A5021455318- Plant Pathogens and Resistance
- Genetic Mapping and Diversity in Plants and Animals
- Plant Disease Resistance and Genetics
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Potato Plant Research
- Wheat and Barley Genetics and Pathology
- Plant Virus Research Studies
- Soil Carbon and Nitrogen Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Plant Pathogens and Fungal Diseases
- RNA and protein synthesis mechanisms
- Soil and Water Nutrient Dynamics
- Chromosomal and Genetic Variations
- Pharmacogenetics and Drug Metabolism
- Glycosylation and Glycoproteins Research
- Engineering and Agricultural Innovations
- Protein Structure and Dynamics
- Agricultural Development and Policies
- Mycotoxins in Agriculture and Food
- Genetic diversity and population structure
- Phosphorus and nutrient management
- Soil Management and Crop Yield
- Plant Taxonomy and Phylogenetics
- Crop Yield and Soil Fertility
University of Wisconsin–Madison
2015-2024
University of Wisconsin System
2013-2015
UMR BIOdiversity, GEnes & Communities
2014
Université de Bordeaux
2014
Cornell University
2012-2013
Robert W. Holley Center for Agriculture & Health
2012
Washington State University
2011
Utah State University
2010
California Institute of Technology
2003-2006
Many important traits in plant breeding are polygenic and therefore recalcitrant to traditional marker-assisted selection. Genomic selection addresses this complexity by including all markers the prediction model. A key method for genomic of values is ridge regression (RR), which equivalent best linear unbiased (BLUP) when genetic covariance between lines proportional their similarity genotype space. This additive model can be broadened include epistatic effects using other kernels, such as...
Genomic selection (GS) uses genomewide molecular markers to predict breeding values and make selections of individuals or lines prior phenotyping. Here we show that genotyping‐by‐sequencing (GBS) can be used for de novo genotyping panels develop accurate GS models, even the large, complex, polyploid wheat ( Triticum aestivum L.) genome. With GBS discovered 41,371 single nucleotide polymorphisms (SNPs) in a set 254 advanced from CIMMYT's semiarid program. Four different methods were evaluated...
Abstract The additive relationship matrix plays an important role in mixed model prediction of breeding values. For genotype X (loci columns), the product XX′ is widely used as a realized matrix, but scaling this ambiguous. Our first objective was to derive proper such that mean diagonal element equals 1+f, where f inbreeding coefficient current population. result formula involving covariance for sampling genomic loci, which must be estimated with markers. second investigate whether...
Genome-wide association studies (GWAS) are widely used in diploid species to study complex traits diversity and breeding populations, but GWAS software tailored autopolyploids is lacking. The objectives of this research were (i) develop an R package for based on the + mixed model, (ii) validate with simulated data, (iii) analyze a panel tetraploid potatoes. A unique feature package, called GWASpoly, its ability model different types polyploid gene action, including additive, simplex...
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, tolerance abiotic biotic stresses. Germplasm collections provide a source phenotypic diversity, but characterization these resources is required increase their utility for programs. We used barley SNP iSelect platform with 7,842 SNPs genotype 2,417 accessions sampled from the USDA National Small Grains Collection 33,176 accessions. Most in this core...
Cultivated potato is a clonally propagated autotetraploid species with highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome revealed extensive allelic diversity, altered coding and transcript sequences, preferential allele expression, structural variation that collectively result in complex transcriptome predicted proteome, which are distributed across the homologous chromosomes. Wild contribute to diversity tetraploid cultivars,...
Intense structuring of plant breeding populations challenges the design training set (TS) in genomic selection (GS). An important open question is how TS should be constructed from multiple related or unrelated small biparental families to predict progeny individual crosses. Here, we used a five interconnected maize (Zea mays L.) doubled-haploid (DH) lines derived four parents systematically investigate composition affects prediction accuracy for A total 635 DH genotyped with 16,741...
Abstract Summary: Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean absolute error between consensus map linkage each population. This minimization is performed subject inequality constraints that ensure ordering markers in preserved. When marker order...
Prediction accuracy of genomic selection (GS) has been previously evaluated through simulation and cross‐validation; however, validation based on progeny performance in a plant breeding program not investigated thoroughly. We several prediction models dynamic barley population comprised 647 six‐row lines using four traits differing genetic architecture 1536 single nucleotide polymorphism (SNP) markers. The were divided into six sets designated as one parent set five consecutive...
Abstract As one of the world’s most important food crops, potato (Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including use SNP arrays to determine allele dosage at thousands markers. By combining genotype and pedigree information with phenotype data for economically traits, objectives this study were (1) partition genetic variance into additive vs. nonadditive components, (2) accuracy genome-wide prediction. Between 2012 2017, a training population 571 clones...
ABSTRACT Previous research on genomic selection (GS) has focused predicting unphenotyped lines. Genomic can also improve the accuracy of phenotyped lines at low heritability, e.g., in a preliminary yield trial (PYT). Our first objective was to estimate this effect within biparental family, using multilocation data for barley ( Hordeum vulgare L.) and maize Zea mays L.). We found that increased with training population size higher an unbalanced design spread across multiple locations than...
Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting performance new lines. However, when datasets that are over time space, there is increasing exposure different genotype – environment combinations interactions may make predictions less accurate. Global cross-validated genomic prediction accuracies be high large but individual years a forward-prediction approach, or locations, often much...
Abstract Remote sensing is revolutionizing the phenotyping of agricultural field trials, but for many researchers, extraction plot‐level results a bottleneck. We have developed R package FIELDimageR as user‐friendly tool to analyze orthomosaic images containing plots. The basic workflow involves cropping and rotating image, followed by creation shapefile based on experimental design. includes functions calculate number plants per plot, canopy cover percentage, vegetation indices, plant...
Abstract The computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in three‐dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well predicts disruption, we have shuffled distantly‐related β‐lactamases PSE‐4 and TEM‐1 at 13 sites create library 2 14 (16,384) chimeras examined which ones retain lactamase function. Sequencing genes ampicillin‐selected clones revealed...
Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many constraints natural selection. We have created an family comprising 3,000 P450 heme proteins that correctly fold incorporate a cofactor by recombining three cytochromes at seven crossover locations chosen minimize structural disruption. Members this differ any known sequence average 72 as 109 amino acids. Most (>73%) properly folded chimeric are...
Estimation of allele dosage, using genomic data, in autopolyploids is challenging and current methods often result the misclassification genotypes. Some progress has been made when SNP arrays, but major challenge next generation sequencing data. Here we compare use read depth as continuous parameterization with ploidy parameterizations context selection (GS). Additionally, different sources information to build relationship matrices were compared. A real breeding population autotetraploid...
Abstract In diploid species, many multiparental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. these populations, haplotype reconstruction has used as a standard practice the power of QTL detection in comparison with marker-based association analysis. However, such software tools for polyploid species are few limited single biparental F1 population. this study, statistical framework implemented PolyOrigin connected...
Significant hectarage of certified organic dryland wheat ( Triticum aestivum L.) is planted in the western United States. Yields are severely constrained by lack precipitation, so many farmers do not grow cover crops or apply fertilizer due to inability recoup application costs short term. Composts have a strong carryover effect, however, and long‐term benefits infrequent applications soil quality, yield, economics on wheat–fallow systems been evaluated. Soils were sampled 2008 2010 from...
Abstract Mid‐density targeted genotyping‐by‐sequencing (GBS) combines trait‐specific markers with thousands of genomic at an attractive price for linkage mapping and selection. A 2.5K GBS assay potato ( Solanum tuberosum L.) was developed using the DArTag technology later expanded to 4K targets. Genomic were selected from Infinium single nucleotide polymorphism (SNP) array maximize genome coverage rates. The SNP platforms produced equivalent dendrograms in a test set 298 tetraploid samples,...
Protein function can be tuned using laboratory evolution, in which one rapidly searches through a library of proteins for the properties interest. In site-directed recombination, n crossovers are chosen an alignment p parents to define set p(n + 1) peptide fragments. These fragments then assembled combinatorially create pn+1 proteins. We have developed computational algorithm enrich these libraries folded while maintaining appropriate level diversity evolution. For given parents, our selects...
The development of germplasm with resistance to common scab and cold-induced sweetening is a high priority for the potato ( L.) industry. A mapping population was developed from mating two individuals diploid family generated by crossing susceptible cultivated clone US-W4 highly resistant wild relative Bitter) '524-8'. Progeny were evaluated in replicated field trials. Tubers scored percentage surface area lesions, lesion type, sweetening, average tuber weight, dry matter. Plants vine...
R/StageWise enables fully efficient, two-stage analysis of multi-environment, multi-trait datasets for genomic selection, including support dominance heterosis and polyploidy. Plant breeders interested in selection often face challenges to utilizing multi-trait, multi-environment datasets. R package StageWise was developed go beyond the capabilities most specialized software prediction, without requiring programming skills needed more general-purpose mixed models. As name suggests, one core...