A5079313615- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Plant Reproductive Biology
- Genetic diversity and population structure
- Plant Molecular Biology Research
- Plant and animal studies
- Gene expression and cancer classification
- Chromosomal and Genetic Variations
- Plant Disease Resistance and Genetics
- Genetic Associations and Epidemiology
- Evolution and Genetic Dynamics
- Berry genetics and cultivation research
- Ocean Acidification Effects and Responses
- Crop Yield and Soil Fertility
- Animal Behavior and Reproduction
- Physiological and biochemical adaptations
- Morphological variations and asymmetry
- Horticultural and Viticultural Research
- Plant nutrient uptake and metabolism
- Plant biochemistry and biosynthesis
- Marine Bivalve and Aquaculture Studies
- Genomics and Phylogenetic Studies
- Plant Taxonomy and Phylogenetics
- Seed Germination and Physiology
University of California, Davis
2015-2025
Plant (United States)
2016-2023
ORCID
2021
Duke University
2008-2019
The origins of maize were the topic vigorous debate for nearly a century, but neither current genetic model nor earlier archaeological models account totality available data, and recent work has highlighted potential contribution wild relative, Zea mays ssp. mexicana . Our population analysis reveals that origin modern can be traced to an admixture between ancient in highlands Mexico some 4000 years after domestication began. We show variation is key component diversity, both at individual...
The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. depends on patterns dormancy release or induction by cold interacts with flowering-time variation construct different life histories. To characterize the genetic basis climatic associations natural in chilling responses associated life-history syndromes, we selected 559 fully sequenced accessions model annual species Arabidopsis thaliana from across wide...
Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt dynamic environments. To understand this cellular diversity, we profiled tomato root translatomes. Using xylem differentiation in tomato, examples functional innovation, repurposing, conservation transcription factors are described, relative the model plant Arabidopsis. Repurposing innovation genes further observed within an exodermis regulatory network illustrate its function....
Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness evolvability within gene regulatory network underlying of larval skeleton in sea urchin Strongylocentrotus purpuratus. find extensive variation expression this throughout a natural population, some which has heritable basis. Switch-like predominate during early development, variation, may promote...
Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress alter the contribution of additive genetic variation gene expression during development purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic change scenarios. first measured embryos by RNA-seq characterize molecular signatures mild, chronic temperature unbiased manner. found increase from 12 18 °C caused...
Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental physiological mechanisms link genotype phenotype. However, classical analytical techniques poorly suited to quantitative of where the number traits assayed per individual reach many thousand. Here, we derive a Bayesian sparse factor estimating covariance matrix...
Linear mixed effect models are powerful tools used to account for population structure in genome-wide association studies (GWASs) and estimate the genetic architecture of complex traits. However, fully-specified computationally demanding common simplifications often lead reduced power or biased inference. We describe Grid-LMM (https://github.com/deruncie/GridLMM), an extendable algorithm repeatedly fitting linear that multiple sources heterogeneity, such as additive non-additive variance,...
Chromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying inversion’s In study, we used large-scale transcriptomic data dissect importance of 13 Mb inversion locus ( Inv4m ) found almost exclusively highland populations maize Zea mays ssp. ). was introgressed into from...
Large-scale phenotype data can enhance the power of genomic prediction in plant and animal breeding, as well human genetics. However, statistical foundation multi-trait is based on multivariate linear mixed effect model, a tool notorious for its fragility when applied to more than handful traits. We present MegaLMM, framework associated software package model analyses virtually unlimited number Using three examples with real data, we show that MegaLMM leverage thousands traits at once...
Native Americans domesticated maize ( Zea mays ssp. ) from lowland teosinte parviglumis parviglumis) in the warm Mexican southwest and brought it to highlands of Mexico South America where was exposed lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites plant responses low-temperature phosphorus availability have been suggested influence Here, we combined linkage mapping with genome scans identify High PhosphatidylCholine 1 HPC1 ), a...
Abstract Incorporating measurements on correlated traits into genomic prediction models can increase accuracy and selection gain. However, multi-trait are complex prone to overfitting which may result in a loss of relative single-trait prediction. Cross-validation is considered the gold standard method for selecting tuning both plant animal breeding. When used appropriately, cross-validation gives an accurate estimate model, effectively choose among disparate based their expected performance...
Abstract Threats to crop production due climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations wild relatives, and ex situ germplasm collections, separating alleles from linked deleterious variants that impact agronomic traits is challenging has limited utility these diverse resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting...
Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions of interest researchers breeders. To determine the prevalence strength local adaptation maize landraces, we performed a reciprocal transplant experiment across an elevational gradient Mexico. We grew 120 grouped into four (Mexican Highland, Mexican Lowland, South American Lowland), common gardens collected phenotypes...
Abstract Genotype-by-environment interactions are a significant challenge for crop breeding as well being important understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment in maize multiparent advanced generation intercross population grown across 5 environments. We found that contributed much genotypic effects to variation some agronomically traits. To understand how correlations between traits change environments, estimated...
Summary Many plant populations exhibit synchronous flowering, which can be advantageous in reproduction. However, molecular mechanisms underlying flowering synchrony remain poorly understood. We studied the role of known vernalization‐response and flower‐promoting pathways facilitating synchronized Arabidopsis thaliana . Using vernalization‐responsive Col‐ FRI genotype, we experimentally varied germination dates daylength among individuals to test field controlled environments. assessed...
Phenomic Selection is a new paradigm in plant breeding that uses high-throughput phenotyping technologies and machine learning models to predict traits of individuals make selections. This can allow breeders evaluate more plants higher throughput accurately, resulting faster rates gain reduced labor costs. However, Prediction are frequently benchmarked against Genomic using cross-validation demonstrate their usefulness breeders. We argue this inappropriate for two reasons: 1) Differences the...
Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect in natural populations. A possible explanation these observations mutant phenotypes and fitness may depend upon the specific environmental conditions which a exposed. Here, we tested this hypothesis by growing flowering time mutants Arabidopsis thaliana multiple field sites seasons quantify their effects realistic conditions. By constructing environment-specific...
Integration of multi-omics data improved prediction accuracies oat agronomic and seed nutritional traits in multi-environment trials distantly related populations addition to the single-environment prediction. Multi-omics has been shown be superior genomic with genome-wide DNA-based genetic markers (G) for predicting phenotypes. However, most existing studies were based on historical datasets from one environment; therefore, they unable evaluate efficiency populations. To fill those gaps, we...
The widely recounted story of the origin cultivated strawberry (Fragaria × ananassa) oversimplifies complex interspecific hybrid ancestry highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into three-century-long domestication history strawberry, we reconstructed genealogy as deeply possible-pedigree records were assembled for 8,851 individuals, including 2,656 developed since 1775. parents individuals with unverified or missing...
Summary The genetic basis of growth and development is often studied in constant laboratory environments; however, the environmental conditions that organisms experience nature are much more dynamic. We examined how daily temperature fluctuations, average temperature, day length vernalization influence flowering time 59 genotypes Arabidopsis thaliana with allelic perturbations known to affect time. For a subset genotypes, we also assessed treatment effects on morphology growth. identified 17...
Variation in the social environment can have profound effects on survival and reproduction wild mammals. However, we know little about degree to which these are influenced by genetic differences among individuals, conversely, environmental variation mediates reaction norms. To better understand relationships, investigated potential for dominance rank, connectedness group size modify of gene expression baboons Amboseli basin. We found evidence a number gene-environment interactions (GEIs)...