aimed to fit several nonlinear mixed models for SC measurements of five different breeds to better predict testicular growth. Data of SC (cm), body weight (BW; kg), and age (A; days), farm location, sire and dam, and birth dates of 169,094 beef bulls were collected from five breeds: Nelore (N) (n = 110,814); Angus (AA) (n = 6541); Brangus (BA) (n = 42,910); Polled Hereford and Hereford (HH) (n = 4640); and Braford (BH) (n = 7480). Data comprise a total of 8640 sires and 115,172 dams and grouped in 2908 contemporary groups (CG). The full model development for SC was defined as: SC = CG + A + A*A + BW + BW*BW + Ɛ. Bulls from HH (34.1 ± 3.2) and AA (33.5 ± 3.0) had the highest value of SC, followed by BH (32.2 ± 3.7), BA (30.6 ± 4.1), and N (26.9 ± 3.6). There was a curvilinear effect of BW on the SC measurements of HH and AA bulls, reaching the maximum point around 600 kg, whether both breeds presented a similar testicular growth pattern. In British breeds, inflection points of average daily SC growth of 0.039 and 0.042 cm/kg were obtained from 700 kg HH and 600 kg AA bulls, respectively. Scrotal circumference values of 0.042 and 0.046 cm/kg reaching the maximum growth point at 450 kg BW were obtained for BH and BA bulls, respectively. We also observed SC values of 0.044 and 0.048 cm/d reaching the maximum growth point at 550 d of age for BH and BA bulls, respectively. Thus, estimate testicular size at maturity should be measured between 500 and 600 kg BW in British genotypes and between 550 and 600 d in Bos indicus and crossbreeds animals. Therefore, SC adjustment can be used by breed-specific criteria associated with BW and/or age to determine testis growth as a selection criterion in beef cattle breeding programs.

Across-sex genomic-assisted genetic correlations for sex-influenced traits in Brahman cattle

Background

This study aimed at estimating genetic parameters of sex-influenced production traits, evaluating the impact of genotype-by-sex interaction, and identifying the selection criteria that could be included in multiple-trait genetic evaluation to increase the rate of genetic improvement in both sexes. To achieve this goal, we used 10 male and 10 female phenotypes, which were measured in a population of 2111 Australian Brahman cattle genotyped at high-density.

Results

Heritability estimates ranged from very low (0.03 ± 0.03 for cows’ days to calving at first calving opportunity, DC1), to moderate (0.33 ± 0.08 for cows’ adult body weight, AWTc), and to high (0.95 ± 0.07 for cows’ hip height, HHc). Genetic correlation (r_g) estimates between male and female homologous traits were favorable and ranged from moderate to high values, which indicate that selection for any of the traits in one sex would lead to a correlated response with the equivalent phenotype in the other sex. However, the estimated direct response was greater than the indirect response. Moreover, Pearson correlations between estimated breeding values obtained from each sex separately and from female and male homologous traits combined into a single trait in univariate analysis ranged from 0.74 to 0.99, which indicate that small ranking variation might appear if male and female traits are included as single or separate phenotypes. Genetic correlations between male growth and female reproductive traits were not significant, ranging from − 0.07 ± 0.13 to 0.45 ± 0.65. However, selection to improve HHc and AWTc in cows may reduce the percentage of normal sperm at 24 months of age (PNS24), possibly due to correlated effects in the same traits in males, which are related to late maturing animals.

Conclusions

Hip height in cows and PNS24, as well as blood insulin-like growth factor 1 (IGF1) concentration in bulls at 6 months of age are efficient selection criteria to improve male growth and female reproductive traits, simultaneously. In the presence of genotype-by-sex interactions, selection for traits in each sex results in high rates of genetic improvement, however, for the identification of animals with the highest breeding value, data for males and females may be considered a single trait.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0482-6) contains supplementary material, which is available to authorized users.

Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle

Multitrait meta-analyses are a strategy to produce more accurate genome-wide association studies, especially for complex phenotypes. We carried out a meta-analysis study for traits related to sexual precocity in tropical beef cattle (Nellore and Brahman) aiming to identify important genomic regions affecting these traits. The traits included in the analyses were age at first calving (AFC), early pregnancy (EP), age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference (SC). The traits AFC, EP, and SCN were measured in Nellore cattle, while AGECL, PPAI, and SCB were measured in Brahman cattle. Meta-analysis resulted in 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10-5 (false discovery rate [FDR] < 0.05). Within 0.5 Mb of the significant SNP, candidate genes were annotated and analyzed for functional enrichment. Most of the closest genes to the SNP with higher significance in each chromosome have been associated with important roles in reproductive function. They are TSC22D2, KLF7, ARHGAP29, 7SK, MAP3K5, TLE3, WDR5, TAF3, TMEM68, PPP1R15B, NR2F2, GALR1, SUFU, and KCNU1. We did not observe any significant SNP in BTA5, BTA12, BTA17, BTA18, BTA19, BTA20, BTA22, BTA23, BTA25, and BTA28. Although the majority of significant SNPs are in BTA14, it was identified significant associations in multiple chromosomes (19 out of 29 autosomes), which is consistent with the postulation that reproductive traits are complex polygenic phenotypes. Five proposed association regions harbor the majority of the significant SNP (76%) and were distributed over four chromosomes (P < 1.39 × 10-5, FDR < 0.05): BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. These regions harbored key genes related to reproductive function. Moreover, these genes were enriched for functional groups associated with immune response, maternal-fetal tolerance, pregnancy maintenance, embryo development, fertility, and response to stress. Further studies including other breeds and precocity traits could confirm the importance of these regions and identify new candidate regions for sexual precocity in beef cattle.

Genetic parameters, predictions, and rankings for semen production traits in a Thailand multi-breed dairy population using genomic-polygenic and polygenic models

The objectives were to compare estimates of variance components, genetic parameters, prediction accuracies, and rankings of bulls for semen volume (VOL), number of sperm (NS), and motility (MOT) using genomic-polygenic (GPRM) and polygenic repeatability models (PRM). The dataset comprised 13,535 VOL, 12,773 NS, and 12,660 MOT from 131 bulls collected from 2001 to 2017 in the Semen Production and Dairy Genetic Evaluation Center of the Dairy Farming Promotion Organization of Thailand. Genotypic data encompassed 76,519 actual and imputed SNP from 72 animals. The three-trait GPRM and PRM included the fixed effects of contemporary group, ejaculate order, age of bull, ambient temperature, and heterosis. Random effects were animal additive genetic, permanent environmental, and residual. Variance components and genetic parameters were estimated using AIREMLF90. GPRM heritabilities were slightly greater than PRM for MOT (0.27 compared with 0.24), and slightly less for VOL (0.11 compared with 0.12), and NS (0.17 compared with 0.19). Repeatabilities were slightly less for GPRM than PRM (0.44 compared with 0.45 for MOT, 0.26 compared with 0.28 for NS, and 0.20 compared with 0.21 for VOL). Additive genetic correlations were high between NS and MOT (GPRM: 0.76, PRM: 0.78), moderate between VOL and NS (GPRM: 0.43, PRM: 0.55), and near zero between VOL and MOT (GPRM: -0.13, PRM: 0.04). Rank correlations between GPRM and PRM estimated breeding values (EBV) were high for all traits. The similarity between GPRM and PRM results suggested that SNP data from the small number of genotyped animals had a minimal impact on genetic predictions in this population.

Morphological defects, sperm DNA integrity, and protamination of bovine spermatozoa

The association between sperm morphology characteristics and DNA conformation and integrity is still controversial. In bulls, major morphological sperm abnormalities have been associated with reduced fertility, and morphological assessment is used to provide an indication of potential fertility of the individual. Sperm DNA fragmentation and damage has a negative effect on embryo development and subsequently fertility, with bull spermatozoa generally displaying low levels of DNA damage and tight chromatin. However, sensitive methods for detecting chromatin damage may reveal associations with morphological defects. The objective was to determine whether morphological sperm abnormalities and variables expressing sperm DNA integrity and protamination are correlated in bulls, using the sperm chromatin structure assay (SCSA) and the sperm protamine deficiency assay (SPDA). Electroejaculated samples (n = 1009) from two-year-old tropically adapted bulls were split and fixed and submitted to microscopic sperm morphology assessment, and snap-frozen for sperm nuclear integrity assessments by SPDA and SCSA. For SPDA, the variables were defective (MCB) and deprotaminated (HCB), and for SCSA, the variables were DNA fragmentation index (DFI) and high DNA stainability (HDS). HCB correlated with DFI; τKen²  = 0.317 and HDS; 0.098, and MCB correlated with DFI; 0.183 (p < 0.001). The percentage of morphological normal spermatozoa was correlated negatively to DFI; τKen²  = -0.168, MCB; -0.116 and HCB; -0.137 (p < 0.001). HCB and DFI were both positively correlated to head defects, proximal droplets, and spermatogenic immaturity, but not to distal droplets, vacuoles, or diadems. Sperm DNA integrity and protamination, using the SCSA and SPDA, respectively, in bulls show associations with morphological parameters, particularly with head shape abnormalities and indicators of spermatogenic immaturity, including proximal droplets. The vacuoles and diadem defects were not correlated with sperm nuclear integrity, and hence, these are likely physiological features that may not directly affect sperm chromatin configuration.

Review: Ontology and endocrinology of the reproductive system of bulls from fetus to maturity

This review focuses on current understanding of prenatal, prepubertal and post-pubertal development of the male reproductive system of cattle. The critical developmental events occur during the first 3 to 4 months of gestation and the first ~6 to 9 months after birth. The Wilms Tumor-1 and SRY proteins play critical roles in early development and differentiation of the fetal testis, which in turn drives gestational development of the entire male reproductive system. The hypothalamic-pituitary-gonadal axis matures earlier in the bovine fetus than other domestic species with descent of the testes into the scrotum occurring around the 4th month of gestation. An array of congenital abnormalities affecting the reproductive system of bulls has been reported and most are considered to be heritable, although the mode of inheritance in most cases has not been fully defined. Early postnatal detection of most of these abnormalities is problematic as clinical signs are generally not expressed until after puberty. Development of genomic markers for these abnormalities would enable early culling of affected calves in seedstock herds. The postnatal early sustained increase in lutenising hormone secretion cues the rapid growth of the testes in the bull calf leading to the onset of puberty. There is good evidence that both genetic and environmental factors, in particular postnatal nutrition, control or influence development and maturation of the reproductive system. For example, in Bos taurus genotypes which have had sustained genetic selection pressure applied for fertility, and where young bulls are managed on a moderate to high plane of nutrition puberty typically occurs at 8 to 12 months of age. However, in many Bos indicus genotypes where there has been little selection pressure for fertility and where young bulls are reared on a low plane of nutrition, puberty typically occurs between 15 to 17 months. Our understanding of the control and expression of sexual behavior in bulls is limited, particularly in B. indicus genotypes.

Multiple-trait genomewide mapping and gene network analysis for scrotal circumference growth curves in Brahman cattle

Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals. Because SC is a sex-limited trait, identifying the underlying genomics of growth curve parameters will allow selection across both males and females. We reported the first multitrait genomewide association study (GWAS) of estimated growth curve parameters for SC data in Brahman cattle. Five widely used nonlinear models were tested to fit a total of 3,612 SC records, measured at 6, 12, 18, and 24 mo of age. The von Bertalanffy model, individually fitted for each animal, best fit this SC data. Parameter estimates SC at maturity (A) and K as well as SC at all ages were jointly analyzed in a GWAS to identify 1-Mb regions most strongly associated with each trait. Heritabilities were 0.25 for K and 0.32 for A and ranged from 0.51 to 0.72 for SC at 6 (SC6), 12 (SC12), 18 (SC18), and 24 mo of age (SC24). An overlapping window on chromosome 14 explaining around 0.8% of genetic variance for K, SC12, SC18, and SC24 was observed. The major positional candidate genes within 1 Mb upstream and downstream of this overlapping window were , , , and . Windows of 1 Mb explaining more than 0.4% of each trait on chromosomes 1, 3, 6, 7, 14, 17, 18, 24, 25, and 26 were identified. Pathways and net-work analyses were indicated through transcription factors playing a role on fertility traits: , , , , , , and . Further validation studies on larger populations or other breeds are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with scrotal growth and male fertility in cattle.

Genetic analysis of docility score of Australian Angus and Limousin cattle

The temperament of cattle is believed to affect the profitability of the herd through impacting production costs, meat quality, reproduction, maternal behaviour and the welfare of the animals and their handlers. As part of the national beef cattle genetic evaluation in Australia by BREEDPLAN, 50 935 Angus and 50 930 Limousin calves were scored by seedstock producers for temperament using docility score. Docility score is a subjective score of the animal’s response to being restrained and isolated within a crush, at weaning, and is scored on a scale from 1 to 5 with 1 representing the quiet and 5 the extremely nervous or anxious calves. Genetic parameters for docility score were estimated using a threshold animal model with four thresholds (five categories) from a Bayesian analysis carried out using Gibbs sampling in THRGIBBS1F90 with post-Gibbs analysis in POSTGIBBSF90. The heritability of docility score on the observed scale was 0.21 and 0.39 in Angus and Limousin, respectively. Since the release of the docility breeding value to the Australian Limousin population there has been a favourable trend within the national herd towards more docile cattle. Weak but favourable genetic correlations between docility score and the production traits indicates that docility score is largely independent of these traits and that selection to improve temperament can occur without having an adverse effect on growth, fat, muscle and reproduction.

Peri-conception and first trimester diet modifies reproductive development in bulls

Nutritional perturbation during gestation alters male reproductive development in rodents and sheep. In cattle both the developmental trajectory of the feto–placental unit and its response to dietary perturbations is dissimilar to that of these species. This study examined the effects of dietary protein perturbation during the peri-conception and first trimester periods upon reproductive development in bulls. Nulliparous heifers (n = 360) were individually fed a high- or low-protein diet (HPeri and LPeri) from 60 days before conception. From 24 until 98 days post conception, half of each treatment group changed to the alternative post-conception high- or low-protein diet (HPost and LPost) yielding four treatment groups in a 2 × 2 factorial design. A subset of male fetuses (n = 25) was excised at 98 days post conception and fetal testis development was assessed. Reproductive development of singleton male progeny (n = 40) was assessed until slaughter at 598 days of age, when adult testicular cytology was evaluated. Low peri-conception diet delayed reproductive development: sperm quality was lowered during pubertal development with a concomitant delay in reaching puberty. These effects were subsequent to lower FSH concentrations at 330 and 438 days of age. In the fetus, the low peri-conception diet increased the proportion of seminiferous tubules and decreased blood vessel area in the testis, whereas low first trimester diet increased blood vessel number in the adult testis. We conclude that maternal dietary protein perturbation during conception and early gestation may alter male testis development and delay puberty in bulls.

Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle

Genomic selection is becoming a standard tool in livestock breeding programs, particularly for traits that are hard to measure. Accuracy of genomic selection can be improved by increasing the quantity and quality of data and potentially by improving analytical methods. Adding genotypes and phenotypes from additional breeds or crosses often improves the accuracy of genomic predictions but requires specific methodology. A model was developed to incorporate breed composition estimated from genotypes into genomic selection models. This method was applied to age at puberty data in female beef cattle (as estimated from age at first observation of a corpus luteum) from a mix of Brahman and Tropical Composite beef cattle. In this dataset, the new model incorporating breed composition did not increase the accuracy of genomic selection. However, the breeding values exhibited slightly less bias (as assessed by deviation of regression of phenotype on genomic breeding values from the expected value of 1). Adding additional Brahman animals to the Tropical Composite analysis increased the accuracy of genomic predictions and did not affect the accuracy of the Brahman predictions.

Multi-Trait GWAS and New Candidate Genes Annotation for Growth Curve Parameters in Brahman Cattle

Understanding the genetic architecture of beef cattle growth cannot be limited simply to the genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the whole growth trajectory over time using a growth curve approach. For such an approach, the parameters that are used to describe growth curves were treated as phenotypes under a GWAS model. Data from 1,255 Brahman cattle that were weighed at birth, 6, 12, 15, 18, and 24 months of age were analyzed. Parameter estimates, such as mature weight (A) and maturity rate (K) from nonlinear models are utilized as substitutes for the original body weights for the GWAS analysis. We chose the best nonlinear model to describe the weight-age data, and the estimated parameters were used as phenotypes in a multi-trait GWAS. Our aims were to identify and characterize associated SNP markers to indicate SNP-derived candidate genes and annotate their function as related to growth processes in beef cattle. The Brody model presented the best goodness of fit, and the heritability values for the parameter estimates for mature weight (A) and maturity rate (K) were 0.23 and 0.32, respectively, proving that these traits can be a feasible alternative when the objective is to change the shape of growth curves within genetic improvement programs. The genetic correlation between A and K was -0.84, indicating that animals with lower mature body weights reached that weight at younger ages. One hundred and sixty seven (167) and two hundred and sixty two (262) significant SNPs were associated with A and K, respectively. The annotated genes closest to the most significant SNPs for A had direct biological functions related to muscle development (RAB28), myogenic induction (BTG1), fetal growth (IL2), and body weights (APEX2); K genes were functionally associated with body weight, body height, average daily gain (TMEM18), and skeletal muscle development (SMN1). Candidate genes emerging from this GWAS may inform the search for causative mutations that could underpin genomic breeding for improved growth rates.

Seminal plasma proteins and their relationship with percentage of morphologically normal sperm in 2-year-old Brahman (Bos indicus) bulls

The objective was to determine the relationship between seminal plasma proteins and sperm morphology in Bos indicus bulls of the Brahman breed. Fifty-six 24-month-old Australian Brahman bulls were electroejaculated and samples were examined to determine the percentage of morphologically normal sperm (PNS24) and the seminal plasma protein composition was identified and quantified by 2-D gel electrophoresis. The total integrated optical density of 152 seminal plasma protein spots (SPPs) across all gels was determined using the PDQuest software version 8.0 (Bio Rad, USA). Using a single regression mixed model with the density of individual spots as a covariate for PNS24, 17 SPPs were significantly associated with PNS24 (p<0.05). A multiple regression analyses of these SPPs, using three models; non-parametric Tree Model, Generalized Additive Model, and a step-wise selection method were conducted, and 6 SPPs could be used to predict PNS24; four SPPs had positive and two had negative association with PNS24. Together these spots explained 35% of the phenotypic variation in PNS24. Using mass spectrometry (MALDI-ToF and TripleToF-MS) the SPPs with positive relationship contained mainly apolipoprotein A-I (1310), protein DJ-1 and glutathione peroxidase 3 (2308), phosphoglycerate kinase 1 (6402) and apolipoprotein A-I and secretoglobin family 1D member (8008). The SPPs inversely associated with PNS24 were clusterin/seminal plasma protein A3 (1411) and epididymal secretory protein E1 (8108). This is the first comprehensive report on the association between seminal plasma protein composition in Bos indicus Brahman bulls and sperm morphology.

Non-synonymous mutations mapped to chromosome X associated with andrological and growth traits in beef cattle

Background

Previous genome-wide association analyses identified QTL regions in the X chromosome for percentage of normal sperm and scrotal circumference in Brahman and Tropical Composite cattle. These traits are important to be studied because they are indicators of male fertility and are correlated with female sexual precocity and reproductive longevity. The aim was to investigate candidate genes in these regions and to identify putative causative mutations that influence these traits. In addition, we tested the identified mutations for female fertility and growth traits.

Results

Using a combination of bioinformatics and molecular assay technology, twelve non-synonymous SNPs in eleven genes were genotyped in a cattle population. Three and nine SNPs explained more than 1% of the additive genetic variance for percentage of normal sperm and scrotal circumference, respectively. The SNPs that had a major influence in percentage of normal sperm were mapped to LOC100138021 and TAF7L genes; and in TEX11 and AR genes for scrotal circumference. One SNP in TEX11 was explained ~13% of the additive genetic variance for scrotal circumference at 12 months. The tested SNP were also associated with weight measurements, but not with female fertility traits.

Conclusions

The strong association of SNPs located in X chromosome genes with male fertility traits validates the QTL. The implicated genes became good candidates to be used for genetic evaluation, without detrimentally influencing female fertility traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1595-0) contains supplementary material, which is available to authorized users.

Sperm protamine deficiency correlates with sperm DNA damage in Bos indicus bulls

The primary purpose of spermatozoa is to deliver the paternal DNA to the oocyte at fertilization. During the complex events of fertilization, if the spermatozoon penetrating the oocyte contains compromised or damaged sperm chromatin, the subsequent progression of embryogenesis and foetal development may be affected. Variation in sperm DNA damage and protamine content in ejaculated spermatozoa was reported in the cattle, with potential consequences to bull fertility. Protamines are sperm-specific nuclear proteins that are essential to packaging of the condensed paternal genome in spermatozoa. Sperm DNA damage is thought to be repaired during the process of protamination. This study investigates the potential correlation between sperm protamine content, sperm DNA damage and the subsequent relationships between sperm chromatin and commonly measured reproductive phenotypes. Bos indicus sperm samples (n = 133) were assessed by two flow cytometric methods: the sperm chromatin structure assay (SCSA) and an optimized sperm protamine deficiency assay (SPDA). To verify the SPDA assay for bovine sperm protamine content, samples collected from testis, caput and cauda epididymidis were analyzed. As expected, mature spermatozoa in the cauda epididymidis had higher protamine content when compared with sperm samples from testis and caput epididymidis (p < 0.01). The DNA fragmentation index (DFI), determined by SCSA, was positively correlated (r = 0.33 ± 0.08, p < 0.05) with the percentage of spermatozoa that showed low protamine content using SPDA. Also, DFI was negatively correlated (r = -0.21 ± 0.09, p < 0.05) with the percentage of spermatozoa with high protamine content. Larger scrotal circumference contributes to higher sperm protamine content and lower content of sperm DNA damage (p < 0.05). In conclusion, sperm protamine content and sperm DNA damage are closely associated. Protamine deficiency is likely to be one of the contributing factors to DNA instability and damage, which can affect bull fertility.

Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle

Background

Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69–77 and 81–92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped.

Results

To further characterise these regions, a bioinformatic approach was undertaken to identify novel non-synonymous SNP within the QTL regions of interest in Brahman cattle. After SNP discovery, we used conventional molecular assay technologies to perform studies of two candidate genes in both breeds. Non-synonymous SNP mapped to Testis-expressed gene 11 (Tex11) were associated (P < 0.001) with scrotal circumference in both breeds, and associations with percentage of normal sperm cells were also observed (P < 0.05). Evidence for recent selection was found as Tex11 SNP form a haplotype segment of Bos taurus origin that is retained within Brahman and Tropical Composite cattle with greatest reproductive potential.

Conclusions

Association of non-synonymous SNP presented here are a first step to functional genetic studies. Bovine species may serve as a model for studying the role of Tex11 in male fertility, warranting further in-depth molecular characterisation.

Genetics of early and lifetime annual reproductive performance in cows of two tropical beef genotypes in northern Australia

Reproduction records from 2137 cows first mated at 2 years of age and recorded through to 8.5 years of age were used to study the genetics of early and lifetime reproductive performance from two genotypes (1020 Brahman and 1117 Tropical Composite) in tropical Australian production systems. Regular ultrasound scanning of the reproductive tract, coupled with full recording of mating, calving and weaning histories, allowed a comprehensive evaluation of a range of reproductive traits. Results showed components traits of early reproductive performance had moderate to high heritabilities, especially in Brahmans. The heritability of lactation anoestrous interval in 3-year-old cows was 0.51 ± 0.18 and 0.26 ± 0.11 for Brahman and Tropical Composite, respectively. Heritabilities of binary reproductive output traits (conception rate, pregnancy rate, calving rate and weaning rate) from first and second matings were generally moderate to high on the underlying scale. Estimates ranged from 0.15 to 0.69 in Brahman and 0.15 to 0.34 in Tropical Composite, but were considerably lower when expressed on the observed scale, particularly for those traits with high mean levels. Heritabilities of lifetime reproduction traits were low, with estimates of 0.11 ± 0.06 and 0.07 ± 0.06 for lifetime annual weaning rate in Brahman and Tropical Composite, respectively. Significant differences in mean reproductive performance were observed between the two genotypes, especially for traits associated with anoestrus in first-lactation cows. Genetic correlations between early-in-life reproductive measures and lifetime reproduction traits were moderate to high. Genetic correlations between lactation anoestrous interval and lifetime annual weaning rate were –0.62 ± 0.24 in Brahman and –0.87 ± 0.32 in Tropical Composite. The results emphasise the substantial opportunity that exists to genetically improve weaning rates in tropical beef cattle breeds by focusing recording and selection on early-in-life female reproduction traits, particularly in Brahman for traits associated with lactation anoestrus.

Multi-trait assessment of early-in-life female, male and genomic measures for use in genetic selection to improve female reproductive performance of Brahman cattle

Early-in-life female and male measures with potential to be practical genetic indicators were chosen from earlier analyses and examined together with genomic measures for multi-trait use to improve female reproduction of Brahman cattle. Combinations of measures were evaluated on the genetic gains expected from selection of sires and dams for each of age at puberty (AGECL, i.e. first observation of a corpus luteum), lactation anoestrous interval in 3-year-old cows (LAI), and lifetime annual weaning rate (LAWR, i.e. the weaning rate of cows based on the number of annual matings they experienced over six possible matings). Selection was on an index of comparable records for each combination. Selection intensities were less than theoretically possible but assumed a concerted selection effort was able to be made across the Brahman breed. The results suggested that substantial genetic gains could be possible but need to be confirmed in other data. The estimated increase in LAWR in 10 years, for combinations without or with genomic measures, ranged from 8 to 12 calves weaned per 100 cows from selection of sires, and from 12 to 15 calves weaned per 100 cows from selection of sires and dams. Corresponding reductions in LAI were 60–103 days or 94–136 days, and those for AGECL were 95–125 or 141–176 days, respectively. Coat score (a measure of the sleekness or wooliness of the coat) and hip height in females, and preputial eversion and liveweight in males, were measures that may warrant wider recording for Brahman female reproduction genetic evaluation. Pregnancy-test outcomes from Matings 1 and 2 also should be recorded. Percentage normal sperm may be important to record for reducing LAI and scrotal size and serum insulin-like growth factor-I concentration in heifers at 18 months for reducing AGECL. Use of a genomic estimated breeding value (EBV) in combination with other measures added to genetic gains, especially at genomic EBV accuracies of 40%. Accuracies of genomic EBVs needed to approach 60% for the genomic EBV to be the most important contributor to gains in the combinations of measures studied.

Genetic relationships between steer performance and female reproduction and possible impacts on whole herd productivity in two tropical beef genotypes

Steer growth and carcass composition, and female reproductive performance have been identified as key aspects of productivity by breeders of tropically adapted beef cattle in Australia. Research has also demonstrated that traits describing meat quality and feed intake and efficiency are of economic importance to Australia’s beef industry. The present study aimed to determine genetic relationships of traits describing steer growth, feed intake and efficiency, carcass composition and meat quality with female reproductive performance in two genotypes of tropically adapted beef cattle. Female reproduction traits describing outcomes of first (Mating 1) and second (Mating 2) annual matings and lifetime reproduction (averaged over 6 matings) were analysed for 1020 Brahman (BRAH) and 1117 Tropical Composite (TCOMP) females. Steer traits were available for 1007 BRAH and 1210 TCOMP half-sibs of the females evaluated for reproductive performance, and measurements of liveweight and body composition for 1025 BRAH and 1520 TCOMP bull progeny of the same females were included in the analysis. Results demonstrated that selection to increase steer carcass weight and eye muscle area and decrease carcass fat depth would have no significant unfavourable impact on female reproductive performance for both genotypes. Measures of liveweight, eye muscle area and P8 fat depth in young BRAH bulls, however, were only moderately correlated with steer carcass equivalents (rg = 0.28 to 0.55) and results showed that selection on the basis of bull measurements alone may negatively affect female lifetime annual calving rate (rg = –0.44 to –0.75) if both were not included in a multi-trait genetic evaluation and considered when making selection decisions. More favourable (lower) net feed intake in BRAH steers was genetically associated with lower Mating 1 weaning rate (rg = 0.76) and higher days to calving (rg = –0.50), although this did not significantly affect lifetime annual calving or weaning rate (rg = 0.10 and 0.29, respectively). For TCOMP, higher steer carcass P8 fat depth was unfavourably genetically associated with female Mating 2 weaning rate (rg = –0.76), although these relationships were not as strong for weaning rate at Mating 1 or when averaged over the animals lifetime (rg = 0.43 and –0.13, respectively). Lower (more favourable) shear force (a measure of tenderness) also displayed a significant genetic association with higher (less favourable) Mating 1 days to calving in TCOMP and, while standard errors were high, tended to be unfavourably associated with other measures of female reproduction evaluated for the present study. Steer growth, carcass composition, meat quality and residual feed intake and female reproduction could be improved simultaneously if measurements describing both are included in a multi-trait genetic evaluation. Results of the present study also showed that expanding female reproduction traits to include descriptors of first and second mating outcomes, as well as lifetime reproductive performance, would allow a fuller account to be taken of genetic relationships of male traits with female reproduction.

Genetic relationships of female reproduction with growth, body composition, maternal weaning weight and tropical adaptation in two tropical beef genotypes

The genetic relationships of female reproduction with growth and body composition, tropical adaptation traits and maternal weaning weight (descriptive of genetic potential milk production) were estimated in 1027 Brahman (BRAH) and 1132 Tropical Composite (TCOMP) females. Female reproduction was evaluated at puberty, as outcomes of the first and second annual mating periods (Mating 1 and Mating 2, which commenced when females averaged 27 and 39 months of age, respectively), as well as annual averages over up to six matings. Traits evaluated included age at puberty, Mating 1 and 2 pregnancy rate, weaning rate and days to calving, and lifetime annual calving and weaning rate. Traits describing growth and body composition (liveweight, hip height, ultrasound-scanned P8 fat depth and eye muscle area, subjective body condition score and blood IGF-I concentration) were measured in the animals as heifers (at ~18 months of age), and again at the start of Mating 2. Traits describing tropical adaptation included coat-length scores in both genotypes and, in BRAH, buffalo fly lesion scores. Previously reported analyses of these data identified heifer IGF-I and coat and buffalo-fly-lesion scores as potential genetic indicators for age at puberty in BRAH. The results of the present study found that exploiting these relationships would have no unfavourable genetic consequences for later female reproduction and, in some cases, may be indicators of female reproduction, when evaluated as outcomes of Matings 1 or 2, or as lifetime annual calving or weaning rates. For BRAH, heifer liveweight was a genetic indicator for Mating 1 weaning rate (rg = 0.70), and, while standard errors were high, there were also positive genetic correlations of heifer hip height, eye muscle area and blood IGF-I concentration with Mating 1 weaning rate (rg = 0.61, 0.58 and 0.43, respectively). For TCOMP, significant genetic relationships of heifer growth, body composition and tropical adaptation traits with female reproduction were virtually absent, suggesting that there is less opportunity to identify earlier in life measures as genetic indicators of reproduction for this genotype. Higher maternal weaning weight was significantly genetically related to lower lifetime annual weaning rate (rg = –0.50) in BRAH, and with lower Mating 2 calving and weaning rate (rg = –0.72 and –0.59, respectively) in TCOMP, which will need to be considered when making selection decisions that affect genetic milk in these genotypes. Importantly, the results presented revealed no strong genetic antagonisms of heifer growth and body composition traits with female reproduction, suggesting that selection could be undertaken to improve these simultaneously.

Genetic correlations of young bull reproductive traits and heifer puberty traits with female reproductive performance in two tropical beef genotypes in northern Australia

Genetic correlations of young bull and heifer puberty traits with measures of early and lifetime female reproductive performance were estimated in two tropical beef cattle genotypes. Heifer age at puberty was highly (rg = –0.71 ± 0.11) and moderately (rg = –0.40 ± 0.20) genetically correlated with pregnancy rate at first annual mating (mating 1) and lifetime annual calving rate, respectively in Brahman (BRAH). In Tropical Composite (TCOMP), heifer age at puberty was highly correlated with reproductive outcomes from the first re-breed (mating 2), mainly due to its association with lactation anoestrous interval (rg = 0.72 ± 0.17). Scrotal circumference were correlated with heifer age at puberty (rg = –0.41 ± 0.11 at 12 months in BRAH; –0.30 ± 0.13 at 6 months in TCOMP) but correlations were lower with later female reproduction traits. Bull insulin-like growth factor-I was correlated with heifer age at puberty (rg = –0.56 ± 0.11 in BRAH; –0.43 ± 0.11 in TCOMP) and blood luteinising hormone concentration was moderately correlated with lactation anoestrous interval (rg = 0.59 ± 0.23) in TCOMP. Semen quality traits, including mass activity, motility and percent normal sperm were genetically correlated with lactation anoestrus and female lifetime female reproductive traits in both genotypes, but the magnitudes of the relationships differed with bull age at measurement. Preputial eversion and sheath scores were genetically associated with lifetime calving and weaning rates in both genotypes. Several of the early-in-life male and female measures examined were moderately to highly genetically correlated with early and lifetime female reproduction traits and may be useful as indirect selection criteria for improving female reproduction in tropical breeds in northern Australia.

Genome-wide association study for inhibin, luteinizing hormone, insulin-like growth factor 1, testicular size and semen traits in bovine species

The fertility of young bulls impacts on reproduction rates, farm profit and the rate of genetic progress in beef herds. Cattle researchers and industry therefore routinely collect data on the reproductive performance of bulls. Genome-wide association studies were carried out to identify genomic regions and genes associated with reproductive traits measured during the pubertal development of Tropical Composite bulls, from 4 to 24 months of age. Data from 1 085 bulls were collected for seven traits: blood hormone levels of inhibin at 4 months (IN), luteinizing hormone following a gonadotropin releasing hormone challenge at 4 months (LH), insulin-like growth factor 1 at 6 months (IGF1), scrotal circumference at 12 months (SC), sperm motility at 18 months (MOT), percentage of normal spermatozoa at 24 months (PNS) and age at a scrotal circumference of 26 cm (AGE26, or pubertal age). Data from 729 068 single-nucleotide polymorphisms were used in the association analysis. Significant polymorphism associations were discovered for IN, IGF1, SC, AGE26 and PNS. Based on these associations, INHBE, INHBC and HELB are proposed as candidate genes for IN regulation. Polymorphisms associated with IGF1 mapped to the PLAG1 gene region, validating a reported quantitative trait locus on chromosome 14 for IGF1. The X chromosome contained most of the significant associations found for SC, AGE26 and PNS. These findings will contribute to the identification of diagnostic genetic markers and informed genomic selection strategies to assist breeding of cattle with improved fertility. Furthermore, this work provides evidence contributing to gene function annotation in the context of male fertility.

Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle

A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10(-4) ). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.