A5035009865- Genetic Mapping and Diversity in Plants and Animals
- Nuts composition and effects
- Bioenergy crop production and management
- Horticultural and Viticultural Research
- Plant and Fungal Interactions Research
- Genetics and Plant Breeding
- Genetic and phenotypic traits in livestock
- Wheat and Barley Genetics and Pathology
- Crop Yield and Soil Fertility
- Rice Cultivation and Yield Improvement
- Plant responses to elevated CO2
- Plant Water Relations and Carbon Dynamics
- Soybean genetics and cultivation
- Legume Nitrogen Fixing Symbiosis
- Biofuel production and bioconversion
- Plant Pathogens and Fungal Diseases
- Genomics and Phylogenetic Studies
- Wine Industry and Tourism
- Nematode management and characterization studies
- Plant Disease Resistance and Genetics
- Plant Molecular Biology Research
- Genetic and Environmental Crop Studies
- Fermentation and Sensory Analysis
- Plant Stress Responses and Tolerance
- Plant Physiology and Cultivation Studies
University of California, Davis
2018-2025
Plant (United States)
2019-2024
University of Missouri
2023
University of Illinois Urbana-Champaign
2012-2021
Institute of Crop Science
2019
Center for Genomic Science
2008-2019
Urbana University
2014-2018
Goodwin College
2015-2016
Energy Biosciences Institute
2013-2014
Cornell University
2006-2011
Advancements in next-generation sequencing technology have enabled whole genome re-sequencing many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to approaches for with large complex genomes such as barley wheat. Genotyping-by-sequencing (GBS) has been developed a tool association studies genomics-assisted breeding range including those genomes. GBS uses restriction enzymes targeted complexity reduction followed by...
Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering with set 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly million were assayed eight environments but showed no evidence any single large-effect quantitative loci (QTLs). Instead, we identified numerous small-effect QTLs shared among families; however, allelic effects differ...
Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and improve agricultural efficiency sustainability. We crossed 25 diverse inbred maize lines B73 reference line, capturing a total 136,000 recombination events. Variation for frequencies was observed among families, influenced by local (cis) variation. identified evidence numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated...
Accelerating crop improvement in sorghum, a staple food for people semiarid regions across the developing world, is key to ensuring global security context of climate change. To facilitate gene discovery and molecular breeding we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) 971 worldwide accessions that adapted diverse agroclimatic conditions. Using this genome-wide SNP map, population structure with respect geographic origin morphological type identified patterns...
The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its wine. Here, we characterize genome-wide patterns genetic variation in over 1,000 samples grape, Vitis vinifera subsp. , wild relative, V. sylvestris from US Department Agriculture germplasm collection. We find support a Near East origin present evidence introgression local as moved into Europe. High levels diversity rapid linkage disequilibrium (LD) decay have...
Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic phenotypic diversity of sorghum [ Sorghum bicolor (L.) Moench] panel suitable association mapping, comprised 377 accessions representing all major cultivated races (tropical lines from diverse geographic climatic regions), important U.S. breeding their progenitors. Accessions were phenotyped eight traits, levels population structure familial...
High-throughput, noninvasive field phenotyping has revealed genetic variation in crop morphological, developmental, and agronomic traits, but rapid measurements of the underlying physiological biochemical traits are needed to fully understand plant-environment interactions. This study tested application leaf hyperspectral reflectance (λ = 500–2,400 nm) as a high-throughput approach for accurate assessment photosynthetic maize (Zea mays). Leaf were measured with standard wet-laboratory...
We compared the genetic architecture of thirteen maize morphological traits in a large population recombinant inbred lines. Four from male inflorescence (tassel) and three female (ear) were measured studied using linkage genome-wide association analyses to flowering leaf previously same population. Inflorescence loci have larger effects than loci, ear are tassel effects. Ear trait models also lower predictive ability tassel, flowering, or models. Pleiotropic identified that control...
Significance Crop yields are dependent on the number of lateral primordia made by inflorescence. In maize unbranched mutants, excess at expense stem cells located in center meristem. Ultimately, mutant meristem lacks enough to regenerate and thus, terminates prematurely. This study shows that duplicate transcription factors unbranched2 unbranched3 function together decrease rate initiation, thus giving time regenerate. Variants gene affect different aspects initiation control crop yield.
We compare genomic selection methods that use correlated traits to help predict biomass yield in sorghum, and find trait-assisted performs best. Genomic (GS) is usually performed on a single trait, but can also focal trait through indirect or multi-trait GS. In this study, we pre-breeding population of sorghum strategies improve prediction yield, the trait. Correlated include moisture, plant height measured at monthly intervals between planting harvest, area under growth progress curve....
Of the four major dwarfing genes described in sorghum, only Dw3 has been cloned. We used association mapping to characterize phenotypic effects of dw3 mutation and fine map a second, epistatic QTL on sorghum chromosome 9 (Sb-HT9.1). Our panel 378 inbreds includes 230 conversion (SC) lines, which are exotic lines that have introgressed with quantitative trait loci (QTL) from common parent. The causal associates reduced lower internode length an elongation apex, consistent its role as auxin...
Abstract Background Sorghum is a tropical C 4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism photoperiod-insensitivity. Quantitative trait loci these traits have been introgressed from dwarf donor into hundreds of diverse sorghum landraces yield the Conversion lines. Here, we report first comprehensive genomic analysis molecular changes underlying this adaptation. Results We apply genotyping-by-sequencing 1,160 lines their...
Next-generation DNA sequencing (NGS) produces vast amounts of sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed library preparation methods NGS have helped solve this problem, however, by combining the use reduced representation libraries with sample barcoding genome-wide genotype from a common set markers across large number samples. Here we such method, called genotyping-by-sequencing (GBS), produce mapping in an F1...
Genomic selection (GS) is a breeding method that uses marker–trait models to predict unobserved phenotypes. This study developed GS for predicting traits associated with resistance Fusarium head blight (FHB) in wheat ( Triticum aestivum L.). We used genotyping‐by‐sequencing (GBS) identify 5054 single‐nucleotide polymorphisms (SNPs), which were then treated as predictor variables analysis. compared how the prediction accuracy of genomic‐estimated values (GEBVs) was affected by (i) five...
Fusarium head blight (FHB) is one of the most important wheat ( Triticum aestivum L.) diseases worldwide, and host resistance displays complex genetic control. A genome‐wide association study (GWAS) was performed on 273 winter breeding lines from midwestern eastern regions United States to identify chromosomal associated with FHB resistance. Genotyping‐by‐sequencing (GBS) used 19,992 single‐nucleotide polymorphisms (SNPs) covering all 21 chromosomes. Marker–trait associations were different...
Members of the genus Juglans are monecious wind-pollinated trees in family Juglandaceae with highly heterozygous genomes, which greatly complicates genome sequence assembly. The genomes interspecific hybrids usually comprised haploid parental species. We exploited this attribute to avoid heterozygosity and sequenced an hybrid microcarpa × J. regia using a novel combination single-molecule sequencing optical mapping technologies. resulting assemblies both were remarkably complete including...
Abstract Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum studied as feedstock for biofuel forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve intrinsic water use efficiency (iWUE) biomass production. Phenotyping to discover genotype-to-phenotype associations remains bottleneck in understanding the mechanistic basis natural variation gs iWUE. This study addressed...