A5022260166- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Effects of Environmental Stressors on Livestock
- Animal Behavior and Welfare Studies
- Rice Cultivation and Yield Improvement
- Gene expression and cancer classification
- Sesame and Sesamin Research
- Genetics, Bioinformatics, and Biomedical Research
- Wheat and Barley Genetics and Pathology
- Genetic Associations and Epidemiology
- Soybean genetics and cultivation
- Meat and Animal Product Quality
- Spectroscopy and Chemometric Analyses
- Remote Sensing in Agriculture
- Animal Nutrition and Physiology
- Smart Agriculture and AI
- Bioinformatics and Genomic Networks
- Genetic diversity and population structure
- Plant-Microbe Interactions and Immunity
- Nematode management and characterization studies
- Cancer-related molecular mechanisms research
- Sugarcane Cultivation and Processing
- Genomics and Phylogenetic Studies
- Data Analysis with R
Virginia Tech
2018-2025
The University of Tokyo
2025
JDSU (United States)
2023
University of Nebraska–Lincoln
2014-2020
University of Missouri
2016
University of Wisconsin–Madison
2011-2015
Precision animal agriculture is poised to rise prominence in the livestock enterprise domains of management, production, welfare, sustainability, health surveillance, and environmental footprint. Considerable progress has been made use tools routinely monitor collect information from animals farms a less laborious manner than before. These efforts have enabled sciences embark on technology-driven discoveries improve agriculture. However, growing amount complexity data generated by fully...
The livestock industry in Türkiye is vital to the country’s agricultural sector and economy. In particular, sheep products are an important source of income livelihood for many Turkish smallholder farmers semi-arid highland areas. one largest producers world its production system heavily dependent on indigenous breeds. Given importance Türkiye, a systematic literature review breeding genetic improvement country needed development optimization programs using modern approaches, such as genomic...
Abstract Prediction of complex traits using molecular genetic information is an active area in quantitative genetics research. In the postgenomic era, many types -omic (e.g., transcriptomic, epigenomic, methylomic, and proteomic) data are becoming increasingly available. Therefore, evaluating utility this massive amount prediction interest. DNA methylation, covalent change a molecule without affecting its underlying sequence, one quantifiable form epigenetic modification. We used methylation...
The accessibility of high-throughput phenotyping platforms in both the greenhouse and field, as well relatively low cost unmanned aerial vehicles, has provided researchers with an effective means to characterize large populations throughout growing season. These longitudinal phenotypes can provide important insight into plant development responses environment. Despite use these new approaches breeding, genomic prediction models for is limited major crop species. objective this study was...
Recent work has suggested that the performance of prediction models for complex traits may depend on architecture target traits. Here we compared several with respect to their ability predicting phenotypes under various statistical architectures gene action: (1) purely additive, (2) additive and dominance, (3) two-locus epistasis, (4) epistatic settings. Simulation a real chicken dataset were used. Fourteen compared: BayesA, BayesB, BayesC, Bayesian LASSO, ridge regression, elastic net,...
Understanding the genetic basis of dynamic plant phenotypes has largely been limited because a lack space and labor resources needed to record traits, often destructively, for large number genotypes. However, recent advent image-based phenotyping platforms provided science community with an effective means nondestructively evaluate morphological, developmental, physiological processes at regular, frequent intervals plants throughout development. The statistical frameworks typically used...
Summary A higher minimum (night‐time) temperature is considered a greater limiting factor for reduced rice yield than similar increase in maximum (daytime) temperature. While the physiological impact of high night (HNT) has been studied, genetic and molecular basis HNT stress response remains unexplored. We examined phenotypic variation mature grain size (length width) diverse set accessions under stress. Genome‐wide association analysis identified several HNT‐specific loci regulating as...
Abstract Global nighttime temperatures are rising at twice the rate of daytime and pose a challenge for rice (Oryza sativa) production. High temperature (HNT) stress affects yield by reducing grain weight, size, fertility. Although genes associated with these parameters have been identified characterized under normal temperatures, genetic basis weight regulation HNT remains less explored. We examined natural variation single (SGW) imposed during development. A genome-wide association...
In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms ORA have been proposed. Recently, Medical Subject Headings (MeSH) terms, which are annotations PubMed documents, used ORA. MeSH enables the extraction broader meaning from lists expected to become exhaustive resource However, existing still not sufficient several reasons.In this work, we developed original...
Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity studies in literature that report genetic or genomic parameters, especially case sheep populations. To investigate architecture acid composition sheep, we conducted genome-wide association (GWAS) estimated heritabilities for profile Longissimus dorsi muscle 216 male sheep. Genomic heritability estimates content ranged from 0.25 to 0.46, indicating substantial variation exists evaluated traits....
Genome-wide association studies have been deemed successful for identifying statistically associated genetic variants of large effects on complex traits. Past found enrichment trait-associated SNPs in functionally annotated regions, while depletion was reported intergenic regions (IGR). However, no systematic examination connections between genomic and predictive ability phenotypes has carried out. In this study, we partitioned based their annotation to characterize that deliver low high...
Arguably, genotypes and phenotypes may be linked in functional forms that are not well addressed by the linear additive models standard quantitative genetics. Therefore, developing statistical learning for predicting phenotypic values from all available molecular information capable of capturing complex genetic network architectures is great importance. Bayesian kernel ridge regression a non-parametric prediction model proposed this purpose. Its essence to create spatial distance-based...
With the advent of high-throughput phenotyping platforms, plant breeders have a means to assess many traits for large breeding populations. However, understanding genetic interdependencies among high-dimensional in statistically robust manner remains major challenge. Since multiple phenotypes likely share mutual relationships, elucidating economically important can better inform decisions and accelerate improvement plants. The objective this study was leverage confirmatory factor analysis...
Recent advancements in phenomics coupled with increased output from sequencing technologies can create the platform needed to rapidly increase abiotic stress tolerance of crops, which increasingly face productivity challenges due climate change. In particular, high-throughput phenotyping (HTP) enables researchers generate large-scale data temporal resolution. Recently, a random regression model (RRM) was used longitudinal rice projected shoot area (PSA) dataset an optimal growth environment....
Plant breeders seek to develop cultivars with maximal agronomic value, which is often assessed using numerous, genetically correlated traits. As intervention on one trait will affect the value of another, breeding decisions should consider relationships among traits in context putative causal structures (i.e., networks). While multi-trait genome-wide association studies (MTM-GWAS) can infer genetic signals at multivariate scale, standard MTM-GWAS does not accommodate network structure...
Abstract Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing diversification. Rice consumed by more than 3 billion people. For rice, thermal sensitivity reproductive development filling well‐documented, while knowledge concerning impact stress (HS) on early seed limited. Here,...
Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor determines shape (including area, perimeter, length, width, circularity, centroid), color with capability to process a large number images in time-efficient manner. In context, our application...
Abstract Average daily gain is an indicator of the growth rate, feed efficiency, and current health status livestock species including pigs. Continuous monitoring in pigs aids producers to optimize their performance while ensuring animal welfare sustainability, such as reducing stress reactions waste. Computer vision has been used predict live body weight from video images without direct handling pig. In most studies, videos were taken immobilized at a weighing station or feeding area...
Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.) one oldest oil-crops in world. Despite its economic agricultural importance, it an 'orphan crop-plant' that has undergone limited modern selection, and, as a consequence preserved wide diversity. Here we established new sesame panel (SCHUJI) contains 184 genotypes representing phenotypic variation geographically distributed. We harnessed...