Aisaku Arakawa
YOU?
Author Swipe
View article: Genome-wide variation reveal that goats were introduced into Asia via multiple migrations
Genome-wide variation reveal that goats were introduced into Asia via multiple migrations Open
In recent world-wide studies on the autosomal genetic diversity of goats, Asian goats were represented only by Southwest Asian, Pakistani and Chinese breeds. We have collected 55 K genome-wide SNP genotypes for 12 South/Southeast Asian and…
View article: Genome-wide variation reveal that goats were introduced into Asia via multiple migrations
Genome-wide variation reveal that goats were introduced into Asia via multiple migrations Open
In recent world-wide studies on the autosomal genetic diversity of goats, Asian goats were represented only by Southwest Asian, Pakistani and Chinese breeds. We have collected 55K genome-wide SNP genotypesfor 12 South/Southeast Asian and 2…
View article: Assessment of genetic diversity and inbreeding in the Okinawa indigenous Agu pig through pedigree analysis
Assessment of genetic diversity and inbreeding in the Okinawa indigenous Agu pig through pedigree analysis Open
Objective: The objective of this study was to clarify the changes in genetic diversity and inbreeding over the years as well as to identify the causes of genetic diversity loss using the pedigree of Okinawa indigenous Agu pigs.Methods: The…
View article: Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan
Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan Open
Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars ( Sus scrofa leucomystax ) in…
View article: Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle Open
Background Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and…
View article: Sawai et al_microsatellite data.xlsx
Sawai et al_microsatellite data.xlsx Open
Microsatellite genotyping data (30 loci) and geographical locations of 1,062 samples from wild boar (Sus scrofa leucomystax) in Japan. The data were analysed in the article: "Assessing population structure and migration patterns of wild bo…
View article: Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle
Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle Open
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 o…
View article: Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data
Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data Open
Background Multi-trait genetic parameter estimation is an important topic for target traits with few records and with a low heritability and when the genetic correlation between target and secondary traits is strong. However, estimating co…
View article: Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome
Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome Open
The Vietnamese native pig (VnP)—a porcine breed with a small body—has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), whi…
View article: An R package VIGoR for joint estimation of multiple linear learners with variational Bayesian inference
An R package VIGoR for joint estimation of multiple linear learners with variational Bayesian inference Open
Summary An R package that can implement multiple linear learners, including penalized regression and regression with spike and slab priors, in a single model has been developed. Solutions are obtained with fast minorize-maximization algori…
View article: Additional file 2 of Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data
Additional file 2 of Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data Open
Additional file 2. RStan code for the NUTS algorithm with an IW prior of a multi-trait animal model.
View article: Additional file 1 of Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data
Additional file 1 of Performance of the No-U-Turn sampler in multi-trait variance component estimation using genomic data Open
Additional file 1. RStan code for the NUTS algorithm with an LKJ prior of a multi-trait animal model. RStan is the R interface to Stan. The user writes the analysis model in the test.stan file and runs Stan by using test.stan in R. The use…
View article: Inbreeding and selection response in a small population of honeybee under incomplete reproductive isolation
Inbreeding and selection response in a small population of honeybee under incomplete reproductive isolation Open
繁殖隔離が不完全なミツバチの小集団における選抜反応と近交係数を予測する理論を開発した．得られた理論を用いて，国内の養蜂家が保有する蜂群規模を想定した選抜計画に適用して育種の効率を評価した．数値計算の結果，繁殖隔離が不完全であっても雄の90%以上が隔離できれば，顕著な遺伝的改良量が得られることが示された．また，養蜂場外からの雄の流入は，近交係数の上昇を抑える上で有効であることも示された．
View article: Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes Open
Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate foren…
View article: Differential Metabolomics Profiles Identified by CE-TOFMS between High and Low Intramuscular Fat Amount in Fattening Pigs
Differential Metabolomics Profiles Identified by CE-TOFMS between High and Low Intramuscular Fat Amount in Fattening Pigs Open
The amount of intramuscular fat (IMF) present in the loin eye area is one of the most important characteristics of high-quality pork. IMF measurements are currently impractical without a labor-intensive process. Metabolomic profiling could…
View article: The phenotypic characteristics and relational database for Vietnamese native pig populations
The phenotypic characteristics and relational database for Vietnamese native pig populations Open
Although there are a number of Vietnamese native pig (VnP) populations, some are on the verge of extinction, and therefore adequate management and conservation are necessary. In this study, we conducted a field survey of VnP populations an…
View article: Tunings for leapfrog integration of Hamiltonian Monte Carlo for estimating genetic parameters
Tunings for leapfrog integration of Hamiltonian Monte Carlo for estimating genetic parameters Open
A Hamiltonian Monte Carlo algorithm is a Markov Chain Monte Carlo method that is considered more effective than the conventional Gibbs sampling method. Hamiltonian Monte Carlo is based on Hamiltonian dynamics, and it follows Hamilton’s equ…
View article: Association of a polymorphism in SREBP1 with fatty acid composition and lipogenic gene expression in beef cattle breeds
Association of a polymorphism in SREBP1 with fatty acid composition and lipogenic gene expression in beef cattle breeds Open
Background Sterol regulatory element-binding protein 1 (SREBP1) plays an important role in the lipogenesis and fatty acid (FA) composition in fat cells and is consequently considered to influence the nutritional quality of beef. SREBP1 reg…
View article: Evaluation of the genetic structure of indigenous Okinawa Agu pigs using microsatellite markers
Evaluation of the genetic structure of indigenous Okinawa Agu pigs using microsatellite markers Open
This study revealed a substantial loss of genetic diversity among Agu pigs due to inbreeding. Our data also suggest that Agu pigs have a distinctive genetic structure, although gene flows from European breeds were observed.
View article: MOESM1 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values
MOESM1 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values Open
Additional file 1. RStan code for the NUTS algorithm. RStan is the R interface to Stan. The user writes the analysis model in the test.stan file and runs Stan by using test.stan in R. The user needs to input the following parameters; J: n…
View article: MOESM4 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values
MOESM4 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values Open
Additional file 4. Simulated data with a heritability of 0.5.
View article: MOESM2 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values
MOESM2 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values Open
Additional file 2. Simulated data with a heritability of 0.1.
View article: MOESM3 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values
MOESM3 of Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values Open
Additional file 3. Simulated data with a heritability of 0.3.
View article: Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region
Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region Open
This study confirmed that the East Asian lineage is dominant in the maternal genetic background of the Agu population, supporting the hypothesis that the ancestors of the Agu pig were introduced from the Asian continent.
View article: Differences in gene expression profiles for subcutaneous adipose, liver, and skeletal muscle tissues between Meishan and Landrace pigs with different backfat thicknesses
Differences in gene expression profiles for subcutaneous adipose, liver, and skeletal muscle tissues between Meishan and Landrace pigs with different backfat thicknesses Open
Backfat thickness is one of the most important traits of commercially raised pigs. Meishan pigs are renowned for having thicker backfat than Landrace pigs. To examine the genetic factors responsible for the differences, we first produced f…
View article: Distinct correlations between lipogenic gene expression and fatty acid composition of subcutaneous fat among cattle breeds
Distinct correlations between lipogenic gene expression and fatty acid composition of subcutaneous fat among cattle breeds Open
These results suggest that the relationships between FA composition and lipogenic gene expression are influenced by breed and sex. The opposite relationship between SCD isoforms suggests a compensatory regulation of total SCD activity, whi…
View article: Effects of correcting missing daily feed intake values on the genetic parameters and estimated breeding values for feeding traits in pigs
Effects of correcting missing daily feed intake values on the genetic parameters and estimated breeding values for feeding traits in pigs Open
Daily feed intake ( DFI ) is an important consideration for improving feed efficiency, but measurements using electronic feeder systems contain many missing and incorrect values. Therefore, we evaluated three methods for correcting missing…