Kosuke Hamazaki
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View article: Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding
Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding Open
Breeding perennial fruit trees like apple is constrained by long generation times and limited population sizes, which often lead to repeated use of a few elite cultivars and consequently narrow genetic diversity. To better understand how s…
View article: DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies
DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies Open
Motivation Differentiable programming frameworks like PyTorch and JAX revolutionized biological modeling. A foremost merit is that multiple components programmed separately can be put together so that the parameters are jointly optimized. …
View article: Optimizing progeny allocation strategies in breeding schemes while updating genomic prediction models
Optimizing progeny allocation strategies in breeding schemes while updating genomic prediction models Open
Genomic selection has revolutionized breeding by enabling the early identification of superior individuals using genome-wide markers, enhancing breeding efficiency and accelerating variety development. Over the past decade, new selection a…
View article: Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding
Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding Open
With the increasing ability to integrate pedigree and genomic data, it is essential to evaluate their potential to uncover valuable genetic insights that can drive the advancement of crop breeding and conservation of genetic diversity. Ped…
View article: Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations
Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations Open
In the breeding programs of self-pollinated plants, achieving genetic improvement in multiple traits can be challenging when relying solely on a single biparental population. Interpopulation crosses are employed to integrate favorable alle…
View article: DiffBreed: Automatic differentiation enables efficient gradient-based optimization of breeding strategies
DiffBreed: Automatic differentiation enables efficient gradient-based optimization of breeding strategies Open
Motivation Differentiable programming frameworks like PyTorch and JAX revolutionized biological modeling. A foremost merit is that multiple components programmed separately can be put together so that the parameters are jointly optimized. …
View article: Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines
Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines Open
In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior indiv…
View article: High-throughput Phenotyping of Soybean Biomass: Conventional Trait Estimation and Novel Latent Feature Extraction Using UAV Remote Sensing and Deep Learning Models
High-throughput Phenotyping of Soybean Biomass: Conventional Trait Estimation and Novel Latent Feature Extraction Using UAV Remote Sensing and Deep Learning Models Open
High throughput phenotyping serves as a framework to reduce chronological costs and accelerate breeding cycles. In this study, we developed models to estimate the phenotypes of biomass-related traits in soybean ( Glycine max ) using unmann…
View article: Cross Potential Selection: A Proposal for Optimizing Crossing Combinations in Recurrent Selection Based on the Ability of Future Inbred Lines
Cross Potential Selection: A Proposal for Optimizing Crossing Combinations in Recurrent Selection Based on the Ability of Future Inbred Lines Open
In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior indiv…
View article: AI-assisted selection of mating pairs through simulation-based optimized progeny allocation strategies in plant breeding
AI-assisted selection of mating pairs through simulation-based optimized progeny allocation strategies in plant breeding Open
Emerging technologies such as genomic selection have been applied to modern plant and animal breeding to increase the speed and efficiency of variety release. However, breeding requires decisions regarding parent selection and mating pairs…
View article: Development of a novel GWAS method to detect QTL effects interacting with the discrete and continuous population structure
Development of a novel GWAS method to detect QTL effects interacting with the discrete and continuous population structure Open
Although GWAS has been a key technology to identify causal genes, the current standard GWAS model still has problems that need to be solved. Among them, the population structure is one of the most severe problems when detecting QTLs in GWA…
View article: High-Throughput Phenotyping of Soybean Biomass: Conventional Trait Estimation and Novel Latent Feature Extraction Using UAV Remote Sensing and Deep Learning Models
High-Throughput Phenotyping of Soybean Biomass: Conventional Trait Estimation and Novel Latent Feature Extraction Using UAV Remote Sensing and Deep Learning Models Open
High-throughput phenotyping serves as a framework to reduce chronological costs and accelerate breeding cycles. In this study, we developed models to estimate the phenotypes of biomass-related traits in soybean (Glycine max) using unmanned…
View article: Assessing the Potential for Genome-Assisted Breeding in Red Perilla Using Quantitative Trait Locus Analysis and Genomic Prediction
Assessing the Potential for Genome-Assisted Breeding in Red Perilla Using Quantitative Trait Locus Analysis and Genomic Prediction Open
Red perilla is an important medicinal plant used in Kampo medicine. The development of elite varieties of this species is urgently required. Medicinal compounds are generally considered target traits in medicinal plant breeding; however, s…
View article: Assessing the potential for genome-assisted breeding in red perilla using quantitative trait locus analysis and genomic prediction
Assessing the potential for genome-assisted breeding in red perilla using quantitative trait locus analysis and genomic prediction Open
Red perilla is an important medicinal plant used in Kampo medicine, and the development of elite varieties of this species is urgently necessary. Medicinal compounds are generally considered target traits in medicinal plant breeding; howev…
View article: Random regression for modeling soybean plant response to irrigation changes using time-series multispectral data
Random regression for modeling soybean plant response to irrigation changes using time-series multispectral data Open
Plant response to drought is an important yield-related trait under abiotic stress, but the method for measuring and modeling plant responses in a time series has not been fully established. The objective of this study was to develop a met…
View article: Evaluating drought tolerance stability in soybean by the response of irrigation change captured from time-series multispectral data
Evaluating drought tolerance stability in soybean by the response of irrigation change captured from time-series multispectral data Open
This study investigated a method to evaluate the drought tolerance stability of a genotype in a single environmental trial by capturing the plant response to irrigation changes. Genotypes that exhibit stable phenotypes under various drough…
View article: AI-assisted selection of mating pairs through simulation-based optimized progeny allocation strategies in plant breeding
AI-assisted selection of mating pairs through simulation-based optimized progeny allocation strategies in plant breeding Open
Emerging technologies such as genomic selection have been applied to modern plant and animal breeding to increase the speed and efficiency of variety release. However, breeding requires decisions regarding parent selection and mating pairs…
View article: Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population
Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population Open
To enrich carotenoids, especially β-cryptoxanthin, in juice sac tissues of fruits via molecular breeding in citrus, allele mining was utilized to dissect allelic variation of carotenoid metabolic genes and identify an optimum allele on the…
View article: Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs
Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs Open
Key message We propose a novel approach to the Bayesian optimization of multi-variate genomic prediction models based on secondary traits to improve accuracy gains and phenotyping costs via efficient Pareto frontier estimation. Multivariat…
View article: Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population
Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population Open
In sorghum [Sorghum bicolor (L.) Moench], hybrid cultivars for the biofuel industry are desired. Along with selection based on testcross performance, evaluation of the breeding population per se is also important for the success of hybrid …
View article: Choosing the optimal population for a genome‐wide association study: A simulation of whole‐genome sequences from rice
Choosing the optimal population for a genome‐wide association study: A simulation of whole‐genome sequences from rice Open
A genome‐wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS (e.g. population structure, sample size, and sequence analysis and field testing costs) need to be considered. Mixed populations con…
RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method Open
Difficulty in detecting rare variants is one of the problems in conventional genome-wide association studies (GWAS). The problem is closely related to the complex gene compositions comprising multiple alleles, such as haplotypes. Several s…
View article: Choosing the optimal population for a genome-wide association study: a simulation using whole-genome sequences from rice
Choosing the optimal population for a genome-wide association study: a simulation using whole-genome sequences from rice Open
A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS, e.g. population structure, sample size, and sequence analysis and field testing costs, need to be considered. Mixture populations c…
View article: Haplotype-based genome wide association study using a novel SNP-set method : RAINBOW
Haplotype-based genome wide association study using a novel SNP-set method : RAINBOW Open
Background Diffculty in detecting rare variants is one of the problems in conventional genome wide association studies (GWAS). The problem is closely related to the complex gene compositions comprising multiple alleles, such as haplotypes.…