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Most downloaded papers related to "ivan baxter," all time

in category plant biology

14 results found. For more information, click each entry to expand.

1: Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters
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Posted to bioRxiv 01 Mar 2016

Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters
1,841 downloads plant biology

Ruairidh J. H. Sawers, Simon F Svane, Clement Quan, Mette Grønlund, Barbara Wozniak, Eliécer González-Muñoz, Ricardo A. Chávez Montes, Ivan Baxter, Jerome Goudet, Iver Jakobsen, Uta Paszkowski

Plant interactions with arbuscular mycorrhizal fungi have long attracted interest for their potential to promote more efficient use of mineral resources in agriculture. Their widespread use, however, remains limited by understanding of the processes that determine the outcome of the symbiosis. In this study, variation in growth response to mycorrhizal inoculation was characterized in a panel of diverse maize lines. A panel of thirty maize lines was evaluated with and without inoculation with arbuscular mycorrhizal fungi. The line Oh43 was identified to show superior response and, along with five other reference lines, was characterized in greater detail in a split-compartment system, using 33P to quantify mycorrhizal phosphorus uptake. Changes in relative growth between non-inoculated and inoculated plants indicated variation in host capacity to profit from the symbiosis. Shoot phosphate content, abundance of intra-radical and root-external fungal structures, mycorrhizal phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters varied among lines. Larger growth responses in Oh43 were correlated with extensive development of root-external hyphae, accumulation of specific Pht1 transcripts and a high level of mycorrhizal phosphorus uptake. The data indicate that host genetic factors influence fungal growth strategy with an impact on plant performance.

2: The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome
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Posted to bioRxiv 13 Apr 2016

The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome
1,164 downloads plant biology

Alexandra B Asaro, Gregory R Ziegler, Cathrine Ziyomo, Owen A Hoekenga, Brian P Dilkes, Ivan Baxter

Plants obtain soil-resident elements that support growth and metabolism via water-mediated flow facilitated by transpiration and active transport processes. The availability of elements in the environment interact with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms influencing elemental accumulation will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 x Mo17 (IBM) recombinant inbred population grown in 10 different environments spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci controlling seed elemental accumulation. While a set of these QTL were found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.

3: Canopy position has a profound effect on soybean seed composition
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Posted to bioRxiv 06 Jan 2016

Canopy position has a profound effect on soybean seed composition
921 downloads plant biology

Steven C Huber, Kunzhi Li, Randall Nelson, Alexander Ulyanov, Catherine M. DeMuro, Ivan Baxter

Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with the canopy position where they were produced. In studies with 10 cultivars grown over a 3-yr period, we found that seeds produced at the top of the canopy have higher concentrations of protein but less oil and lower concentrations of minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Among cultivars, mean protein concentration (average of different positions) correlated positively with mean concentrations of S, Zn and Fe, but not other minerals. Therefore, on a whole plant basis, the uptake and allocation of S, Zn and Fe to seeds correlated with the production and allocation of reduced N to seed protein; however, the reduced N and correlated minerals (S, Zn and Fe) showed different patterns of allocation among node positions. For example, while mean concentrations of protein and Fe correlated positively, the two parameters correlated negatively in terms of variation with canopy position. Altering the microenvironment within the soybean canopy by removing neighboring plants at flowering increased protein concentration in particular at lower node positions and thus altered the node-position gradient in protein (and oil) without altering the distribution of Mg, Fe and Cu, suggesting different underlying control mechanisms. Metabolomic analysis of developing seeds at different positions in the canopy suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds and may explain the increased protein accumulation in seeds produced at the top of the canopy. Our results establish node-position variation in seed constituents and provide a new experimental system to identify genes controlling key aspects of seed composition. In addition, our results provide an unexpected and simple approach to link agronomic practices to improve human nutrition and health in developing countries because food products produced from seeds at the bottom of the canopy contained higher Fe concentrations than products from the top of the canopy. Therefore, using seeds produced in the lower canopy for production of iron-rich soy foods for human consumption could be important when plants are the major source of protein and human diets can be chronically deficient in Fe and other minerals.

4: A genetic link between leaf carbon isotope composition and whole-plant water use efficiency in the C4 grass Setaria
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Posted to bioRxiv 20 Mar 2018

A genetic link between leaf carbon isotope composition and whole-plant water use efficiency in the C4 grass Setaria
816 downloads plant biology

Patrick Z Ellsworth, Max J Feldman, Ivan Baxter, Asaph Cousins

Genetic selection for whole plant water use efficiency (yield per transpiration; WUEplant) in any crop-breeding program requires high throughput phenotyping of component traits of WUEplant such as transpiration efficiency (TEi; CO2 assimilation rate per stomatal conductance). Leaf carbon stable isotope composition ( δ13Cleaf) has been suggested as a potential proxy for WUEplant because both parameters are influenced by TEi. However, a genetic link between δ13Cleaf and WUEplant in a C4 species is still not well understood. Therefore, a high throughput phenotyping facility was used to measure WUEplant in a recombinant inbred line (RIL) population of the C4 grasses Setaria viridis and S. italica to determine the genetic relationship between δ13Cleaf, WUEplant, and TEi under well-watered and water-limited growth conditions. Three quantitative trait loci (QTL) for δ13Cleaf were found to co-localize with transpiration, biomass accumulation, and WUEplant. WUEplant calculated for each of the three δ13Cleaf allele classes was negatively correlated with δ13Cleaf as would be predicted when TEi is driving WUEplant. These results demonstrate that δ13Cleaf is genetically linked to WUEplant through TEi and can be used as a high throughput proxy to screen for WUEplant in these C4 species.

5: A curated list of genes that control elemental accumulation in plants.
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Posted to bioRxiv 31 Oct 2018

A curated list of genes that control elemental accumulation in plants.
753 downloads plant biology

Lauren Whitt, Felipe Ricachenevsky, Gregory R Ziegler, Stephan Clemens, Elsbeth Walker, Franciscus Johannes Maria Maathuis, Philip Kear, Ivan Baxter

Knowledge of the genes and alleles underlying elemental composition will be required to understand how plants interact with their environment. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with the phenotype in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change elemental uptake. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 96 known genes covering 4 species and 23 elements and their 596 orthologs in 8 species. Most of the genes were identified in the model plant Arabidopsis thaliana and transporter coding genes as well as genes that affect the accumulation of iron and zinc are overrepresented in the current list.

6: Coordinated Changes In The Accumulation Of Metal Ions In Maize (Zea mays ssp. mays L.) In Response To Inoculation With The Arbuscular Mycorrhizal Fungus Funneliformis mosseae
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Posted to bioRxiv 08 May 2017

Coordinated Changes In The Accumulation Of Metal Ions In Maize (Zea mays ssp. mays L.) In Response To Inoculation With The Arbuscular Mycorrhizal Fungus Funneliformis mosseae
700 downloads plant biology

M. Rosario Ramirez-Flores, Ruben Rellan-Alvarez, Barbara Wozniak, Mesfin-Nigussie Gebreselassie, Iver Jakobsen, Victor Olalde-Portugal, Ivan Baxter, Uta Paszkowski, Ruairidh J.H. Sawers

Arbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of nineteen elements was determined in the roots and leaves of a panel of thirty maize varieties, grown under phosphorus limiting conditions, with, or without, inoculation with the fungus Funneliformis mosseae. Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a coordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants.

7: High-throughput profiling and analysis of plant responses over time to abiotic stress
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Posted to bioRxiv 01 May 2017

High-throughput profiling and analysis of plant responses over time to abiotic stress
682 downloads plant biology

Kira M Veley, Jeffrey C. Berry, Sarah J. Fentress, Daniel P. Schachtman, Ivan Baxter, Rebecca Bart

Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. Here we describe strategies for identifying shape, color and ionomic indicators of plant nitrogen use efficiency. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity) and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, both in terms of biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis we present a novel approach to quantifying color-based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low cost and high throughput option for characterizing G x E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.

8: Elemental Accumulation in Kernels of the Maize Nested Association Mapping Panel Reveals Signals of Gene by Environment Interactions
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Posted to bioRxiv 20 Jul 2017

Elemental Accumulation in Kernels of the Maize Nested Association Mapping Panel Reveals Signals of Gene by Environment Interactions
536 downloads plant biology

Gregory R Ziegler, Philip J. Kear, Di Wu, Catherine Ziyomo, Alexander Lipka, Michael A. Gore, Owen A Hoekenga, Ivan Baxter

Elemental accumulation in seeds is the product of a combination of environment and a wide variety of genetically controlled physiological processes. We measured the kernel elemental composition of the Nested Association Mapping (NAM) of maize (Zea mays L.) grown in 4 different environments. Analysis of variance revealed strong effects of genotype, environment and genotype by environment interactions. Using Joint-linkage mapping on a set of 7000 markers we identified 354 quantitative trait loci (QTL) across 20 elements, four environments and a combination of the environments. Leveraging 20 M SNPs derived from genome resequencing on the parents of the population, genome-wide association mapping studies (GWAS) detected 8573 loci. While most of the GWAS SNPs were located near genes not previously implicated in elemental regulation, several SNPs were located next to orthologs of well-characterized elemental regulation genes

9: Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria
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Posted to bioRxiv 27 Oct 2016

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria
518 downloads plant biology

Max J Feldman, Rachel E Paul, Darshi Banan, Jennifer F Barrett, Jose Sebastian, Muh-Ching Yee, Hui Jiang, Alexander E Lipka, Thomas P Brutnell, José R. Dinneny, Andrew DB Leakey, Ivan Baxter

Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed twelve controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor vertical growth throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

10: Trait components of whole plant water use efficiency are defined by unique, environmentally responsive genetic signatures in the model C4 grass Setaria
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Posted to bioRxiv 15 Dec 2017

Trait components of whole plant water use efficiency are defined by unique, environmentally responsive genetic signatures in the model C4 grass Setaria
483 downloads plant biology

Max J Feldman, Patrick Z Ellsworth, Noah Fahlgren, Malia A Gehan, Asaph B Cousins, Ivan Baxter

Plant growth and water use are interrelated processes influenced by the genetic control of both plant morphological and biochemical characteristics. Improving plant water use efficiency (WUE) to sustain growth in different environments is an important breeding objective that can improve crop yields and enhance agricultural sustainability. However, genetic improvements of WUE using traditional methods have proven difficult due to low throughput and environmental heterogeneity encountered in field settings. To overcome these limitations the study presented here utilizes a high-throughput phenotyping platform to quantify plant size and water use of an interspecific Setaria italica x Setaria viridis recombinant inbred line population at daily intervals in both well-watered and water-limited conditions. Our findings indicate that measurements of plant size and water use in this system are strongly correlated; therefore, a linear modeling approach was used to partition this relationship into predicted values of plant size given water use and deviations from this relationship at the genotype level. The resulting traits describing plant size, water use and WUE were all heritable and responsive to soil water availability, allowing for a genetic dissection of the components of plant WUE under different watering treatments. Linkage mapping identified major loci underlying two different pleiotropic components of WUE. This study indicates that alleles controlling WUE derived from both wild and domesticated accessions of the model C4 species Setaria can be utilized to predictably modulate trait values given a specified precipitation regime.

11: High fidelity detection of crop biomass QTL from low-cost imaging in the field
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Posted to bioRxiv 14 Jun 2017

High fidelity detection of crop biomass QTL from low-cost imaging in the field
380 downloads plant biology

Darshi Banan, Rachel Paul, Max Feldman, Mark Holmes, Hannah Schlake, Ivan Baxter, Andrew DB Leakey

Above-ground biomass production is a key target for studies of crop abiotic stress tolerance, disease resistance and yield improvement. However, biomass is slow and laborious to evaluate in the field using traditional destructive methods. High-throughput phenotyping (HTP) is widely promoted as a potential solution that can rapidly and non-destructively assess plant traits by exploiting advances in sensor and computing technology. A key potential application of HTP is for quantitative genetics studies that identify loci where allelic variation is associated with variation in crop production. And, the value of performing such studies in the field, where environmental conditions match that of production farming, is recognized. To date, HTP of biomass productivity in field trials has largely focused on expensive and complex methods, which — even if successful — will limit their use to a subset of wealthy research institutions and companies with extensive research infrastructure and highly-trained personnel. Even with investment in ground vehicles, aerial vehicles and gantry systems ranging from thousands to millions of dollars, there are very few examples where Quantitative trait loci (QTLs) detected by HTP of biomass production in a field-grown crop are shown to match QTLs detected by direct measures of biomass traits by destructive harvest techniques. Until such proof of concept for HTP proxies is generated it is unlikely to replace existing technology and be widely adopted. Therefore, there is a need for methods that can be used to assess crop performance by small teams with limited training and at field sites that are remote or have limited infrastructure. Here we use an inexpensive and simple, miniaturized system of hemispherical imaging and light attenuation modeling to identify the same set of key QTLs for biomass production as traditional destructive harvest methods applied to a field-grown Setaria mapping population. This provides a case study of a HTP technology that can deliver results for QTL mapping without high costs or complexity.

12: Increased temperatures may safeguard the nutritional quality of crops under future elevated CO2 concentrations
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Posted to bioRxiv 20 Jun 2018

Increased temperatures may safeguard the nutritional quality of crops under future elevated CO2 concentrations
350 downloads plant biology

Iris H. Köhler, Steven Huber, Carl J. Bernacchi, Ivan R. Baxter

Iron (Fe) and zinc (Zn) deficiencies are a global human health problem that may worsen by growth of crops at elevated atmospheric CO2 concentration (eCO2). However, climate change will also involve higher temperature, but it is unclear how the combined effect of eCO2 and higher temperature will affect the nutritional quality of food crops. To begin to address this question, we grew soybean (Glycine max) in a Temperature by Free-Air CO2 Enrichment (T-FACE) experiment in 2014 and 2015 under ambient (400 μmol mol-1) and elevated (600 μmol mol-1) CO2 concentration and under ambient and elevated temperatures (+2.7 °C day and +3.4°C at night). In our study, eCO2 significantly decreased Fe concentration in soybean seeds in both seasons (-8.7% and -7.7%) and Zn concentration in one season (-8.9%) while higher temperature (at ambient CO2 concentration) had the opposite effect. The combination of eCO2 with elevated temperature generally restored seed Fe and Zn concentrations to levels obtained under ambient CO2 and temperature conditions, suggesting that the potential threat to human nutrition by increasing CO2 concentration may not be realized. In general, seed Fe concentration was negatively correlated with yield suggesting inherent limitations to increasing seed Fe. In addition, we confirm our previous report that the concentration of seed storage products and several minerals varies with node position at which the seeds developed. Overall, these results demonstrate the complexity of predicting climate change effects on food security when various environmental parameters change in an interactive manner.

13: Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome
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Posted to bioRxiv 31 Dec 2017

Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome
237 downloads plant biology

Alexandra B Asaro, Brian P Dilkes, Ivan Baxter

Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads the ionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. To examine the genetic basis of covariation in the accumulation of multiple elements, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. We compared quantitative trait loci (QTL) determining single-element variation to QTL that predict variation in principal components (PCs) of multiple-element covariance. Single-element and multivariate approaches detected partially overlapping sets of loci. In addition to loci co-localizing with single-element QTL, multivariate traits within environments were controlled by loci with significant multi-element effects not detectable using single-element traits. Gene-by-environment interactions underlying multiple-element covariance were identified through QTL analyses of principal component models of ionome variation. In addition to interactive effects, growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.

14: Genomewide association study reveals transient loci underlying the genetic architecture of biomass accumulation under cold stress in Sorghum.
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Posted to bioRxiv 08 Sep 2019

Genomewide association study reveals transient loci underlying the genetic architecture of biomass accumulation under cold stress in Sorghum.
161 downloads plant biology

Nadia Shakoor, Erica Agnew, Greg Ziegler, Scott Lee, Cesar Lizarraga, Noah Fahlgren, Ivan Baxter, Todd C. Mockler

Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy because of its potential for high biomass yields. However, in its early growth phases, sorghum is sensitive to cold stress, preventing early planting in temperate environments. Cold temperature adaptability is vital for the successful cultivation of both bioenergy and grain sorghum at higher latitudes and elevations, and for early season planting or to extend the growing season. Identification of genes and alleles that enhance biomass accumulation of sorghum grown under early cold stress would enable the development of improved bioenergy sorghum through breeding or genetic engineering. We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP is a collection of densely genotyped and racially, geographically, and phenotypically diverse accessions. The plants were weighed, watered, and imaged daily to measure growth dynamics and water use efficiency (WUE). Daily, non-destructive imaging allowed for a temporal analysis of growth-related traits in response to cold stress. We performed a genome-wide association study (GWAS) to identify candidate genomic intervals and genes controlling response to early cold stress. GWAS identified transient quantitative trait loci (QTL) strongly associated with each growth-related trait, permitting an investigation into the genetic basis of cold stress response at different stages of development. The analysis identified a priori and novel candidate genes associated with growth-related traits and the temporal response to cold stress.


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