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.

One of the key profit drivers in any animal breeding program is fertility as it contributes directly to the progeny produced. Typically, fertility traits are hard to quantify and lowly heritable so they are often ignored in breeding programs. The inclusion of male fertility traits could allow for selection on heritable traits that are easy to measure and implement in a commercial breeding program. The utilization of male fertility traits could improve overall fertility and production. Bull breeding soundness evaluation traits were heritable, ranging from low to high, allowing for genetic improvement in those traits. Seven traits were recommended as selection criteria in a breeding program, which included two physical traits and five sperm traits. Implementing these seven traits in a breeding program would allow for a higher calving rate and associated increased profits.

Cross-species enhancer prediction using machine learning.

Cis-regulatory elements (CREs) are non-coding parts of the genome that play a critical role in gene expression regulation. Enhancers, as an important example of CREs, interact with genes to influence complex traits like disease, heat tolerance and growth rate. Much of what is known about enhancers come from studies of humans and a few model organisms like mouse, with little known about other mammalian species. Previous studies have attempted to identify enhancers in less studied mammals using comparative genomics but with limited success. Recently, Machine Learning (ML) techniques have shown promising results to predict enhancer regions. Here, we investigated the ability of ML methods to identify enhancers in three non-model mammalian species (cattle, pig and dog) using human and mouse enhancer data from VISTA and publicly available ChIP-seq. We tested nine models, using four different representations of the DNA sequences in cross-species prediction using both the VISTA dataset and species-specific ChIP-seq data. We identified between 809,399 and 877,278 enhancer-like regions (ELRs) in the study species (11.6-13.7% of each genome). These predictions were close to the ~8% proportion of ELRs that covered the human genome. We propose that our ML methods have predictive ability for identifying enhancers in non-model mammalian species. We have provided a list of high confidence enhancers at https://github.com/DaviesCentreInformatics/Cross-species-enhancer-prediction and believe these enhancers will be of great use to the community.

Genomic Analysis of Purebred and Crossbred Angus Cows Quantifies Heterozygosity, Breed, and Additive Effects on Components of Reproduction.

Multiple studies have quantified the production differences of Hereford Angus crossbreds compared to purebred Angus for a range of traits including growth, carcass, and reproductive traits. This study aims to quantify breed and heterosis effects on maternal performance using genomics. Thirty Hereford and thirty Angus sires were mated to 1100 Angus heifers and cows in a large commercial herd run on pasture at Musselroe Bay, Tasmania, Australia. Approximately 1650 calves were born. Heifers were weaned, scanned for attainment of puberty prior to joining at approximately 15 months of age, joined, and then recorded for status of pregnancy, calving, lactating, 2nd pregnancy, and weaning of second calf. Heterozygosity effects were significant for heifer pre-joining weight and height as well as proportion pubertal. Breed differences were significant for the same traits plus pregnancy rate at second joining and proportion rearing two calves. Genetic parameters were reported for 13 traits. On average, higher genetic merit (Estimated Breeding Value, EBV percentile) Hereford bulls were used than Angus for growth and puberty, but they were similar for fat and reproduction. Days to calving BREEDPLAN EBVs of the sires were related to puberty and reproduction. Scrotal size BREEDPLAN EBVs of the sires were related to attainment of puberty genomic EBVs calculated. In summary, breed differences in growth and puberty were due to heterosis, but there was an advantage of Hereford genes for reproductive performance. Ongoing emphasis on selection for reduced days to calving and estimation of multi-breed EBVs is important.

Evidence of marbling as a single connected entity in beef striploins.

Serial sections of Angus striploins that varied in marbling were analysed in three dimensions to assess potential differences in intramuscular fat structure. The majority of the intramuscular fat appeared to be connected along the 100 mm of muscle in both the highly marbled and less marbled striploins. Thus, rather than having dispersed individual flecks of marbling, the intramuscular fat was a single entity within the striploin. The local shape patterns of this entity varied with marbling level in that the structure had an increased diameter in the highly marbled striploins. However, the amount of branching in the intramuscular fat did not vary with the level of marbling. The results suggest that marbling may occur along an internal structure, such as the vascular system or interstitium, in the longissimus muscle. It is postulated that when beef marbling increases, additional intramuscular fat is not deposited in isolated sites but along this internal structure, widening the existing entity rather than changing the shape.

Widespread differential maternal and paternal genome effects on fetal bone phenotype at mid-gestation.

Parent-of-origin-dependent (epi)genetic factors are important determinants of prenatal development that program adult phenotype. However, data on magnitude and specificity of maternal and paternal genome effects on fetal bone are lacking. We used an outbred bovine model to dissect and quantify effects of parental genomes, fetal sex, and nongenetic maternal effects on the fetal skeleton and analyzed phenotypic and molecular relationships between fetal muscle and bone. Analysis of 51 bone morphometric and weight parameters from 72 fetuses recovered at day 153 gestation (54% term) identified six principal components (PC1-6) that explained 80% of the variation in skeletal parameters. Parental genomes accounted for most of the variation in bone wet weight (PC1, 72.1%), limb ossification (PC2, 99.8%), flat bone size (PC4, 99.7%), and axial skeletal growth (PC5, 96.9%). Limb length showed lesser effects of parental genomes (PC3, 40.8%) and a significant nongenetic maternal effect (gestational weight gain, 29%). Fetal sex affected bone wet weight (PC1, p < 0.0001) and limb length (PC3, p < 0.05). Partitioning of variation explained by parental genomes revealed strong maternal genome effects on bone wet weight (74.1%, p < 0.0001) and axial skeletal growth (93.5%, p < 0.001), whereas paternal genome controlled limb ossification (95.1%, p < 0.0001). Histomorphometric data revealed strong maternal genome effects on growth plate height (98.6%, p < 0.0001) and trabecular thickness (85.5%, p < 0.0001) in distal femur. Parental genome effects on fetal bone were mirrored by maternal genome effects on fetal serum 25-hydroxyvitamin D (96.9%, p < 0.001) and paternal genome effects on alkaline phosphatase (90.0%, p < 0.001) and their correlations with maternally controlled bone wet weight and paternally controlled limb ossification, respectively. Bone wet weight and flat bone size correlated positively with muscle weight (r = 0.84 and 0.77, p < 0.0001) and negatively with muscle H19 expression (r = -0.34 and -0.31, p < 0.01). Because imprinted maternally expressed H19 regulates growth factors by miRNA interference, this suggests muscle-bone interaction via epigenetic factors.

Major effect of retinal short-chain dehydrogenase reductase (RDHE2) on bovine fat colour.

Beef with yellow fat is considered undesirable by consumers in most European and Asian markets. ß-Carotene is the major carotenoid deposited in the adipose tissue and milk fat of cattle (Bos taurus), which can result in the yellowness. The effects of retinal short-chain dehydrogenase reductase (RDHE2) and ß, ß-carotene 9',10-dioxygenase (BCO2) were considered jointly as major candidate genes for causing the yellow fat colour, based on their genomic locations in the fat colour quantitative trait loci (QTL) and their roles in the metabolism of ß-carotene. In a secondary pathway, BCO2 cleaves ß-carotene into retinoic acid, the most potent form of vitamin A. RDHE2 converts trans-retinol to trans-retinal, a less active form of vitamin A. We evaluated the effects of two amino acid variants of the RDHE2 gene (V6A and V33A) along with a mutation in the BCO2 gene that results in a stop codon (W80X) in seven cattle populations. The RDHE2 V6A genotype affected several fat colour traits but the size of the effect varied in the populations studied. The genotype effect of the RDHE2 V33A variant was observed only in New Zealand samples of unknown breed. In general, the individual effects of RDHE2 V6A and V33A SNPs genotypes were greater in the random New Zealand samples than in samples from pedigreed Jersey-Limousin backcross progeny, accounting for 8-17 % of the variance in one population. Epistasis between the BCO2 W80X and RDHE2 variants was observed, and in some populations this explained more of the variation than the effects of the individual RDHE2 variants.

Joint modeling of additive and non-additive (genetic line) effects in multi-environment trials.

A statistical approach for the analysis of multi-environment trials (METs) is presented, in which selection of best performing lines, best parents, and best combination of parents can be determined. The genetic effect of a line is partitioned into additive, dominance and residual non-additive effects. The dominance effects are estimated through the incorporation of the dominance relationship matrix, which is presented under varying levels of inbreeding. A computationally efficient way of fitting dominance effects is presented which partitions dominance effects into between family dominance and within family dominance line effects. The overall approach is applicable to inbred lines, hybrid lines and other general population structures where pedigree information is available.

Fatty acid synthase effects on bovine adipose fat and milk fat.

A quantitative trait locus (QTL) was identified by linkage analysis on bovine Chromosome 19 that affects the fatty acid, myristic acid (C14:0), in subcutaneous adipose tissue of pasture-fed beef cattle (99% level: experiment-wise significance). The QTL was also shown to have significant effects on ten fatty acids in the milk fat of pasture-fed dairy cattle. A positional candidate gene for this QTL was identified as fatty acid synthase (FASN), which is a multifunctional enzyme with a central role in the metabolism of lipids. Five single nucleotide polymorphisms (SNPs) were identified in the bovine FASN gene, and animals were genotyped for FASN SNPs in three different cattle resource populations. Linkage and association mapping results using these SNPs were consistent with FASN being the gene underlying the QTL. SNP substitution effects for C14:0 percentage were found to have an effect in the opposite direction in adipose fat to that in milk fat. It is concluded that SNPs in the bovine FASN gene are associated with variation in the fatty acid composition of adipose fat and milk fat.