Showing papers by "Seiichiro Ogawa published in 2022"

Inferring genetic characteristics of Japanese Black cattle populations using genome-wide single nucleotide polymorphism markers

Abstract: This study attempted to infer the population structure of Japanese Black cattle by using genotype data on 33,063 genomewide single nucleotide polymorphism (SNP) markers of totally 4,348 fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. We evaluated allele frequency, heterozygosity, linkage disequilibrium, correlation of linkage phase, and genotype concordance among the steers. The distribution of allele frequencies in the steers sampled in Hyogo differed from the others, showing >10% of the SNPs as monomorphic. Observed heterozygosity was lowest and degree of linkage disequilibrium was highest in Hyogo. Genotypes were more similar among Hyogo steers than between other steer pairs. These results show the genetic characteristics of the Japanese Black cattle populations inferred from genotype data on genome-wide SNPs obtained using a commercial chip.

Genetic relationship between superovulatory response traits and carcass traits in Japanese Black cattle.

Abstract: We estimated the genetic correlations between superovulatory response traits and carcass traits in Japanese Black cattle. As regards the superovulatory response traits in cows, we analyzed the phenotypic records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donors between 2008 and 2018. As regards the carcass traits in fattened animals, we analyzed the phenotypic records for cold carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, estimated yield percent, and marbling score for 1448 progenies derived from 596 donors and slaughtered between 2004 and 2020. Variance components were estimated using single-trait and two-trait animal models and the restricted maximum likelihood approach. The estimated genetic correlations with the carcass traits ranged from -0.05 to 0.04 for TNE and from -0.14 to 0.04 for NGE, and their standard errors ranged from 0.10 to 0.14. These results imply that the genetic relationship between the superovulatory response traits in Japanese Black donor cows and the carcass traits in their fattened progenies was weak to negligible. Therefore, we concluded that selecting donors with superior genetic ability for superovulatory responses would not have antagonistic effects on carcass performance in their fattened progenies.

Genetic relationship of female reproductive traits with calf weight and carcass traits in Japanese Black cattle population in Miyagi prefecture

Abstract: 宮城県黒毛和種集団の雌性繁殖形質，子牛市場出荷時体重および枝肉形質に関する遺伝的パラメーターを推定した．雌性繁殖形質として初産月齢45,334件，妊娠期間283,621件，空胎期間238,287件，分娩間隔238,287件の記録を用いた．これら分娩による産子240,160頭分の子牛市場出荷時体重の記録を用いた．さらにこのうち122,910頭分の枝肉重量，ロース芯面積，バラの厚さ，皮下脂肪の厚さ，歩留基準値およびBMSナンバーの記録を用いた．遺伝率の推定には単形質アニマルモデル，遺伝相関の推定には2形質アニマルモデルを用いた．枝肉形質および子牛市場出荷時体重と雌性繁殖形質との推定遺伝相関は，初産月齢で−0.161～0.038，妊娠期間で−0.069～0.127，分娩間隔で−0.113～0.051といずれも弱く無視できる程度であった．本結果は，生産性と再生産性の同時改良に際し有用と期待される．

Subtractive manufacturing with swelling induced stochastic folding of sacrificial materials for fabricating complex perfusable tissues in multi-well plates.

Abstract: Organ-on-a-chip systems that recapitulate tissue-level functions have been proposed to improve in vitro-in vivo correlation in drug development. Significant progress has been made to control the cellular microenvironment with mechanical stimulation and fluid flow. However, it has been challenging to introduce complex 3D tissue structures due to the physical constraints of microfluidic channels or membranes in organ-on-a-chip systems. Inspired by 4D bioprinting, we develop a subtractive manufacturing technique where a flexible sacrificial material can be patterned on a 2D surface, swell and shape change when exposed to aqueous hydrogel, and subsequently degrade to produce perfusable networks in a natural hydrogel matrix that can be populated with cells. The technique is applied to fabricate organ-specific vascular networks, vascularized kidney proximal tubules, and terminal lung alveoli in a customized 384-well plate and then further scaled to a 24-well plate format to make a large vascular network, vascularized liver tissues, and for integration with ultrasound imaging. This biofabrication method eliminates the physical constraints in organ-on-a-chip systems to incorporate complex ready-to-perfuse tissue structures in an open-well design.

An attempt of using public ambient temperature data in swine genetic evaluation for litter-size traits at birth in Japan†

Abstract: Context Large-scale genetic evaluation is promising for efficiently improving sow lifetime productivity, and therefore, a reasonable operational model should be pursued to analyse phenotypic data collected from around Japan, where unique seasonality exists. However, the information on establishing the model is currently insufficient. Aims To obtain the fundamental information on using ambient temperature information in developing the model for routine swine genetic evaluation in Japan, by analysing total number born, number born alive, and number stillborn collected at a Japanese farm, together with off-farm ambient temperature measured at the nearest Automated Meteorological Data Acquisition System station. Methods Five repeatability animal models were exploited, considering the effects of farrowing season (Model 1), farrowing month (Model 2), quadratic regressions of daily maximum ambient temperature of farrowing day (Model 3), season and temperature (Model 4), or month and temperature (Model 5). Key results Patterns of the effects of daily maximum temperature of farrowing day estimated using Model 3 were similar to those of farrowing season by Model 1 and those of farrowing month by Model 2. Adding the effect of daily maximum temperature of farrowing day (Models 4 and 5) could explain phenotypic variability better than only considering either of farrowing season or month (Models 1 and 2). Estimated heritability was stable among the models and the rank correlation of predicted breeding values among models was >0.98 for all traits. Conclusions The results indicated the possibility that using public ambient temperature can capture a large part of the phenotypic variability in litter-size traits at birth caused by seasonality in Japan. Implications This study could support the availability of public meteorological data in the development of flexible operational models for future swine genetic evaluation in Japan.

Heritability and genetic correlation estimates of semen production traits with litter traits and pork production traits in purebred Duroc pigs

Abstract: Abstract We estimated heritabilities of semen production traits and their genetic correlations with litter traits and pork production traits in purebred Duroc pigs. Semen production traits were semen volume, sperm concentration, proportion of morphologically normal sperms, total number of sperm, and total number of morphologically normal sperm. Litter traits at farrowing were total number born, number born alive, number stillborn, total litter weight at birth, mean litter weight at birth, and piglet survival rate at birth. Litter traits at weaning were litter size at weaning, total litter weight at weaning, mean litter weight at weaning, and piglet survival rate from birth to weaning. Pork production traits were average daily gain, backfat thickness, and loin muscle area. We analyzed 45,913 semen collection records of 896 boars, 6,950 farrowing performance records of 1,400 sows, 2,237 weaning performance records of 586 sows, and individual growth performance records of 9,550 animals measured at approximately 5 mo of age. Heritabilities were estimated using a single-trait animal model. Genetic correlations were estimated using a 2-trait animal model. Estimated heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of estimated genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.

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

Abstract: 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. Genomic heritabilities estimated using model 1 were moderate to high. The sums of the proportions of the additive genetic variance explained by each autosome to the total genetic variance estimated by using model 2 were >90%. For carcass weight, the proportions explained by Bos taurus autosomes 6, 8, and 14 were higher than those explained by the remaining autosomes. In some cases, the estimated proportion was close to 0. The results obtained from model 2 could provide a novel insight into the genetic architecture, such as heritability per chromosome, of carcass traits in Japanese Black cattle, although further careful investigation would be required.

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

Abstract: 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. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results.

Genomic prediction for carcass traits in Japanese Black cattle considering mixed structure of subpopulations

Abstract: We performed Bayesian clustering analysis using STRUCTURE software with genotype data on 33,063 commercial single nucleotide polymorphism (SNP) markers in 4,348 Japanese Black fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. When the number of the assumed clusters in STRUCTURE was 2, the steers from Hyogo prefecture were clearly separated from the others. This indicates the usefulness of the STRUCTURE analysis with commercial SNP markers for the clarifications of the difference of the genetic constitutions of each prefecture. Next, genomic predictions for carcass traits were conducted using a statistical model including the proportions of the clusters as partial linear regressions. Genomic breeding values predicted by the model without the STRUCTURE covariates were likely to be divided into the part of explaining the STRUCTURE analysis and the remaining part. This result shows the possibility that the accuracy of genomic prediction depends on the degree of information of the genomic population structure.

Study on the Ignition Method for n-Octane Pyrolysis Fuel in a Scramjet Engine

Abstract: In scramjet engines, ignition must take place within a residence time on the order of milliseconds. In this study, secure ignition conditions for speci fi ed n-octane pyrolysis fuel components used in autoignition or forced-ignition by plasma jet torch in a high-speed fl ow were numerically investigated. First, the ignition delay time within the combustor and cavity fl ame-holder was estimated using chemical reaction analysis. Three fuel components (n-C 8 H 18 , all pyrolysis fuel (15 components, decomposition rate under 11%)), and pyrolysis gas fuel (eight gas fuel components, decomposition rate under 11%) could not self-ignite within the combustor and cavity residence time. Secondly, ignition using a plasma jet torch in the cavity was numerically investigated. In the case of forced-ignition by plasma jet torch, all pyrolysis fuel (No. 3) and n-C 8 H 18 could ignite within the cavity residence time with less input energy than pyrolysis gas fuel (No. 3) under three kinds of Mach number fl ight conditions ( M 0 = 4, 6, and 8). Moreover, the e ff ect of shortening the ignition delay time by raising the plasma jet torch gas temperature and O radical rate within the cavity was investigated. Ignition of the three kinds of mixture fuel was more greatly a ff ected by the torch injection temperature than the O radical rate in the cavity under all Mach number fl ight conditions.

Genetic and genomic analysis of oxygen consumption in mice.

Abstract: We estimated genetic parameters for oxygen consumption (OC), OC per metabolic body weight (OCMBW) and body weight at three through 8 weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. With respect to OC, estimated direct heritability was moderate (0.32) and the estimated proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance was very low (0.01), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes through selective signature detection with the results of pooled whole-genome resequencing using pooled DNA samples from high and low OC mice. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP-binding proteins (Ndufa12, Sdhc, Atp10b, etc.), Prr16 encoding Largen protein, Cry1 encoding a key component of the circadian core oscillator and so on. The results, although careful interpretation must be required, could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement, and therefore feed efficiency.

Effect of ambient temperature on average daily gain of pigs evaluated using public weather data and a plateau‐linear regression model

Abstract: Abstract We performed a plateau‐linear regression model analysis of the average daily gain (ADG) of pigs on daily average temperature at the end of performance testing (T). Records for performance testing between 30 kg and 105 kg of 2268 purebred Duroc pigs raised at the National Livestock Breeding Center Miyazaki Station were used. Off‐farm ambient temperatures were measured at the nearest Automated Meteorological Data Acquisition System station at Kobayashi, Miyazaki (Kobayashi station). A plateau‐linear regression equation was obtained in which ADG decreased by 12.6 g for every 1°C when T > 21.1°C. We calculated the expected age in day at the end of testing (D105) using the regression equation obtained and T observed at the Kobayashi station in 2020. The number of days that D105 was prolonged due to higher T was 125 days, corresponding to approximately one third of the year. These results could contribute to planning and management of stable pork production in response to heat in Japan.

Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

Abstract: The genetic contribution with respect to autosomal genes has been widely used to evaluate the genetic diversity of a target population. Here, we developed a method to calculate the genetic contribution with respect to genes on sex chromosomes and mitochondrial DNA through pedigree analysis. To demonstrate the performance, we applied the methods for calculating genetic contributions to example pedigree data. To verify the results of genetic contribution calculations, we performed gene-dropping simulations mimicking flows of genes on autosomes, X and Y chromosomes, and mitochondrial DNA, and then compared the results from the simulation with the corresponding genetic contributions. To investigate the effect of pedigree error, we compared the results of genetic contribution calculations using pedigree data with and without errors. The results of gene-dropping simulation showed good agreement with the results of the genetic contribution calculation. The effect of pedigree errors on the calculation of genetic contribution depended on the error rate. Since the patterns of the genetic contributions of such genes might be different from those on autosomes, the novel approach could provide new information on the genetic composition of populations. The results are expected to contribute to the development of methods for sustainable breeding and population management.

An attempt of using public ambient temperature data in swine genetic evaluation for litter size traits at birth in Japan

Abstract: To obtain the fundamental information on using ambient temperature information in developing the model for routine swine genetic evaluation in Japan, we analyzed total number born (TNB), number born alive (NBA), and number stillborn (NSB) collected at a Japanese farm, together with off-farm ambient temperature measured at a nearest Automated Meteorological Data Acquisition System station. Five repeatability animal models were exploited, considering the effects of farrowing season (model 1), farrowing month (model 2), quadratic regressions of daily maximum ambient temperature of farrowing day (model 3), season and temperature (model 4), or month and temperature (model 5). Patterns of the effects of daily maximum temperature of farrowing day estimated using model 3 was similar to those of farrowing season by model 1 and those of farrowing month by model 2. Adding the effect of daily maximum temperature of farrowing day (models 4 and 5) could explain phenotypic variability greater than only considering either of farrowing season and month (models 1 and 2). Estimated heritability was stable among the models and the rank correlation of predicted breeding values between models was >0.98 for all traits. The results indicate the possibility that using public ambient temperature can capture a large part of the phenotypic variability in litter size traits at birth caused by the seasonality in Japan and do not harm, at least, the performance of genetic evaluation. This study could support the availability of public meteorological data in flexible developing operational models for future swine genetic evaluation in Japan.

Genetic and genomic analysis of oxygen consumption in mice

Abstract: We estimated genetic parameters of oxygen consumption (OC), OC per metabolic body weight (OCMBW), and body weight at three through eight weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental, and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. For OC, estimated direct heritability was moderate (0.32) and estimated maternal heritability and proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance were very low (both <0.03), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes by performing pool-seq using pooled DNA samples from mice in high and low OC lines and selective signature detection. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP-binging proteins (Ndufa12, Sdhc, Atp10b, etc.), Prr16 encoding Largen protein, Cry1 encoding a key component of the circadian core oscillator, and so on. The results could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement and therefore feed efficiency.

Myeloperoxidase expression in diencephalon is potentially associated with fear-related behavior in chicks of laying hen.

Abstract: Preventing feather pecking (FP) in adult laying hens is important for the welfare of intensively poultry farming. Fear-related behavior in growing female layer chicks may predict FP in adult hens. In this study, in two representative laying breeds (White Leghorn [WL] and Rhode Island Red [RIR]) that have different FP frequencies, we identified a candidate gene associated with fear-related behavior in chicks and FP in adult hens. In the tonic immobility test and open-field test, the behavioral activity was lower in WL chicks than in RIR chicks (P < 0.01), suggesting that WL chicks were more fearful than RIR chicks. Based on previous studies, 51 genes that have been found to be differentially expressed in the brain between high- and low-FP populations were chosen, and their expression levels were screened in the chick diencephalon. This analysis revealed that myeloperoxidase (MPO) gene expression level was higher in WL chicks than that in RIR chicks (P < 0.05). Furthermore, STRING analysis predicted the gene network including MPO and MPO-related genes and revealed the association of these genes with fear-related behavior. These results suggest that MPO is potentially associated with fear-related behavior in growing female layer chicks and FP in adult hens.