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bioRxiv2016

PARAQUAT TOLERANCE3 is an E3 ligase and acts as a negative regulator of oxidative stress response

Oxidative damage could be caused in plant cells when biotic and abiotic stresses are imposed. While the response to oxidative stress is well studied, little is known about how the activated response is switched off when oxidative stress is diminished. By studying Arabidopsis mutant paraquat tolerance3, we identified the genetic locus PARAQUAT TOLERANCE3 (PQT3) as a major negative regulator of oxidative stress tolerance. PQT3, encoding an E3 ligase, is rapidly down-regulated by oxidative stress. PQT3 has E3 ubiquitin ligase activity in ubiquitination assay. Subsequently, we identified PRMT4b as a PQT3-interacting protein. By histone methylation, PRMT4b may regulate the expression of APX1 and GPX1, encoding two key enzymes against oxidative stress. Moreover, PQT3 is able to recognize PRMT4b for targeted degradation via 26S proteasome. Therefore, we have identified PQT3 as an E3 ligase that acts as a negative regulator of activated response to oxidative stress.

Plant Biology↗

bioRxiv2016

Characterization and Transposon Mutagenesis of the Maize (Zea mays) Pho1 Gene Family

Phosphorus is an essential nutrient for all plants, but also one of the least mobile, and consequently least available, in the soil. Plants have evolved a series of molecular, metabolic and developmental adaptations to increase the acquisition of phosphorus and to maximize the efficiency of use within the plant. In Arabidopsis (Arabidopsis thaliana), the AtPHO1 protein regulates and facilitates the distribution of phosphorus within the plant. To investigate the role of PHO1 in maize (Zea mays), the B73 reference genome was searched for homologous sequences and four genes identified that were designated ZmPho1;1, ZmPho1;2a, ZmPho1;2b and ZmPho1;3. ZmPho1;2a and ZmPho1;2b are the most similar to AtPho1, and represent candidate co-orthologs that we hypothesize to have been retained following whole genome duplication. Tissue-and phosphate-specific differences in the accumulation of ZmPho1;2a and ZmPho1;2b transcripts were observed, indicating regulatory divergence. Furthermore, evidence was obtained for the phosphate-regulated production of anti-sense transcripts associated with both ZmPho1;2a and ZmPho1;2b, suggesting the possibility of regulatory crosstalk between paralogs. To characterize functional divergence between ZmPho1;2a and ZmPho1;2b, a program of transposon mutagenesis was initiated using the Ac/Ds system, and, here, we report the generation of novel alleles of ZmPho1;2a and ZmPho1;2b.

Plant Biology↗

bioRxiv2016

A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification

Quantitative Trait Locus (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the Solanum pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennelli. This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous Hidden Markov Model for genotyping the lines, and by using state of the art sparse regression techniques for QTL mapping.

Plant Biology↗

bioRxiv2016

Pooled enrichment sequencing identifies diversity and evolutionary pressures at NLR resistance genes within a wild tomato population.

Nod-like Receptors (NLRs) are Nucleotide-binding domain and Leucine rich Repeats (NB-LRR)-containing proteins that are important in plant resistance signaling. Many of the known pathogen Resistance (R)-genes in plants are NLRs and they can recognise directly or indirectly pathogen molecules. As such, divergence and copy number variants at these genes is found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild non-model species, it is necessary to identify the full range of NLRs and infer their evolutionary history.\n\nHere we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species S. pennellii. We use a combination of enrichment sequencing and pooling of ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different of mapping and SNP calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of {pi}N/{pi}s ratios and differing site frequency spectra. We compare our observed rate of heterozygosity to expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat.

Plant Biology↗

bioRxiv2016

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

O_LIPlant interactions with arbuscular mycorrhizal fungi have long excited interest for their potential to promote more efficient use of mineral resources in agricultural production. Their use, however, remains limited, in part because of a lack of understanding of the factors that determine symbiotic outcome. In this work, variation in response to arbuscular mycorrhizal colonization was characterized a panel of genetically diverse maize inbred lines.\nC_LIO_LIThe parents of the maize Nested Association Mapping population were evaluated, with and without colonization, in early vegetative stages. Subsequently, six lines with contrasting phenotypes were selected for further characterization, including quantification of fungal colonization, mycorrhiza-mediated phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters.\nC_LIO_LIThe relative growth of lines changed between non-inoculated and inoculated plants, indicative of variation in host capacity to profit from symbiosis. Patterns of Pht1 transcript accumulation varied among lines, and were correlated with outcome.\nC_LIO_LILarger growth responses were correlated with more extensive development of root-external hyphae, increased accumulation of specific Pht1 transcripts and a high level of mycorrhiza-mediated phosphorus uptake. The data suggest that host genetic factors influence fungal growth strategy with subsequent impact on plant biomass production.\nC_LI

Plant Biology↗

bioRxiv2016

A Sister of PIN1 gene in tomato (Solanum lycopersicum) defines organ initiation patterns by maintaining epidermal auxin flux

The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One of the main contributors to auxin localization is the auxin efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis has revealed that PIN1 genes are split into two sister clades; PIN1 and the relatively uncharacterized Sister-Of-PIN1 (SoPIN1). In this paper we identify entire-2 as a loss-of-function SlSoPIN1a (Solyc10g078370) mutant in Solanum lycopersicum. The entire-2 plants are unable to specify proper leaf initiation leading to a frequent switch from the wild type spiral phyllotactic pattern to distichous and decussate patterns. Leaves in entire-2 are large and less complex and the leaflets display spatial deformities in lamina expansion, vascular development, and margin specification. During sympodial growth in entire-2 the specification of organ position and identity is greatly affected resulting in variable branching patterns on the main sympodial and inflorescence axes. To understand how SlSoPIN1a functions in establishing proper auxin maxima we used the auxin signaling reporter DR5::Venus to visualize differences in auxin localization between entire-2 and wild type. DR5::Venus visualization shows a widening of auxin localization which spreads to subepidermal tissue layers during early leaf and flower organogenesis, showing that SoPIN1 functions to focus auxin signaling to the epidermal layer. The striking spatial deformities observed in entire-2 help provide a mechanistic framework for explaining the function of the SoPIN1 clade in angiosperm species.\n\nAuthor SummaryThe plant hormone auxin acts as a positional signal in most plant developmental processes. The PIN-FORMED family of auxin transporters are the main contributors to auxin localization, especially PIN-FORMED1, which has been studied extensively in plant model species Arabidopsis thaliana. Members of the PIN-FORMED gene family have been found in all plant species, but there is a scarcity of mutants described outside Arabidopsis thaliana. Using Solanum lycopersicum (tomato) as a system, this study identifies a loss of function mutant from the Sister-Of-PIN1 clade in the SlSoPIN1a gene. The characterization of this mutant reveals the role of SlSoPIN1a in establishing position of organ initiation during shoot and reproductive development, including a role in establishing proper spiral phyllotaxy. We use an auxin visualization technique to conclude SlSoPIN1a functions in specifying auxin presence in proper cell layers to establish organ and tissue positioning. This work gives further evolutionary context to how PIN-FORMED genes act to establish organogenesis in the plant kingdom.

Plant Biology↗

bioRxiv2016

RNA‐guided endonuclease‐driven mutagenesis in tobacco followed by efficient fixation of mutated sequences in doubled haploid plants

BackgroundCustomizable endonucleases are providing an effective tool for genome engineering. The resulting primary transgenic individuals are typically heterozygous and/or chimeric with respect to any mutations induced. To generate genetically fixed mutants, they are conventionally allowed to self-pollinate, a procedure which segregates individuals into mutant heterozygotes/homozygotes and wild types. The chances of recovering homozygous mutants among the progeny depends not only on meiotic segregation but also on the frequency of mutated germline cells in the chimeric mother plant.\n\nResultsRNA-guided endonuclease-mediated mutagenesis was targeted to the green fluorescent protein gene (gfp) harboured by a transgenic tobacco line. Upon retransformation using a gfp-specific endonuclease construct, the T0 plants were allowed to either self-pollinate, or were propagated via regeneration from in vitro cultured embryogenic pollen which give rise to haploid/doubled haploid plants or from leaf explants that form plants vegetatively. Single or multiple mutations were detected in 80% of the T0 plants. The majority of these mutations proved heritable by each of the three propagation systems used. Regeneration from in vitro cultured embryogenic pollen allowed for homozygous mutants to be produced more efficiently than via sexual reproduction. The recovery of mutations that were not found among sexually produced progeny was shown to be achievable through vegetative plant propagation in vitro. In addition, a number of mutations not detected in the primary gRNA/Cas9-expressing plants were uncovered in the progeny, irrespective of the mode of propagation.\n\nConclusionRegeneration from embryogenic pollen culture provides a convenient method to rapidly generate a variety of genetically fixed mutants following site-directed mutagenesis. Induced mutations that are not sexually transmitted can be recovered through vegetative plant regeneration from somatic tissue.

Plant Biology↗

bioRxiv2016

Dynamics and Control of Phloem Loading of Indoleacetic Acid in Seedling Cotyledons of Ricinus Communis During Germination

During seed germination sugars and auxin are produced from stored precursors or conjugates respectively and transported to the seedling axis. To elucidate the mode of travel of IAA into the phloem a solution of [3H]indoleacetic acid (IAA), together with [14C]sucrose, was injected in the endosperm cavity harboring the cotyledons of germinating seedlings of Ricinus communis. Phloem exudate from the cut hypocotyl was collected and the radioactivity recorded. Sucrose loading in the phloem was inhibited at higher IAA levels, and the rate of filling of the transient pool(s) was reduced by IAA. IAA was detected within 10 minutes, with the concentration increasing over 30 min and reaching a steady-state by 60 min. The kinetics indicated that phloem loading of IAA involving both an active, carrier-based, and a passive, diffusion-based component, with IAA traveling along a pathway containing an intermediary pool, possibly the protoplasts of mesophyll cells. Phloem loading of IAA was altered by sucrose, K+ and a range of non-specific and IAA-specific analogues and inhibitors in a manner that showed that IAA moves into the phloem from the extra cotyledonary solution by multiple pathways, with a carrier mediated pathway playing a principal role.\n\nSummary StatementIndoleacetic acid is transported from the peri-cotyledonary space into the phloem of germinating Ricinus seedlings by both trans-membrane carriers and diffusive pathways, with the cells of the cotyledons forming an intermediate reservoir.

Plant Biology↗

bioRxiv2016

DIRC3 and close to NABP1 Genetics Polymorphisms correlated with Prognostic Survival in Patients with Laryngeal Squamous Cell Carcinoma

Laryngeal squamous cell carcinoma (LSCC) is one of the most common and aggressive malignancies in the upper digestive tract that has a high mortality rate and a poor prognosis. Prognostic factors were determined through multivariate Cox regression analysis. The overall survival rates were calculated by the Kaplan-Meier method. The SPSS statistical software package version 17.0 (SPSS Inc., Chicago, IL, USA) was used for all analyses. Median follow-up was 38 (range 3-122) months and the median survival time was 48 months. We adjusted to confounding factors (total laryngectomy, poor differentiation, T3-T4 stage, N1-N2 stage, III-IV TNM stage) into multivariate Cox proportional hazards model, we confirmed rs11903757 GT genotype (HR = 2.036; 95% CI, 1.071 - 3.872; p = 0.030) and rs966423 TT genotype (HR = 11.677; 95% CI, 3.901 - 34.950; p = 0.000) were significantly correlated with prognostic survival of patients with LSCC compared with rs11903757 TT genotype and rs966423 CC genotype, respectively. Our research provided new evidence for patients with LSCC, it seemed to be the first that demonstrated rs11903757 GT genotype on chromosome 2q32.3 close to NABP1 and rs966423 TT genotype in the intron region of DIRC3 on chromosome 2q35 predict poor prognostic survival in patients with LSCC.

Plant Biology↗

bioRxiv2016

Left-right leaf asymmetry in decussate and distichous phyllotactic systems

Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of a particular chirality are similarly asymmetric relative to each other. Models of auxin flux capable of recapitulating spiral phyllotaxis predict handed auxin asymmetries in initiating leaf primordia with empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend a similar analysis of leaf asymmetry to decussate and distichous phyllotaxy. We found that our simulation models of these two patterns predicted mirrored asymmetries in auxin distribution in leaf primordia pairs. To empirically verify the morphological consequences of asymmetric auxin distribution, we analyzed the morphology of a tomato sister-of-pinformed1a (sopin1a) mutant, entire-2, in which spiral phyllotaxy consistently transitions to a decussate state. Shifts in the displacement of leaflets on the left and right sides of entire-2 leaf pairs mirror each other, corroborating predicted model results. We then analyze the shape of >800 commonivy (Hedera helix) and >3,000 grapevine (Vitis and Ampelopsis spp.) leaf pairs and find statistical enrichment of predicted mirrored asymmetries. Our results demonstrate that left-right auxin asymmetries in models of decussate and distichous phyllotaxy successfully predict mirrored asymmetric leaf morphologies in superficially symmetric leaves.

Plant Biology↗

bioRxiv2016

A mathematical model of non-photochemical quenching to study short-term light memory in plants

Plants are permanently exposed to rapidly changing environments, therefore it is evident that they had to evolve mechanisms enabling them to dynamically adapt to such fluctuations. Here we study how plants can be trained to enhance their photoprotection and elaborate on the concept of the short-term illumination memory in Arabidopsis thaliana. By monitoring fluorescence emission dynamics we systematically observe the extent of non-photochemical quenching (NPQ) after previous light exposure to recognise and quantify the memory effect. We propose a simplified mathematical model of photosynthesis that includes the key components required for NPQ activation, which allows us to quantify the contribution to photoprotection by those components. Due to its reduced complexity, our model can be easily applied to study similar behavioural changes in other species, which we demonstrate by adapting it to the shadow-tolerant plant Epipremnum aureum. Our results indicate that a basic mechanism of short-term light memory is preserved. The slow component, accumulation of zeaxanthin, accounts for the amount of memory remaining after relaxation in darkness, while the fast one, antenna protonation, increases quenching efficiency. With our combined theoretical and experimental approach we provide a unifying framework describing common principles of key photoprotective mechanisms across species in general, mathematical terms.

Plant Biology↗

bioRxiv2016

Genome-Wide Analysis of Single Non-Templated Nucleotides in Plant Endogenous siRNAs and miRNAs

Plant small RNAs are subject to various modifications. Previous reports revealed widespread 3' modifications (truncations and non-templated tailing) of plant miRNAs when the 2'-C-methyltransferase HEN1 is absent. However, non-templated nucleotides in plant heterochromatic siRNAs have not been deeply studied, especially in wild-type plants. We systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing libraries from Arabidopsis. tomato, Medicago, rice, maize, and Physcomitrella. Elevated rates of non-templated nucleotides were observed at the 3' ends of both miRNAs and endogenous siRNAs from wild-type specimens of all species. 'Off-sized' small RNAs, such as 25 and 23 nt siRNAs arising from loci dominated by 24 nt siRNAs, often had very high rates of 3'-non-templated nucleotides. The same pattern was observed in all species that we studied. Further analysis of 24 nt siRNA clusters in Arabidopsis revealed distinct patterns of 3'-non-templated nucleotides of 23 nt siRNAs arising from heterochromatic siRNA loci. This pattern of non-templated 3' nucleotides on 23 nt siRNAs is not affected by loss of known small RNA 3'-end modifying enzymes, and may result from modifications added to longer heterochromatic siRNA precursors.

Plant Biology↗

bioRxiv2016

On the Origin and Evolutionary Consequences of Gene Body DNA Methylation

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (\"gene body methylation; gbM\"), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, the first known instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z and various histone modifications in E. salsugineum and in Arabidopsis thaliana epiRILs found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modifications of chromatin over evolutionary time scales.

Plant Biology↗

bioRxiv2016

Widespread natural variation of DNA methylation within angiosperms

To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time. These results show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Plant Biology↗

bioRxiv2016

Predicting plant biomass accumulation from image-derived parameters

Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologist. However, it is a great challenge to find a suitable model to predict plant biomass in the context of high-throughput phenotyping. In the present study, we constructed several models to examine the quantitative relationship between image-based features and plant biomass accumulation. Our methodology has been applied to three consecutive barley experiments with control and stress treatments. The results proved that plant biomass can be accurately predicted from image-based parameters using a random forest model. The high prediction accuracy based on this model, in particular the cross-experiment performance, is promising to relieve the phenotyping bottleneck in biomass measurement in breeding applications. The relative contribution of individual features for predicting biomass was further quantified, revealing new insights into the phenotypic determinants of plant biomass outcome. Whats more, the methods could also be used to determine the most important image-based features related to plant biomass accumulation, which would be promising for subsequent genetic mapping to uncover the genetic basis of biomass.\n\nOne-sentence SummaryWe demonstrated that plant biomass can be accurately predicted from image-based parameters in the context of high-throughput phenotyping.\n\nFootnotesThis work was supported by the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), the Robert Bosch Stiftung (32.5.8003.0116.0) and the Federal Agency for Agriculture and Food (BEL, 15/12-13, 530-06.01-BiKo CHN) and the Federal Ministry of Education and Research (BMBF, 0315958A and 031A053B). This research was furthermore enabled with support of the European Plant Phenotyping Network (EPPN, grant agreement no. 284443) funded by the FP7 Research Infrastructures Programme of the European Union.

Plant Biology↗

bioRxiv2016

Modification of plant regeneration medium decreases the time for recovery of Solanum lycopersicum cultivar M82 stable transgenic lines

Tomato (Solanum lycopersicum) has rapidly become a valuable model species for a variety of studies including functional genomics. A high-throughput method to obtain transgenic lines sooner than standard methods would greatly advance gene function studies. The goal of this study was to optimize our current transformation method by investigating medium components that would result in a decreased time for recovery of transgenics. For this study, 6-day-old cotyledon explants from Solanum lycopersicum cultivar M82 in vitro-grown seedlings were infected with the Agrobacterium tumefaciens strain LBA4404 containing the binary vector pBI121. This vector contains the {beta}-glucuronidase reporter gene and the neomycin phosphotransferase II selectable marker gene that confers resistance to kanamycin. Modification of our standard plant regeneration medium with indole-3-acetic acid (IAA) at concentrations of either 0.05 mg/l or 0.1 mg/l decreased the recovery time for transgenic lines by 6 weeks as compared to our standard medium that contains zeatin as the only plant growth regulator. We observed 50% and 54% transformation efficiency on plant regeneration medium containing 0.05 mg/l and 0.1 mg/l IAA, respectively. Moreover, addition of 1 mg/l IAA to the root induction medium resulted in earlier root development than medium that did not contain IAA. Addition of IAA to the plant regeneration and rooting media did not have any negative effects on plant development. Recovery of transgenic lines in a shorter time results in higher throughput for the introduction of gene constructs and has the potential to decrease the time and resources needed to complete investigations of gene function.

Plant Biology↗

bioRxiv2016

Prediction of glyphosate resistance level based on EPSPS gene copy number in Kochia scoparia

Glyphosate-resistant (GR) Kochia scoparia has evolved in dryland chemical fallow systems throughout North America and the mechanism involves 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene duplication. Sugarbeet fields in four states were surveyed for K. scoparia in 2013 and tested for glyphosate-resistance level and EPSPS gene copy number. Glyphosate resistance was confirmed in K. scoparia populations collected from sugarbeet fields in Colorado, Wyoming, and Nebraska. The GR samples all had increased EPSPS gene copy number, with median population values up to 11. An empirical model was developed to estimate the level of glyphosate-resistance in K. scoparia based on EPSPS gene copy number. The results suggested that glyphosate susceptibility can be accurately diagnosed using EPSPS gene copy number, and further increases in EPSPS gene copy number could increase resistance levels up to 8-fold relative to susceptible K. scoparia. These trends suggest that continued glyphosate selection pressure is selecting for higher EPSPS copy number and higher resistance levels in K. scoparia. By including multiple K. scoparia samples lacking EPSPS gene duplication, our empirical model provides a more realistic estimate of fold-resistance due to EPSPS gene copy number compared to methods that do not account for normal variation of herbicide response in susceptible biotypes.

Plant Biology↗

bioRxiv2016

The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome

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.\n\nAuthor SummaryPlants take up elements from the soil, a process that is highly regulated by the plants genome. To investigate how maize alters its elemental uptake in response to different environments, we analyzed the kernel elemental content of a population derived from a cross grown 10 different times in six locations. We found that environment had a profound effect on which genetic loci were important for elemental accumulation in the kernel. Our results suggest that to have a full understanding of elemental accumulation in maize kernels and other food crops, we will need to understand the interactions identified here at the level of the genes and the environmental variables that contribute to loading essential nutrients into seeds.

Plant Biology↗