Genetic parameters of behavior traits of beef cattle classified using wearable devices.

With the development of wearable devices, it is now possible to monitor livestock behavior 24 h a day. In this study, we estimated the genetic parameters of the daily duration of six behaviors (feeding, moving, lying, standing, ruminating while lying, and ruminating while standing) in beef cattle, automatically classified using wearable devices. The devices were attached to 332 Japanese beef cattle at two stations for approximately 5 months.

Genomic and phenotypic selection indices for decreased birth weight, shortening fattening period, and regulating total weight gain in beef cattle.

Objective: This study aimed to develop genomic and phenotypic indices for beef cattle selection that afford progeny with reduced birth weight and fattening period. The indices should also allow regulating total weight gain during the fattening period and avoid marked increases of inbreeding.

Methods: Whether addition of constraint on total weight gain to constraints on body weight gain at up to four specific time points during the fattening process was effective for the weight gain until the end of the fattening period was examined in two selection indices with the selection trait being a phenotypic or a genomic breeding value random regression coefficient.

Development of an index that decreases birth weight, promotes postnatal growth and yet minimizes selection intensity in beef cattle.

Objective: The main goal of our current study was to improve the growth curve of meat animals by decreasing the birth weight while achieving a finishing weight that is the same as that before selection but at younger age.

Methods: Random regression model was developed to derive various selection indices to achieve desired gains in body weight at target time points throughout the fattening process. We considered absolute and proportional gains at specific ages (in weeks) and for various stages (i.

Genomic dissection of repeatability considering additive and nonadditive genetic effects for semen production traits in beef and dairy bulls.

The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that nonadditive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and nonadditive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include nonadditive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model.

Predicting the rate of inbreeding in populations undergoing four-path selection on genomically enhanced breeding values.

Objective: A formula is needed that is practical for current livestock breeding methods and that predicts the approximate rate of inbreeding (∆F) in populations where selection is performed according to four-path programs (sires to breed sons, sires to breed daughters, dams to breed sons, and dams to breed daughters). The formula widely used to predict inbreeding neglects selection, we need to develop a new formula that can be applied with or without selection.

Methods: The core of the prediction is to incorporate the long-tern genetic influence of the selected parents in four-selection paths executed as sires to breed sons, sires to breed daughters, dams to breed sons, and dams to breed daughters.

Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size.

Background: Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed.

Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle.

Intensive use of a few elite sires has increased the risk of the manifestation of deleterious recessive traits in cattle. Substantial genotyping data gathered using single-nucleotide polymorphism (SNP) arrays have identified the haplotypes with homozygous deficiency, which may compromise survival. We developed Japanese Black cattle haplotypes (JBHs) using SNP array data (4843 individuals) and identified deleterious recessive haplotypes using exome sequencing of 517 sires.

Genetic and genomic analyses for predicted methane-related traits in Japanese Black steers.

The objectives of this study were to estimate genetic parameters and to perform a genome-wide association study (GWAS) for predicted methane-related traits in Japanese Black steers. The methane production and yield traits were predicted using on-farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane-related traits during the total fattening period (52 weeks).

Genome-wide association study and genomic evaluation of feed efficiency traits in Japanese Black cattle using single-step genomic best linear unbiased prediction method.

The objectives of this study were to better understand the genetic architecture and the possibility of genomic evaluation for feed efficiency traits by (i) performing genome-wide association studies (GWAS), and (ii) assessing the accuracy of genomic evaluation for feed efficiency traits, using single-step genomic best linear unbiased prediction (ssGBLUP)-based methods. The analyses were performed in residual feed intake (RFI), residual body weight gain (RG), and residual intake and body weight gain (RIG) during three different fattening periods. The phenotypes from 4,578 Japanese Black steers, which were progenies of 362 progeny-tested bulls and the genotypes from the bulls were used in this study.

Development of a structural growth curve model that considers the causal effect of initial phenotypes.

Background: Growth curves have been widely used in genetic analyses to gain insights into the growth characteristics of both animals and plants. However, several questions remain unanswered, including how the initial phenotypes affect growth and what is the duration of any such impact. For beef cattle production in Japan, calves are procured from farms that specialize in reproduction and then moved to other farms where they are fattened to achieve their market/purchase value.

Effects of preselection of genotyped animals on reliability and bias of genomic prediction in dairy cattle.

Objective: Models for genomic selection assume that the reference population is an unselected population. However, in practice, genotyped individuals, such as progeny-tested bulls, are highly selected, and the reference population is created after preselection. In dairy cattle, the intensity of selection is higher in males than in females, suggesting that cows can be added to the reference population with less bias and loss of accuracy.

Selection on milk production and conformation traits during the last two decades in Japan.

Objective: The purpose of this study was to compare intended and actual yearly genetic gains for milk production and conformation traits and to investigate the simple selection criterion practiced among milk production and conformation traits during the last two decades in Japan. Learning how to utilize the information on intended and actual genetic gains during the last two decades into the genomic era is vital.

Methods: Genetic superiority for each trait for four paths of selection (sires to breed bulls [SB], sires to breed cows [SC], dams to breed bulls [DB], and dams to breed cows [DC]) was estimated.

Evaluation of feed efficiency traits for genetic improvement in Japanese Black cattle.

We evaluated the genetic relationships (1) among feed efficiency traits with different fattening periods, (2) between feed efficiency traits and growth traits, and (3) between feed efficiency traits and carcass traits, to determine the influence of genetic factors on feed efficiency traits. In total, 4,578 Japanese Black cattle from a progeny testing program were used. Residual feed intake (RFI), residual BW gain (RG), and residual intake and BW gain (RIG) were defined as feed efficiency traits, and were measured for the first half (approximately 9 to 15 months of age), latter half (approximately 15 to 21 months of age), and total period of fattening (approximately 9 to 21 months of age).

Effects of selection index coefficients that ignore reliability on economic weights and selection responses during practical selection.

Objective: In practical breeding, selection is often performed by ignoring the accuracy of evaluations and applying economic weights directly to the selection index coefficients of genetically standardized traits. The denominator of the standardized component trait of estimated genetic evaluations in practical selection varies with its reliability. Whereas theoretical methods for calculating the selection index coefficients of genetically standardized traits account for this variation, practical selection ignores reliability and assumes that it is equal to unity for each trait.

Ubiquitylation-independent ER-associated degradation of an AE1 mutant associated with dominant hereditary spherocytosis in cattle.

Various mutations in the AE1 (anion exchanger 1, band 3) gene cause dominant hereditary spherocytosis, a common congenital hemolytic anemia associated with deficiencies of AE1 of different degrees and loss of mutant protein from red blood cell membranes. To determine the mechanisms underlying decreases in AE1 protein levels, we employed K562 and HEK293 cell lines and Xenopus oocytes together with bovine wild-type AE1 and an R664X nonsense mutant responsible for dominant hereditary spherocytosis to analyze protein expression, turnover, and intracellular localization. R664X-mutant protein underwent rapid degradation and caused specifically increased turnover and impaired trafficking to the plasma membrane of the wild-type protein through hetero-oligomer formation in K562 cells.