A5070155734- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Forest ecology and management
- Genetic diversity and population structure
- Biochemical Analysis and Sensing Techniques
- Bioenergy crop production and management
- Wheat and Barley Genetics and Pathology
- Berry genetics and cultivation research
- Postharvest Quality and Shelf Life Management
- Plant Water Relations and Carbon Dynamics
- Remote Sensing in Agriculture
- Crop Yield and Soil Fertility
- Growth and nutrition in plants
- Plant Pathogens and Resistance
- Spectroscopy and Chemometric Analyses
- Horticultural and Viticultural Research
- Ruminant Nutrition and Digestive Physiology
- Smart Agriculture and AI
- Plant biochemistry and biosynthesis
- Forest Insect Ecology and Management
- Insect-Plant Interactions and Control
- Food composition and properties
- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
University of Florida
2016-2025
ID Genomics (United States)
2014-2019
U.S. Horticultural Research Laboratory
2019
Institut thématique Génétique, génomique et bioinformatique
2012
Universidade Federal de Viçosa
2007-2012
Brazilian Agricultural Research Corporation
1996-1999
Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, wild accessions. A subset of these accessions was evaluated consumer panels, identifying the that made most important contributions to flavor liking. We found modern contain significantly lower amounts many older Whole-genome sequencing a genome-wide association study permitted...
Genomic selection can increase genetic gain per generation through early selection. is expected to be particularly valuable for traits that are costly phenotype and expressed late in the life cycle of long-lived species. Alternative approaches genomic prediction models may perform differently with distinct properties. Here performance four different original methods differ respect assumptions regarding distribution marker effects, including (i) ridge regression-best linear unbiased...
Featured paper: See also the Commentary by Ellis
• Genomic selection is increasingly considered vital to accelerate genetic improvement. However, it unknown how accurate genomic prediction models remain when used across environments and ages. This knowledge critical for breeders apply this strategy in Here, we evaluated the utility of a Pinus taeda population c. 800 individuals clonally replicated grown on four sites, genotyped 4825 single-nucleotide polymorphism (SNP) markers. Prediction were estimated diameter height at multiple ages...
Progress in the rate of improvement autopolyploid species has been limited compared with diploids, mainly because software and methods to apply advanced prediction selection methodologies autopolyploids are lacking. The objectives this research were (i) develop an R package for construct relationship matrix derived from pedigree information that accounts autopolyploidy double reduction (ii) use estimate level effect autotetraploid blueberry breeding population extensive information. is...
Although they are staple foods in cuisines globally, many commercial fruit varieties have become progressively less flavorful over time. Due to the cost and difficulty associated with flavor phenotyping, breeding programs long been challenged selecting for this complex trait. To address issue, we leveraged targeted metabolomics of diverse tomato blueberry accessions their corresponding consumer panel ratings create statistical machine learning models that can predict sensory perceptions...
Abstract Breeding crops for improved flavor is challenging due to the high cost of sensory evaluation and difficulty connecting experience chemical composition. The main goal this study was identify drivers sweetness consumer liking fresh strawberries ( Fragaria × ananassa ). Fruit 148 strawberry samples from cultivars breeding selections were grown harvested over seven years subjected both analyses. Each panel consisted at least 100 consumers, resulting in more than 15,000 data points per...
The application of quantitative genetics in plant and animal breeding has largely focused on additive models, which may also capture dominance epistatic effects. Partitioning genetic variance into its nonadditive components using pedigree-based models (P-genomic best linear unbiased predictor) (P-BLUP) is difficult with most commonly available family structures. However, the availability dense panels molecular markers makes possible use additive- dominance-realized genomic relationships for...
Summary Genome‐wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These focused largely on analysis common variants despite abundance rare polymorphisms several species, and their potential role trait variation. Here, we conducted first GWAS Populus deltoides , a genetically diverse keystone forest species North America an important short rotation woody crop for bioenergy industry. We searched associations between eight...
Sweet corn is one of the most important vegetables in United States and Canada. Here, we present a de novo assembly sweet inbred line Ia453 with mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar commercial hybrids developed for processing fresh markets. The ten pseudochromosomes cover 92% total 99% estimated genome size, scaffold N50 222.2 Mb. reference completely assembles large structural variation that created mutant sh2-R allele. Furthermore,...
ABSTRACT Quantitative genetic analyses aim to estimate parameters and breeding values select superior parents, families, individuals. For these estimates a relationship matrix derived from the pedigree typically is used in mixed model framework. However, complex, multistep process errors are common. Because reduce accuracy of parameter affect gain, it important correct errors. Here we show that realized (RRM) single nucleotide polymorphism markers based on normality coefficients can be...
Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source nuclear data for studies animal systematics and phylogeography. However, mitochondrial microsatellite variation are still commonly used in various kinds molecular studies, probably will complement genomic years to come. Here we show that besides providing abundant data, UCE is an excellent both sequences loci design complete genomes high depth. Identification dozens...
Pedigrees and dense marker panels have been used to predict the genetic merit of individuals in plant animal breeding, accounting primarily for contribution additive effects. However, nonadditive effects may also affect trait variation many breeding systems, particularly when specific combining ability is explored. Here we models with different priors, including additive-only plus dominance effects, polygenic (height) oligogenic (fusiform rust resistance) traits a structured population...
The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm integrate genomics and breeding. We carried out whole-genome contrasted it genome-wide association study (GWAS) for growth traits in breeding populations Eucalyptus benthamii (n =505) pellita =732). Both species are increasing commercial interest the development germplasm adapted environmental stresses. Predictive ability reached 0.16 E. 0.44 diameter growth. abilities using...
Summary Rapidly enhancing oleoresin production in conifer stems through genomic selection and genetic engineering may increase resistance to bark beetles terpenoid yield for liquid biofuels. We integrated association prediction analyses of flow (g 24 h −1 ) using 4854 single nucleotide polymorphisms ( SNP s) expressed genes within a pedigreed population loblolly pine P inus taeda that was clonally replicated at three sites the s outheastern U nited S tates. Additive variation 2 ≈ 0.12–0.30)...
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...
Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations breeding strategies. occurs many important crops; however, its effects on inheritance agronomic traits are still poorly understood compared with diploid species. Higher levels allelic dosage or more complex interactions between alleles could affect phenotype expression. Hence, present study aimed to dissect genetic basis fruit-related autotetraploid blueberries...
A complete approach for genome-wide selection (GWS) involves reliable statistical genetics models and methods. Reports on this topic are common additive genetic but not additive-dominance models. The objective of paper was (i) to compare the performance 10 predictive (including current proposed modifications), fitted using Bayesian, Lasso Ridge regression approaches; (ii) decompose genomic heritability accuracy in terms three quantitative information sources, namely, linkage disequilibrium...
Abstract Demand for all-natural vanilla flavor is increasing, but its botanical source, Vanilla planifolia , faces critical challenges arising from a narrow germplasm base and supply limitations. Genomics tools are the key to overcoming these limitations by enabling advanced genetics plant breeding new cultivars with improved yield quality. The objective of this work was establish genomic resources needed facilitate analysis diversity among accessions provide resource analyze other...
Alfalfa is planted in more than 30 million hectares worldwide, but despite its popularity temperate regions, it not widely grown subtropical agroecosystems. It critical to improve alfalfa for such considering current predictions of global warming and the increasing demands animal-based products. In this study, we examined diversity present germplasm reported genetic parameters forage production. An initial screening was performed from 2014 2016, evaluating 121 populations different origins....
Whole-genome multiomic profiles hold valuable information for the analysis and prediction of disease risk progression. However, integrating high-dimensional multilayer omic data into risk-assessment models is statistically computationally challenging. We describe a statistical framework, Bayesian generalized additive model ((BGAM), present software inputs models. used BGAM from The Cancer Genome Atlas survival after diagnosis breast cancer. developed sequence studies to (1) compare...
Sweet corn breeding programs, like field corn, focus on the development of elite inbred lines to produce commercial hybrids. For this reason, genomic selection models can help in silico prediction hybrid crosses from lines, which is hypothesized improve test cross scheme, leading higher genetic gain a program. This study aimed explore potential implementing sweet program through within-site across-year and across-site framework. A total 506 hybrids were evaluated six environments...