Evaluating the Efficacy of Target Capture Sequencing for Genotyping in Cattle.

(1) Background: Target capture sequencing (TCS) is potentially a cost-effective way to detect single-nucleotide polymorphisms (SNPs) and an alternative to SNP array-based genotyping. (2) Methods: We evaluated the effectiveness and reliability of TCS in cattle breeding scenarios using 48 female and 8 male samples. DNA was extracted from blood samples, targeted for 71,746 SNPs with TWIST probes, and sequenced on an MGI platform.

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.

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.

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.

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.

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.

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. β-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 β, β-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 β-carotene.

Reporter gene imaging using radiographic contrast from nonradioactive iodide sequestered by the sodium-iodide symporter.

The hypothesis that the human sodium-iodide symporter, NIS, can be used to detect NIS expression using standard radiological techniques was tested using adenoviral transduced NIS expression in human tumor xenografts grown in mice and in a naive dog prostate. Nonradioactive iodide was administered systemically to animals that 1-3 days previously had received a local injection of a replication-competent adenovirus expressing NIS under the control of the CMV promoter. The distribution of radiopacity was assessed in mouse tumors using micro-CT and a clinical X-ray machine and in the prostate of an anesthetized dog using a clinical spiral CT.

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.

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.

Joint modeling of additive and non-additive genetic line effects in single field trials.

A statistical approach is presented for selection of best performing lines for commercial release and best parents for future breeding programs from standard agronomic trials. The method involves the partitioning of the genetic effect of a line into additive and non-additive effects using pedigree based inter-line relationships, in a similar manner to that used in animal breeding. A difference is the ability to estimate non-additive effects.