Former Lab Member
Current position:
Co-Founder and VP of Genomics
at Rev Genomics
Cody Markelz
Co-Founder and VP of Genomics
Rev Genomics
Former Postdoctoral Researcher
More info for Cody Markelz:
Research Interests
I am interested in plants and computers.
Education
| Degree | Field | Institution | Year(s) | Advisor |
|---|---|---|---|---|
| Ph.D. | Plant Biology | University of Illinois | 2007 - 2012 | Andrew Leakey |
| B.S. | Integrative Biology | University of Illinois | 2003 - 2007 | Don Ort |
Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development.
Plant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use hierarchical Bayesian Function-Valued Trait (FVT) models to estimate Brassica rapa growth curves throughout ontogeny, across two treatments, and in two growing seasons. We find genetic variation for plasticity of growth rates and final sizes, but not the inflection point (transition from accelerating to decelerating growth) of growth curves. There are trade-offs between growth rate and duration, indicating that selection for maximum yields at early harvest dates may come at the expense of late harvest yields and vice versa. We generate eigengene modules and determine which are co-expressed with FVT traits using a Weighted Gene Co-expression Analysis. Independently, we seed a Mutual Rank co-expression network model with FVT traits to identify specific genes and gene networks related to FVT. GO-analyses of eigengene modules indicate roles for actin/cytoskeletal genes, herbivore resistance/wounding responses, and cell division, while MR networks demonstrate a close association between metabolic regulation and plant growth. We determine that combining FVT Quantitative Trait Loci (QTL) and MR genes/WGCNA eigengene expression profiles better characterizes phenotypic variation than any single data type (i.e. QTL, gene, or eigengene alone). Our network analysis allows us to employ a targeted eQTL analysis, which we use to identify regulatory hotspots for FVT. We examine cis vs. trans eQTL that mechanistically link FVT QTL with structural trait variation. Colocalization of FVT, gene, and eigengene eQTL provide strong evidence for candidate genes influencing plant height. The study is the first to explore eQTL for FVT, and specifically do so in agroecologically relevant field settings.
Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common <i>Brassica rapa</i> Mapping Population.
is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for arecombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotatedgenome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.
Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.
Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange.
Transcriptional reprogramming and stimulation of leaf respiration by elevated CO2 concentration is diminished, but not eliminated, under limiting nitrogen supply.
Plant respiration responses to elevated CO2 concentration ( [CO2 ] ) have been studied for three decades without consensus about the mechanism of response. Positive effects of elevated [CO2 ] on leaf respiration have been attributed to greater substrate supply resulting from stimulated photosynthesis. Negative effects of elevated [CO2 ] on leaf respiration have been attributed to reduced demand for energy for protein turnover assumed to result from lower leaf N content. Arabidopsis thaliana was grown in ambient (370 ppm) and elevated (750 ppm) [CO2 ] with limiting and ample N availabilities. The stimulation of leaf dark respiration was attenuated in limiting N (+12%) compared with ample N supply (+30%). This response was associated with smaller stimulation of photosynthetic CO2 uptake, but not interactive effects of elevated CO2 and N supply on leaf protein, amino acids or specific leaf area. Elevated [CO2 ] also resulted in greater abundance of transcripts for many components of the respiratory pathway. A greater transcriptional response to elevated [CO2 ] was observed in ample N supply at midday versus midnight, consistent with reports that protein synthesis is greatest during the day. Greater foliar expression of respiratory genes under elevated [CO2 ] has now been observed in diverse herbaceous species, suggesting a widely conserved response.
Developmental stage specificity of transcriptional, biochemical and CO2 efflux responses of leaf dark respiration to growth of Arabidopsis thaliana at elevated [CO2].
Plant respiration responses to elevated growth [CO(2)] are key uncertainties in predicting future crop and ecosystem function. In particular, the effects of elevated growth [CO(2)] on respiration over leaf development are poorly understood. This study tested the prediction that, due to greater whole plant photoassimilate availability and growth, elevated [CO(2)] induces transcriptional reprogramming and a stimulation of nighttime respiration in leaf primordia, expanding leaves and mature leaves of Arabidopsis thaliana. In primordia, elevated [CO(2)] altered transcript abundance, but not for genes encoding respiratory proteins. In expanding leaves, elevated [CO(2)] induced greater glucose content and transcript abundance for some respiratory genes, but did not alter respiratory CO(2) efflux. In mature leaves, elevated [CO(2)] led to greater glucose, sucrose and starch content, plus greater transcript abundance for many components of the respiratory pathway, and greater respiratory CO(2) efflux. Therefore, growth at elevated [CO(2)] stimulated dark respiration only after leaves transitioned from carbon sinks into carbon sources. This coincided with greater photoassimilate production by mature leaves under elevated [CO(2)] and peak respiratory transcriptional responses. It remains to be determined if biochemical and transcriptional responses to elevated [CO(2)] in primordial and expanding leaves are essential prerequisites for subsequent alterations of respiratory metabolism in mature leaves.
Future carbon dioxide concentration decreases canopy evapotranspiration and soil water depletion by field-grown maize.
Maize, in rotation with soybean, forms the largest continuous ecosystem in temperate North America, therefore changes to the biosphere-atmosphere exchange of water vapor and energy of these crops are likely to have an impact on the Midwestern US climate and hydrological cycle. As a C4 crop, maize photosynthesis is already CO2 -saturated at current CO2 concentrations ([CO2 ]) and the primary response of maize to elevated [CO2 ] is decreased stomatal conductance (gs ). If maize photosynthesis is not stimulated in elevated [CO2 ], then reduced gs is not offset by greater canopy leaf area, which could potentially result in a greater ET reduction relative to that previously reported in soybean, a C3 species. The objective of this study is to quantify the impact of elevated [CO2 ] on canopy energy and water fluxes of maize (Zea mays). Maize was grown under ambient and elevated [CO2 ] (550 μmol mol(-1) during 2004 and 2006 and 585 μmol mol(-1) during 2010) using Free Air Concentration Enrichment (FACE) technology at the SoyFACE facility in Urbana, Illinois. Maize ET was determined using a residual energy balance approach based on measurements of sensible (H) and soil heat fluxes, and net radiation. Relative to control, elevated [CO2 ] decreased maize ET (7-11%; P < 0.01) along with lesser soil moisture depletion, while H increased (25-30 W m(-2) ; P < 0.01) along with higher canopy temperature (0.5-0.6 °C). This reduction in maize ET in elevated [CO2 ] is approximately half that previously reported for soybean. A partitioning analysis showed that transpiration contributed less to total ET for maize compared to soybean, indicating a smaller role of stomata in dictating the ET response to elevated [CO2 ]. Nonetheless, both maize and soybean had significantly decreased ET and increased H, highlighting the critical role of elevated [CO2 ] in altering future hydrology and climate of the region that is extensively cropped with these species.
Greater antioxidant and respiratory metabolism in field-grown soybean exposed to elevated O3 under both ambient and elevated CO2.
Antioxidant metabolism is responsive to environmental conditions, and is proposed to be a key component of ozone (O(3)) tolerance in plants. Tropospheric O(3) concentration ([O(3)]) has doubled since the Industrial Revolution and will increase further if precursor emissions rise as expected over this century. Additionally, atmospheric CO(2) concentration ([CO(2)]) is increasing at an unprecedented rate and will surpass 550 ppm by 2050. This study investigated the molecular, biochemical and physiological changes in soybean exposed to elevated [O(3) ] in a background of ambient [CO(2)] and elevated [CO(2)] in the field. Previously, it has been difficult to demonstrate any link between antioxidant defences and O(3) stress under field conditions. However, this study used principle components analysis to separate variability in [O(3)] from variability in other environmental conditions (temperature, light and relative humidity). Subsequent analysis of covariance determined that soybean antioxidant metabolism increased with increasing [O(3)], in both ambient and elevated [CO(2)]. The transcriptional response was dampened at elevated [CO(2)], consistent with lower stomatal conductance and lower O(3) flux into leaves. Energetically expensive increases in antioxidant metabolism and tetrapyrrole synthesis at elevated [O(3)] were associated with greater transcript levels of enzymes involved in respiratory metabolism.
Methamphetamine causes anorexia in Drosophila melanogaster, exhausting metabolic reserves and contributing to mortality.
Methamphetamine (MA) appears to produce neurotoxic effects, in part, through disruptions of energy metabolism. A recent study of the whole-body proteome of Drosophila melanogaster showed many changes in energy metabolism-related proteins, leading us to hypothesize that MA toxicity may cause whole-body disruptions of energy metabolism. To test this, we monitored the response of energy reserves and other metabolites to MA-exposure with and without the addition of dietary glucose. We also monitored changes in feeding behavior, locomotor activity and respiration rates associated with MA-exposure to investigate how MA affects energy balance. We observed that glycogen and triglyceride levels decreased dramatically within 48 hr of MA-exposure, indicating a strongly negative caloric balance. Behavioral assays revealed that MA-treated flies decreased food consumption by 60-80% and exhibited a 2-fold increase in locomotion. Caloric expenditure decreased with MA-exposure, apparently due to a compensatory decrease in resting metabolism, showing that anorexia was the primary driver of the negative caloric balance. Additionally, we observed that glucose supplementation of MA-containing diet increased glycogen reserves by 44% at 48 hr, leading to a commensurate increase in survivorship. We conclude that dietary sugar supplementation enhances survivorship by partially compensating for decreased caloric intake resulting from MA-induced anorexia. The observation that MA produces similar behavioral changes in Drosophila and humans, i.e. increased locomotor activity and anorexia, further supports the use of Drosophila as a model organism for the study of the effects of MA.
Impairment of C(4) photosynthesis by drought is exacerbated by limiting nitrogen and ameliorated by elevated [CO(2)] in maize.
Predictions of future ecosystem function and food supply from staple C(4) crops, such as maize, depend on elucidation of the mechanisms by which environmental change and growing conditions interact to determine future plant performance. To test the interactive effects of elevated [CO(2)], drought, and nitrogen (N) supply on net photosynthetic CO(2) uptake (A) in the world's most important C(4) crop, maize (Zea mays) was grown at ambient [CO(2)] (∼385 ppm) and elevated [CO(2)] (550 ppm) with either high N supply (168 kg N ha(-1) fertilizer) or limiting N (no fertilizer) at a site in the US Corn Belt. A mid-season drought was not sufficiently severe to reduce yields, but caused significant physiological stress, with reductions in stomatal conductance (up to 57%), A (up to 44%), and the in vivo capacity of phosphoenolpyruvate carboxylase (up to 58%). There was no stimulation of A by elevated [CO(2)] when water availability was high, irrespective of N availability. Elevated [CO(2)] delayed and relieved both stomatal and non-stomatal limitations to A during the drought. Limiting N supply exacerbated stomatal and non-stomatal limitation to A during drought. However, the effects of limiting N and elevated [CO(2)] were additive, so amelioration of stress by elevated [CO(2)] did not differ in magnitude between high N and limiting N supply. These findings provide new understanding of the limitations to C(4) photosynthesis that will occur under future field conditions of the primary region of maize production in the world.