A5050250616- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Polysaccharides Composition and Applications
- Genetics and Plant Breeding
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Cancer-related molecular mechanisms research
- Effects of Environmental Stressors on Livestock
- Gut microbiota and health
- Polysaccharides and Plant Cell Walls
- Proteoglycans and glycosaminoglycans research
- Food composition and properties
- Proteins in Food Systems
- Surfactants and Colloidal Systems
- Evolution and Genetic Dynamics
- Viral gastroenteritis research and epidemiology
- Animal Nutrition and Physiology
- Tribology and Lubrication Engineering
- Rheology and Fluid Dynamics Studies
- Herbal Medicine Research Studies
- Metabolomics and Mass Spectrometry Studies
- Celiac Disease Research and Management
- Respiratory viral infections research
- Electrostatics and Colloid Interactions
- Environmental DNA in Biodiversity Studies
University of Maryland, College Park
2023-2025
Norwegian University of Life Sciences
2011-2024
Shanghai Jiao Tong University
2011-2014
Genomic Selection (GS) is a newly developed tool for the estimation of breeding values quantitative traits through use dense markers covering whole genome. For successful application GS, accuracy prediction genomewide value (GW-EBV) key issue to consider. Here we investigated and possible bias GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) phenotypic data 500 Norwegian Red bulls. The study was performed on milk yield, fat protein first lactation mastitis traits, calving...
Summary Previous proposals for a unified approach amalgamating information from animals with or without genotypes have combined the numerator relationship matrix A genomic G estimated markers. These approaches resulted in biased EBV (GEBV), and methodology was developed to overcome these problems. Firstly, matrix, FG , based on linkage analysis derived using same base population as which (i) utilizes scale pedigree (ii) permits regression coefficients used propagate data genotyped...
Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed correct these errors, but it is uncertain if they obtain accuracy needed for high-resolution source tracking foodborne illness outbreaks.
GBLUP (genomic best linear unbiased prediction) uses high-density single nucleotide polymorphism (SNP) markers to construct genomic identity-by-state (IBS) relationship matrices. However, identity-by-descent (IBD) relationships can be accurately calculated for extremely sparse markers. Here, we compare the accuracy of prediction genome-wide breeding values (GW-BV) a sib-evaluated trait in typical aquaculture population, assuming either IBS or IBD matrices, and by varying marker density size...
It is commonly assumed that prediction of genome-wide breeding values in genomic selection achieved by capitalizing on linkage disequilibrium between markers and QTL but also genetic relationships. Here, we investigated the reliability predicting based population-wide information, identity-by-descent relationships within known pedigree, to what extent information improves predictions relationship information. The study was performed milk, fat, protein yield, using genotype data 35 706 SNP...
Abstract Background Understanding the evolutionary forces related to climate changes that have been shaped genetic variation within species has long a fundamental pursuit in biology. In this study, we generated whole-genome sequence (WGS) data from 65 cross-bred and 45 Mongolian cattle. Together with 62 sequences world-wide cattle populations, estimated diversity population structure of populations. addition, performed comparative genomics analyses explore basis underlying adaptation cold...
Genomic prediction is based on the accurate estimation of genomic relationships among and between training animals selection candidates in order to obtain estimates estimated breeding values (GEBV). Various methods have been used predict GEBV population-wide linkage disequilibrium (G IBS ) or sometimes analysis LA ). Here, we propose a novel method relationship matrix using runs homozygosity ROH Runs were derive probabilities multi-locus identity by descent chromosome segments. The accuracy...
Many quantitative traits measured in breeding programs are genetically correlated. The genetic correlations between the indicate that measurement of one trait carries information on others. To benefit from this information, multi-trait genomic prediction (MTGP) is preferable to use. However, MTGP more difficult implement compared single-trait (STGP), and even challenging for goal exploit not only other but also ungenotyped animals. This could be accomplished using both single multistep...
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and profile microbial communities. However, criticized for being too conserved differentiate between distinct species. We argue that inability is not a unique feature of gene. Rather, we observe gradual loss species-level resolution other nearly-universal marker genes as number sequences increases in reference databases. This trend was strongly correlated with how represented taxonomic group database...
Abstract 16S rRNA gene sequence clustering is an important tool in characterizing the diversity of microbial communities. As data sets are growing size, existing algorithms increasingly become analytical bottleneck. Part this bottleneck due to substantial computational cost expended on small clusters and singleton sequences. We propose iterative sampling-based approach that targets largest set, allowing users stop process when sufficient available for specific analysis being targeted....
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and profile microbial communities. The criticized for being too conserved differentiate between distinct species. We argue that inability is not a unique feature of gene. Rather, we observe gradual loss species-level resolution other marker genes as number sequences increases in reference databases. demonstrate this effect through analysis three commonly databases nearly-universal genes: SILVA...