Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle.

We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP. Meanwhile, DK had the highest prediction accuracy for NIRS-based C18:1 and MUFA, but the difference in accuracies between DK and KAML was slight. For all traits, accuracies of RF and CNN were lower than those of GBLUP. The KAML extends GBLUP methods, of which marker effects are weighted, and involves only additive genetic effects; whereas machine learning methods capture non-additive genetic effects. Thus, KAML is the most suitable method for breeding of fatty acid composition in Japanese Black cattle.

A survey of bovine leukemia virus resistant bovine leukocyte antigen (BoLA)-DRB3*009:02 allele-carrying Japanese Black cattle in two prefectures in Japan.

The bovine leukocyte antigen (BoLA) DRB3*009:02 allele is strongly associated with a low/undetectable bovine leukemia virus (BLV) proviral load. Understanding the status of cattle possessing DRB3*009:02 allele is key for BLV control by breeding. We performed a survey of DRB3*009:02-carrying cattle in two prefectures in Japan using a TaqMan assay developed previously. The allele was found in 3.8% (confidence interval (CI): 3.3-4.3) of 6020 Japanese Black female cattle. A prefecture-level difference was found: the allele was observed in 8.6% CI: 7.5-9.9) of 2242 cattle of the birth prefecture B in Kyushu/Okinawa region, and this percentage was significantly higher than those of prefecture C in Kyushu/Okinawa region (1.3% (CI: 0.4-3.4) of 319) and prefecture A in Chugoku region (0.9% (CI: 0.6-1.4) of 2741), respectively. Consideration on the difference in possession of DRB3*009:02 allele is needed to establish the more efficient control strategy of BLV infection in Japanese Black cattle.

Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle.

BACKGROUND: Size of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus, extent to which traits of interest affect accuracy of genomic prediction in Japanese Black cattle remains obscure. This study aimed to explore the size of reference population for expected accuracy of genomic prediction for simulated and carcass traits in Japanese Black cattle using a large amount of samples. RESULTS: A simulation analysis showed that heritability and size of reference population substantially impacted the accuracy of GEBV, whereas the number of quantitative trait loci did not. The estimated numbers of independent chromosome segments (Me) and the related weighting factor (w) derived from simulation results and a maximum likelihood (ML) approach were 1900-3900 and 1, respectively. The expected accuracy for trait with heritability of 0.1-0.5 fitted well with empirical values when the reference population comprised > 5000 animals. The heritability for carcass traits was estimated to be 0.29-0.41 and the accuracy of GEBVs was relatively consistent with simulation results. When the reference population comprised 7000-11,000 animals, the accuracy of GEBV for carcass traits can range 0.73-0.79, which is comparable to estimated breeding value obtained in the progeny test. CONCLUSION: Our simulation analysis demonstrated that the expected accuracy of GEBV for a polygenic trait with low-to-moderate heritability could be practical in Japanese Black cattle population. For carcass traits, a total of 7000-11,000 animals can be a sufficient size of reference population for genomic prediction.

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. We identified seven JBHs with homozygous deficiency. JBH_10 and JBH_17 were associated with the resuming of estrus after artificial insemination, indicating that these haplotypes carried deleterious mutations affecting embryonic survival. The exome data of 517 Japanese Black sires revealed that AC_000165.1:g.85341291C>G of IARS in JBH_8_2, AC_000174.1:g.74743512G>T of CDC45 in JBH_17, and a copy variation region (CNVR_27) of CLDN16 in JBH_1_1 and JBH_1_2 were the candidate mutations. A novel variant AC_000174.1:g.74743512G>T of CDC45 in JBH_17 was located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing. Mating between heterozygotes of JBH_17 indicated that homozygotes carrying the risk allele died around the blastocyst stage. Analysis of frequency of the CDC45 risk allele revealed that its carriers were widespread throughout the tested Japanese Black cattle population. Our approach can effectively manage the inheritance of recessive risk alleles in a breeding population.

Genomic imprinting variances of beef carcass traits and physiochemical characteristics in Japanese Black cattle.

The objective of this study was to estimate variance components related to imprinting for carcass traits and physiochemical characteristics in Japanese Black cattle. The carcass records obtained from 4,220 Japanese Black feedlot cattle included carcass weight (CW), rib eye area (REA), rib thickness, subcutaneous fat thickness, and beef marbling score (BMS), and the physiochemical characteristics were fat, moisture, glycogen per proportion of moisture content, oleic acid, and monounsaturated fatty acids (MUFA). To detect gametic effects, an imprinting model was fitted. High additive heritabilities were estimated for all traits (from 0.516 for glycogen to 0.853 for fat) and were reduced in Mendelian heritability. The range of the differences was from 0.002 (CW) to 0.331 (fat and moisture), and the reductions were due to their imprinting variances. The ratio of the imprinting variance to the total additive genetic variance for REA (0.374), BMS (0.291), fat (0.387), moisture (0.388), and MUFA (0.337) were large (p < 0.05). These imprinting variances were due to the maternal contribution and suggested the existence of maternally expressed genomic imprinting effects on the traits in Japanese Black cattle. Therefore, maternal gametic effects should be considered in breeding programs for Japanese Black cattle.

Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle.

Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position-unassigned SNPs, or "buried SNPs" include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.

An approach of estimating individual growth curves for young thoroughbred horses based on their birthdays.

We propose an approach of estimating individual growth curves based on the birthday information of Japanese Thoroughbred horses, with considerations of the seasonal compensatory growth that is a typical characteristic of seasonal breeding animals. The compensatory growth patterns appear during only the winter and spring seasons in the life of growing horses, and the meeting point between winter and spring depends on the birthday of each horse. We previously developed new growth curve equations for Japanese Thoroughbreds adjusting for compensatory growth. Based on the equations, a parameter denoting the birthday information was added for the modeling of the individual growth curves for each horse by shifting the meeting points in the compensatory growth periods. A total of 5,594 and 5,680 body weight and age measurements of Thoroughbred colts and fillies, respectively, and 3,770 withers height and age measurements of both sexes were used in the analyses. The results of predicted error difference and Akaike Information Criterion showed that the individual growth curves using birthday information better fit to the body weight and withers height data than not using them. The individual growth curve for each horse would be a useful tool for the feeding managements of young Japanese Thoroughbreds in compensatory growth periods.

Anti-inflammatory and Intestinal Barrier-protective Activities of Commensal Lactobacilli and Bifidobacteria in Thoroughbreds: Role of Probiotics in Diarrhea Prevention in Neonatal Thoroughbreds.

We previously isolated the commensal bacteria lactobacilli and bifidobacteria from the Thoroughbred intestine and prepared the horse probiotics LacFi(TM), consisting of Lactobacillus ruminis KK14, L. equi KK 15, L. reuteri KK18, L. johnsonii KK21, and Bifidobacterium boum HU. Here, we found that the five LacFi(TM) constituent strains remarkably suppressed pro-inflammatory interleukin-17 production in mouse splenocytes stimulated with interleukin-6 and transforming growth factor-ß. The protective effects of the probiotic on impaired intestinal barrier function were evaluated in Caco-2 cells treated with tumor necrosis factor-α. Evaluation of transepithelial resistance showed that all the strains exhibited intestinal barrier protective activity, with significant suppression of barrier impairment by L. reuteri KK18. The LacFi(TM) constituent strains were detected in neonatal LacFi(TM)-administered Thoroughbred feces using polymerase chain reaction denaturing gradient gel electrophoresis and culture methods. These five strains were found to be the predominant lactobacilli and bifidobacteria in the intestinal microbiota of LacFi(TM)-administered Thoroughbreds. Administration of LacFi(TM) to neonatal Thoroughbreds decreased diarrhea incidence from 75.9% in the control group (n=29 neonatal Thoroughbreds) to 30.7% in the LacFi(TM)-administered group (n=101 neonatal Thoroughbreds) immediately after birth to 20 weeks after birth. LacFi(TM) treatment also prevented diarrhea especially at and around 4 weeks and from 10 to 16 weeks. The duration of diarrhea was also shorter in the probiotics-administered group (7.4 ± 0.8 days) than in the control group (14.0 ± 3.2 days). These results indicate that the LacFi(TM) probiotics regulates intestinal function and contributes to diarrhea prevention.

Empirical Percentile Growth Curves with Z-scores Considering Seasonal Compensatory Growths for Japanese Thoroughbred Horses.

Percentile growth curves are often used as a clinical indicator to evaluate variations of children's growth status. In this study, we propose empirical percentile growth curves using Z-scores adapted for Japanese Thoroughbred horses, with considerations of the seasonal compensatory growth that is a typical characteristic of seasonal breeding animals. We previously developed new growth curve equations for Japanese Thoroughbreds adjusting for compensatory growth. Individual horses and residual effects were included as random effects in the growth curve equation model and their variance components were estimated. Based on the Z-scores of the estimated variance components, empirical percentile growth curves were constructed. A total of 5,594 and 5,680 body weight and age measurements of male and female Thoroughbreds, respectively, and 3,770 withers height and age measurements were used in the analyses. The developed empirical percentile growth curves using Z-scores are computationally feasible and useful for monitoring individual growth parameters of body weight and withers height of young Thoroughbred horses, especially during compensatory growth periods.

Empirical Growth Curve Estimation Using Sigmoid Sub-functions that Adjust Seasonal Compensatory Growth for Male Body Weight of Thoroughbred Horses.

Thoroughbred horses are seasonal mating animals, raised in northern regions or countries. Foals born yearly in spring generally show a typical seasonal compensatory growth pattern, in which their growth rate declines in the first winter and increases in the next spring. In this study, a new empirical adjustment approach is proposed to adjust for this compensatory growth when growth curve equations are estimated, by using 1,633 male body weights of Thoroughbreds as an illustrating example. Based on general Richards growth curve equation, a new growth curve equation was developed and fit to the weight-age data. The new growth curve equation had a sigmoid sub-function that can adjust the compensatory growth, combined with the Richards biological parameter responsible for the maturity of animals. The unknown parameters included in the equations were estimated by SAS NLMIXED procedure. The goodness of fit was examined by using Akaike's Information Criterion (AIC). The AIC values decreased from 13,053 (general Richards equation) to 12,794 (the newly developed equation), indicating the better fit of the new equation to the weight-age data. The shape of the growth curve was improved during the period of compensatory growth. The proposed method is one of the useful approaches for adjusting seasonal compensatory growth in growth curve estimations for Thoroughbreds, and for their management during the compensatory period. Based on this approach, the optimal growth curve equations can be estimated also for female body weight of Thoroughbreds or other growth traits affected by seasonal compensatory growth.

In vivo effects of intra-articular injection of gelatin hydrogen microspheres containing basic fibroblast growth factor on experimentally induced defects in third metacarpal bones of horses.

OBJECTIVE: To evaluate the effect of intra-articular injection of gelatin hydrogel microspheres containing basic fibroblast growth factor (bFGF) on experimentally induced defects in third metacarpal bones (MC3s) of horses, in vivo. ANIMALS: 6 healthy adult Thoroughbreds. PROCEDURES: Horses were anesthetized, and a hole (diameter, 4.5 mm) was drilled into the medial condyle of both MC3s of each horse. One milliliter (100 microg) of a solution of gelatin hydrogel microspheres (2 mg) containing bFGF was injected into the joint capsule of the right metacarpophalangeal joint of each horse (bFGF joint). One milliliter of saline (0.9% NaCl) solution was injected into the left metacarpophalangeal joint (control joint). Radiography was performed 1 day and 4, 8, 12, and 16 weeks after surgery to evaluate bone defect refilling. Sixteen weeks after surgery, multidetector-row computed tomography (MDRCT) was performed to determine the degree of refilling at the bone defect site. RESULTS: Radiography revealed healing of bone defects at 4 to 12 weeks after surgery in bFGF joints and at 8 to 16 weeks after surgery in control joints. In addition, MDRCT revealed a higher degree of healing in bFGF versus control joints. Mean+/-SD MDRCT score for bFGF joints (411.7+/-135.6 Hounsfield units) was significantly higher than that for control joints (240.8+/-133.1 Hounsfield units). CONCLUSIONS AND CLINICAL RELEVANCE: Treatment of horses with gelatin hydrogel microspheres that contained bFGF enhanced bone regeneration and healing of experimentally induced defects. This treatment strategy may be useful for treating horses with fractures.

Response of biochemical markers of bone metabolism to exercise intensity in thoroughbred horses.

We studied the response of biochemical markers of bone metabolism to exercise intensity in horses. Four horses were walked on a mechanical walker for one week (pre-exercise). Then they performed low-speed exercise on a high-speed treadmill in the first week and medium-speed exercise in the second week and high-speed exercise in the third week of training. We measured two indices of bone resorption, serum hydroxyproline concentration and the urinary deoxypyridinoline/creatinine ratio, and serum osteocalcin (OC) concentration as an index of bone formation. Both indices of bone resorption gradually decreased during the experiment. Serum OC concentration did not change in the first week but was significantly lower in the second and the third weeks compared to in the pre-exercise period and in the first week. These results suggest that the low-speed exercise decreased bone resorption but did not affect bone formation, which possibly results in increasing bone mineral content and strengthening of bones. The high-speed exercise decreased bone formation and bone resorption, i.e., bone turnover was suppressed. The low-speed exercise may be preferable for increasing bone mineral content.

Effect of exercise on iron metabolism in horses.

We investigated the effect of exercise on iron metabolism in horses. Four horses were walked on a mechanical walker for 1 wk (pre-exercise). They then performed moderate exercise on a high-speed treadmill in the first week of the exercise and relative high in the second week and high in the third week. Serum iron was significantly lower in the third week of exercise than in the pre-exercise. Transferrin saturation (TS) was significantly lower in the first and third weeks of exercise than in the pre-exercise. Serum haptoglobin was significantly lower in the first week of exercise than in the pre-exercise and further significantly lower in the second and third weeks than in the first. The packed cell volume did not change during the experiment. The exercise significantly increased the apparent absorption of iron. Urinary iron excretion did not change throughout the experiment. Sweat iron loss did not change during the exercise. The exercise significantly increased iron balance. We considered that hemolysis is induced by moderate exercise and is further enhanced by heavy exercise, which decreases serum iron and TS. However, the increase in iron absorption compensates for the adverse effect of exercise on iron status. Therefore, exercise does not induce anemia in horses.