Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle.

We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited.

Estimation of the autosomal contribution to total additive genetic variability of carcass traits in Japanese Black cattle.

We attempted to estimate the additive genetic variance explained by each autosome, using genotype data of 33,657 single nucleotide polymorphism (SNP) markers in 2271 Japanese Black fattened steers. Traits were cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percentage, and marbling score. Two mixed linear models were used: One is that (model 1) incorporating a genomic relationship matrix (G matrix) constructed by using all available SNPs, and another (model 2), incorporating two G matrices constructed by using the SNPs on one autosome and using those on the remaining autosomes.

An intersection network based on combining SNP coassociation and RNA coexpression networks for feed utilization traits in Japanese Black cattle.

Genome-wide association studies (GWAS) of quantitative traits have detected numerous genetic associations, but they encounter difficulties in pinpointing prominent candidate genes and inferring gene networks. The present study used a systems genetics approach integrating GWAS results with external RNA-expression data to detect candidate gene networks in feed utilization and growth traits of Japanese Black cattle, which are matters of concern. A SNP coassociation network was derived from significant correlations between SNPs with effects estimated by GWAS across 7 phenotypic traits.

Structure and polymorphisms of the major histocompatibility complex in the Oriental stork, Ciconia boyciana.

The major histocompatibility complex (MHC) is highly polymorphic and plays a central role in the vertebrate immune system. Despite its functional consistency, the MHC genomic structure differs substantially among organisms. In birds, the MHCs of Galliformes and the Japanese crested ibis (Pelecaniformes) are well-characterized, but information about other avian MHCs remains scarce.

Genetic Analyses in the Japanese Captive Population of Japanese Crested Ibis () using Pedigree Information.

The Japanese captive population of Japanese crested ibis () was established using 5 founders derived from the Chinese captive population. Its size has increased rapidly, and the maintenance phase is about to start. Thus, this study was designed to perform genetic analyses in this population with pedigree information, considering the adoption of mean kinship strategy as the breeding strategy suited to the maintenance phase.

Estimation of variance and genomic prediction using genotypes imputed from low-density marker subsets for carcass traits in Japanese black cattle.

The influence of genotype imputation using low-density single nucleotide polymorphism (SNP) marker subsets on the genomic relationship matrix (G matrix), genetic variance explained, and genomic prediction (GP) was investigated for carcass weight and marbling score in Japanese Black fattened steers, using genotype data of approximately 40,000 SNPs. Genotypes were imputed using equally spaced SNP subsets of different densities. Two different linear models were used.

Change of fatty acid composition of the lumbar longissimus during the final stage of fattening in the Japanese Black cattle.

Consideration of the shortened fattening period seems to be worthwhile for the realization of profitable beef production. In this study, change of fatty acid composition of the lumbar longissimus during the final stage of fattening was investigated in Japanese Black cattle. Each of 110 fattening animals was sampled three times: the initial two samples were taken by biopsy (25.

Accuracy of imputation of single nucleotide polymorphism marker genotypes from low-density panels in Japanese Black cattle.

Using target and reference fattened steer populations, the performance of genotype imputation using lower-density marker panels in Japanese Black cattle was evaluated. Population imputation was performed using BEAGLE software. Genotype information for approximately 40,000 single nucleotide polymorphism (SNP) markers by Illumina BovineSNP50 BeadChip was available, and imputation accuracy was assessed based on the average concordance rates of the genotypes, varying equally spaced SNP densities, and the number of individuals in the reference population.

Predicting the phenotypic values of physiological traits using SNP genotype and gene expression data in mice.

Predicting phenotypes using genome-wide genetic variation and gene expression data is useful in several fields, such as human biology and medicine, as well as in crop and livestock breeding. However, for phenotype prediction using gene expression data for mammals, studies remain scarce, as the available data on gene expression profiling are currently limited. By integrating a few sources of relevant data that are available in mice, this study investigated the accuracy of phenotype prediction for several physiological traits.

Structure and polymorphism of the major histocompatibility complex class II region in the Japanese Crested Ibis, Nipponia nippon.

The major histocompatibility complex (MHC) is a highly polymorphic genomic region that plays a central role in the immune system. Despite its functional consistency, the genomic structure of the MHC differs substantially among organisms. In birds, the MHC-B structures of Galliformes, including chickens, have been well characterized, but information about other avian MHCs remains sparse.

Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle.

Background: Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poorly studied. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of equally-spaced single nucleotide polymorphisms (SNPs) density on genomic relationship matrix (G matrix), genetic variance explained and GE were investigated using the genotype data of about 40,000 SNPs and two statistical models.

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis.

Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers.

Genome-wide SNP and STR discovery in the Japanese crested ibis and genetic diversity among founders of the Japanese population.

The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management.

Genetic diversity and structure in the Sado captive population of the Japanese crested ibis.

The Japanese crested ibis Nipponia nippon is a critically threatened bird. We assessed genetic diversity and structure in the Sado captive population of the Japanese crested ibis based on 24 and 50 microsatellite markers developed respectively for the same and related species. Of a total of 74 loci, 19 showed polymorphisms in the five founder birds of the population, and therefore were useful for the analysis of genetic diversity and structure.

Estimation of variance components for carcass traits in Japanese Black cattle using 50K SNP genotype data.

Genomic selection using high-density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy-three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score.

The W- and Z-linked EE0.6 sequences used for molecular sexing of captive Japanese crested ibis on Sado Island.

The Japanese crested ibis Nipponia nippon is a critically threatened bird. Accurate sexing is necessary to perform effective management of captive breeding toward a national project for a tentative release of the Japanese crested ibis on Sado Island. A PCR-based sexing method targeting a 0.

QTL/microarray approach using pathway information.

Background: A combined quantitative trait loci (QTL) and microarray-based approach is commonly used to find differentially expressed genes which are then identified based on the known function of a gene in the biological process governing the trait of interest. However, a low cutoff value in individual gene analyses may result in many genes with moderate but meaningful changes in expression being missed.

Results: We modified a gene set analysis to identify intersection sets with significantly affected expression for which the changes in the individual gene sets are less significant.

Non-invasive sampling technique for DNA extraction from captive Japanese Crested Ibis on Sado Island.

The Japanese Crested Ibis Nipponia nippon is a critically threatened bird. The post-hatch eggs of the current captive population of this species on Sado Island have been stored at room temperature for the long-term. In this study, we investigated the suitability of the vascularized chorioallantois membrane from the eggs as a non-invasive DNA source.

Estimation of breeding values from large-sized routine carcass data in Japanese Black cattle using Bayesian analysis.

Volumes of official data sets have been increasing rapidly in the genetic evaluation using the Japanese Black routine carcass field data. Therefore, an alternative approach with smaller memory requirement to the current one using the restricted maximum likelihood (REML) and the empirical best linear unbiased prediction (EBLUP) is desired. This study applied a Bayesian analysis using Gibbs sampling (GS) to a large data set of the routine carcass field data and practically verified its validity in the estimation of breeding values.

Investigation of Gibbs sampling conditions to estimate variance components from Japanese Black carcass field data.

The genetic evaluation using the carcass field data in Japanese Black cattle has been carried out employing an animal model, implementing the restricted maximum likelihood (REML) estimation of additive genetic and residual variances. Because of rapidly increasing volumes of the official data sets and therefore larger memory spaces required, an alternative approach like the REML estimation could be useful. The purpose of this study was to investigate Gibbs sampling conditions for the single-trait variance component estimation using the carcass field data.

Efficient computation of the inverse of gametic relationship matrix for a marked QTL.

Best linear unbiased prediction of genetic merits for a marked quantitative trait locus (QTL) using mixed model methodology includes the inverse of conditional gametic relationship matrix (G-1) for a marked QTL. When accounting for inbreeding, the conditional gametic relationships between two parents of individuals for a marked QTL are necessary to build G-1 directly. Up to now, the tabular method and its adaptations have been used to compute these relationships.

A comparison of interval mapping procedures including the QTL-cluster mapping.

Using the deterministic sampling, patterns of the log-likelihood surfaces expected in some interval mapping procedures for estimating the position of, and the effect for, QTL(s) were investigated for the situations where a single QTL or closely linked QTLs are contained in a chromosome segment bracketed with two markers. The mapping procedures compared were the conventional, likelihood-based interval mapping (IM), the regression interval mapping (RIM), and the QTL-cluster mapping (CM) in which the conditional probabilities of transmission of the whole segment marked by the flanking markers were taken into consideration. The half-sib design was used here, and several cases of the true genetic model were considered, differing in the number of QTLs contained in the marker interval, the linkage phase for the sire, and the magnitude of the QTL(s) effect.

A recursive procedure to compute the gametic relationship matrix and its inverse for marked QTL clusters.

Recently, a variety of mixed linear models have been proposed for marker-assisted prediction of the effects of quantitative trait loci (QTLs) in outbred populations of animals. One of them addresses the effects of a cluster of linked QTLs, or those of a particular chromosomal segment, marked by DNA marker(s) and requires that the inverse of the corresponding gametic relationship matrix whose elements are the conditional expected values of the identity-by-descent (IBD) proportions between gametes for individuals be evaluated. Here, for a model of this type, utilizing the property of the IBD set and using the information on the joint gametogenesis processes at the flanking marker loci, we present a recursive method to systematically calculate the elements of the gametic relationship matrix and its inverse.

Prediction of additive genetic effects for the QTL-cluster on the basis of data on surrounding markers in outbred populations.

This paper described a method for predicting additive effects of a cluster of tightly linked QTLs for outbred populations of animals in the situation where the QTLs are located on a chromosome segment surrounded by multiple linked DNA markers. We present a mixed model method for best linear unbiased prediction (conditional to the marker data) of the additive effects of the QTL-cluster and of the remaining QTLs unlinked to the marker linkage group. This method takes into consideration the identity-by-descent proportion (IBDP) for the particular chromosomal segment, in contrast to some other methods which use IBD probabilities at one specific location.