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.

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.

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.

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.

The spatial and temporal expression of delta-like protein 1 in the rat pituitary gland during development.

An analysis of secreted proteins by the signal sequence trap method using a cDNA library of the rat pituitary anlage at embryonic days (E) 13.5 revealed the abundant expression of delta-like protein 1 (Dlk1) in the pituitary gland. Dlk1, an epidermal growth factor-like repeat protein in preadipocytes, functions in maintaining the preadipose state.

Pnlip encoding pancreatic lipase is a possible candidate for intramuscular fat accumulation QTL in OLETF rat.

A quantitative trait locus (QTL) responsible for intramuscular fat accumulation in Musculus longissimus of Otsuka Long-Evans Tokushima Fatty (OLETF) rat, Imfm, was previously mapped to the approximately 10-cM genomic region between D1Rat166 and D1Rat90 on chromosome 1 using Imfm congenic strain. In this study, we refined the Imfm region to a approximately 2.3-cM genomic region between D1Rat225 and D1Rat90, using 12 informative recombinants selected from 176 (Imfm congenic x F344) F, x Imfm congenic backcross progenies.

Identification of positional candidates for bovine placental genes responsible for early embryonic death during cloning-attempted pregnancy.

Our previous study detected 291 and 77 genes showing early embryonic death-associated elevation and reduction of expression, respectively, in the fetal placenta of the cow carrying somatic nuclear transfer-derived cloned embryo. In this study, we mapped the 10 genes showing the elevation and the 10 genes doing the reduction most significantly, using somatic cell hybrid and bovine draft genome sequence. We then compared the mapped positions for these genes with the genomic locations of bovine quantitative trait loci for still-birth and/or abortion.

Early embryonic death-associated changes in genome-wide gene expression profiles in the fetal placenta of the cow carrying somatic nuclear-derived cloned embryo.

Successful somatic nuclear transfer-derived cloning has been reported in cattle; however, the cloned embryo is highly susceptible to death around day 60 of gestation leading to early embryonic loss. The early embryonic death is postulated to possibly arise in part from an atypical placentation. We have performed cDNA macroarray analysis using 3,353 of the previously cataloged 4,165 genes, in order to characterize the early embryonic death-associated changes in genome-wide gene expression profiles in the fetal placenta of the cow carrying somatic nuclear transfer-derived cloned embryo.

Pnlip encoding pancreatic lipase is possible candidate for obesity QTL in the OLETF rat.

The Otsuka Long-Evans Tokushima Fatty (OLETF) rat exhibits polygenic obesity, and one of quantitative trait loci (QTLs) responsible for a susceptibility to obesity in the OLETF, Nidd6/of, has been mapped to the approximately 10-cM genomic region between D1Rat166 and D1Rat90 on chromosome 1 in (OLETF x normal) F2 intercross. In this study, we have attempted to identify the causal gene for the Nidd6/of QTL. A Nidd6/of congenic strain, constructed by introgressing the OLETF allele on the mapped Nidd6/of region in the normal F344 rat strain, confirmed the existence of the Nidd6/of as obesity QTL.

Bifunctional properties of peroxisome proliferator-activated receptor gamma1 in KDR gene regulation mediated via interaction with both Sp1 and Sp3.

Vascular endothelial growth factor receptor 2 (KDR) plays a critical role in mediating a variety of vasculogenic and angiogenic processes, including diabetic retinopathy. We previously demonstrated that the promoter activity of the KDR gene in retinal capillary endothelial cells (RCECs) was regulated in part by the relative concentration of positive/negative transcription factors Sp1/Sp3. We also reported that the peroxisome proliferator-activated receptor (PPAR)gamma ligand could inhibit intraocular angiogenesis.

Capn10, a candidate gene responsible for type 2 diabetes mellitus in the OLETF rat.

The rat strain Otsuka Long-Evans Tokushima Fatty (OLETF) is an animal model for type 2 diabetes mellitus. Nidd8/of has been identified as one of 14 quantitative trait loci (QTLs) involved in the diabetes by a whole genome search in 160 F2 progenies obtained by mating the OLETF and F344 rats. Comparative mapping between human and rat indicated that the Nidd8/of genomic region, near D9rat21 on rat chromosome 9, contains the calpain10 (Capn10) gene, which is putative type 2 diabetes-susceptibility gene in humans.

A congenic strain (F344.OLETF-Imfm) displays the existence of intramuscular fat accumulation QTL on rat chromosome 1.

A genomic region between D1Wox8 and D1Rat90 on rat chromosome 1 was previously shown to be linked to intramuscular fat accumulation by quantitative trait locus (QTL) analysis using a F2 population derived from the Otsuka Long-Evans Tokushima Fatty (OLETF) rat, which exhibits an increase in the levels of intramuscular fat content in Musculus longissimus, and the F344 rat. There exist two regions showing major and minor lod peaks for linkage to intramuscular fat accumulation, in the chromosomal region. We constructed a congenic strain introgressing the OLETF allele on the minor but not the major lod peak region in the F344 rat strain.

Genomic structure and promoter analysis of the bovine leptin gene.

The product of the leptin gene is a 16-kDa protein secreted by adipose tissue and regulates adiposity. The leptin gene could be a potential candidate gene controlling some proportion of adipose and lean accretion in cattle, and thus, may be referred to as one of genetic factor controlling meat quality determinants such as marbling. We have isolated the bovine leptin gene including its promoter region.

Detection of a quantitative trait locus for intramuscular fat accumulation using the OLETF rat.

The Otsuka Long-Evans Tokushima Fatty (OLETF) rat is an animal model for obese type 2 diabetes. We showed that the OLETF rat exhibits higher levels of intramuscular fat content in Musculus longissimus as compared to the Fischer-344 (F344) rat. Our investigation was designed to identify quantitative trait loci (QTLs) contributing to the increased levels of intramuscular fat content by performing a whole-genome search using 108 F2 intercross obtained by mating the OLETF and the F344 rats.