Publications by authors named "Brian Dilkes"

56 Publications

Metabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plants.

Plant Cell 2021 May;33(3):492-510

Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.

The optimal extraction of information from untargeted metabolomics analyses is a continuing challenge. Here, we describe an approach that combines stable isotope labeling, liquid chromatography- mass spectrometry (LC-MS), and a computational pipeline to automatically identify metabolites produced from a selected metabolic precursor. We identified the subset of the soluble metabolome generated from phenylalanine (Phe) in Arabidopsis thaliana, which we refer to as the Phe-derived metabolome (FDM) In addition to identifying Phe-derived metabolites present in a single wild-type reference accession, the FDM was established in nine enzymatic and regulatory mutants in the phenylpropanoid pathway. To identify genes associated with variation in Phe-derived metabolites in Arabidopsis, MS features collected by untargeted metabolite profiling of an Arabidopsis diversity panel were retrospectively annotated to the FDM and natural genetic variants responsible for differences in accumulation of FDM features were identified by genome-wide association. Large differences in Phe-derived metabolite accumulation and presence/absence variation of abundant metabolites were observed in the nine mutants as well as between accessions from the diversity panel. Many Phe-derived metabolites that accumulated in mutants also accumulated in non-Col-0 accessions and was associated to genes with known or suspected functions in the phenylpropanoid pathway as well as genes with no known functions. Overall, we show that cataloguing a biochemical pathway's products through isotopic labeling across genetic variants can substantially contribute to the identification of metabolites and genes associated with their biosynthesis.
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http://dx.doi.org/10.1093/plcell/koaa046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136897PMC
May 2021

Maize Plants Chimeric for an Autoactive Resistance Gene Display a Cell Autonomous Hypersensitive Response but Non-Cell Autonomous Defense Signaling.

Mol Plant Microbe Interact 2021 Jan 28. Epub 2021 Jan 28.

USDA-ARS, Plant Science Research Unit, Raleigh, North Carolina, United States.

The maize gene Rp1-D21 is a mutant form of the gene Rp1-D that confers resistance to common rust. Rp1-D21 triggers a spontaneous defense response that occurs in the absence of the pathogen and includes a programed cell death called the hypersensitive response (HR). Eleven plants heterozygous for Rp1-D21, in four different genetic backgrounds, were identified that had chimeric leaves with lesioned sectors showing HR abutting green non-lesioned sectors lacking HR. The Rp1-D21 sequence derived from each of the lesioned portions of leaves was unaltered from the expected sequence whereas the Rp1-D21 sequences from nine of the non-lesioned sectors displayed various mutations and we were unable to amplify Rp1-D21 from the other two non-lesioned sectors. In every case, the borders between the sectors were sharp with no transition zone, suggesting that HR and chlorosis associated with Rp1-D21 activity was cell-autonomous. Expression of defense response marker genes was assessed in the lesioned and non-lesioned sectors as well as in near-isogenic plants lacking and carrying Rp1-D21. Defense gene expression was somewhat elevated in non-lesioned sectors abutting sectors carrying Rp1-D21 compared to near-isogenic plants lacking Rp1-D21. This suggests that while the HR itself was cell autonomous, other aspects of the defense response initiated by Rp1-D21 were not.
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http://dx.doi.org/10.1094/MPMI-04-20-0091-RDOI Listing
January 2021

Bracing for sustainable agriculture: the development and function of brace roots in members of Poaceae.

Curr Opin Plant Biol 2021 02 5;59:101985. Epub 2021 Jan 5.

Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, United States. Electronic address:

Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots-subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.
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http://dx.doi.org/10.1016/j.pbi.2020.101985DOI Listing
February 2021

Maize brace roots provide stalk anchorage.

Plant Direct 2020 Nov 8;4(11):e00284. Epub 2020 Nov 8.

Department of Plant and Soil Sciences and the Delaware Biotechnology Institute University of Delaware Newark DE USA.

Mechanical failure, known as lodging, negatively impacts yield and grain quality in crops. Limiting crop loss from lodging requires an understanding of the plant traits that contribute to lodging-resistance. In maize, specialized aerial brace roots are reported to reduce root lodging. However, their direct contribution to plant biomechanics has not been measured. In this manuscript, we use a non-destructive field-based mechanical test on plants before and after the removal of brace roots. This precisely determines the contribution of brace roots to establish a rigid base (i.e. stalk anchorage) that limits plant deflection in maize. These measurements demonstrate that the more brace root whorls that contact the soil, the greater their overall contribution to anchorage, but that the contributions of each whorl to anchorage were not equal. Previous studies demonstrated that the number of nodes that produce brace roots is correlated with flowering time in maize. To determine if flowering time selection alters the brace root contribution to anchorage, a subset of the Hallauer's Tusón tropical population was analyzed. Despite significant variation in flowering time and anchorage, selection neither altered the number of brace root whorls in the soil nor the overall contribution of brace roots to anchorage. These results demonstrate that brace roots provide a rigid base in maize and that the contribution of brace roots to anchorage was not linearly related to flowering time.
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http://dx.doi.org/10.1002/pld3.284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649601PMC
November 2020

Variation in Maize Chlorophyll Biosynthesis Alters Plant Architecture.

Plant Physiol 2020 09 8;184(1):300-315. Epub 2020 Jul 8.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907

Chlorophyll is a tetrapyrrole metabolite essential for photosynthesis in plants. The first committed step of chlorophyll biosynthesis is catalyzed by a multimeric enzyme, magnesium chelatase, the subunit I of which is encoded by the () gene in maize (). A range of chlorophyll contents and net CO assimilation rates can be achieved in maize by combining a semidominant mutant allele of () and a cis-regulatory modifier named () that varies between different inbred lines. We previously demonstrated that these allelic interactions can delay reproductive maturity. In this study, we demonstrate that multiple gross morphological traits respond to a reduction in chlorophyll. We found that stalk width, number of lateral branches (tillers), and branching of the inflorescence decline with a decrease in chlorophyll level. Chlorophyll deficit suppressed tillering in multiple maize mutants, including , , and In contrast to these traits, plant height showed a nonlinear response to chlorophyll levels. Weak suppression of by resulted in a significant increase in mutant plant height. By contrast, enhancement of the severity of the phenotype by the allele resulted in reduced plant height. We demonstrate that the effects of reduced chlorophyll contents on plant growth and development are complex and depend on the trait being measured. We propose that the lack of chlorophyll exerts growth control via energy balance sensing, which is upstream of the known genetic networks for branching and architecture.
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http://dx.doi.org/10.1104/pp.20.00306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479880PMC
September 2020

Endosidin20 Targets the Cellulose Synthase Catalytic Domain to Inhibit Cellulose Biosynthesis.

Plant Cell 2020 07 23;32(7):2141-2157. Epub 2020 Apr 23.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907

Plant cellulose is synthesized by rosette-structured cellulose synthase (CESA) complexes (CSCs). Each CSC is composed of multiple subunits of CESAs representing three different isoforms. Individual CESA proteins contain conserved catalytic domains for catalyzing cellulose synthesis, other domains such as plant-conserved sequences, and class-specific regions that are thought to facilitate complex assembly and CSC trafficking. Because of the current lack of atomic-resolution structures for plant CSCs or CESAs, the molecular mechanism through which CESA catalyzes cellulose synthesis and whether its catalytic activity influences efficient CSC transport at the subcellular level remain unknown. Here, by performing chemical genetic analyses, biochemical assays, structural modeling, and molecular docking, we demonstrate that Endosidin20 (ES20) targets the catalytic site of CESA6 in Arabidopsis (). Chemical genetic analysis revealed important amino acids that potentially participate in the catalytic activity of plant CESA6, in addition to previously identified conserved motifs across kingdoms. Using high spatiotemporal resolution live cell imaging, we found that inhibiting the catalytic activity of CESA6 by ES20 treatment reduced the efficiency of CSC transport to the plasma membrane. Our results demonstrate that ES20 is a chemical inhibitor of CESA activity and trafficking that represents a powerful tool for studying cellulose synthesis in plants.
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http://dx.doi.org/10.1105/tpc.20.00202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7346566PMC
July 2020

Interaction Between Induced and Natural Variation at Delays Reproductive Maturity in Maize.

G3 (Bethesda) 2020 02 6;10(2):797-810. Epub 2020 Feb 6.

Department of Botany and Plant Pathology,

We previously demonstrated that maize () locus encodes a putative -regulatory expression polymorphism at the magnesium chelatase subunit I gene (aka ) that strongly modifies the chlorophyll content of the semi-dominant mutants. The allele of Mo17 inbred line reduces chlorophyll content in the mutants leading to reduced photosynthetic output. mutants in B73 reached reproductive maturity four days later than wild-type siblings. Enhancement of by the Mo17 allele at the QTL delayed maturity further, resulting in detection of a flowering time QTL in two bi-parental mapping populations crossed to The near isogenic lines of B73 harboring the allele from Mo17 delayed flowering of mutants by twelve days. Just as previously observed for chlorophyll content, had no effect on reproductive maturity in the absence of the allele. Loss of chlorophyll biosynthesis in mutants and enhancement by reduced CO assimilation. We attempted to separate the effects of photosynthesis on the induction of flowering from a possible impact of chlorophyll metabolites and retrograde signaling by manually reducing leaf area. Removal of leaves, independent of the mutant, delayed flowering but surprisingly reduced chlorophyll contents of emerging leaves. Thus, defoliation did not completely separate the identity of the signal(s) that regulates flowering time from changes in chlorophyll content in the foliage. These findings illustrate the necessity to explore the linkage between metabolism and the mechanisms that connect it to flowering time regulation.
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http://dx.doi.org/10.1534/g3.119.400838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003087PMC
February 2020

Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome.

Plant Direct 2019 May 10;3(5):e00139. Epub 2019 May 10.

Donald Danforth Plant Science Center St. Louis Missouri.

The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype-by-environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. 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 , the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. 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. QTL influencing trait covariation were detected at loci that were not found by mapping single-element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi-element traits that were determined by both genetic and environmental factors as well as genotype-by-environment interactions. Growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.
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http://dx.doi.org/10.1002/pld3.139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589523PMC
May 2019

A Modifier of the Allele Uncovers a Cryptic Phenotypic Impact of -regulatory Variation in Maize.

G3 (Bethesda) 2019 02 7;9(2):375-390. Epub 2019 Feb 7.

Center for Plant Biology, Purdue University, IN 47907

Forward genetics determines the function of genes underlying trait variation by identifying the change in DNA responsible for changes in phenotype. Detecting phenotypically-relevant variation outside protein coding sequences and distinguishing this from neutral variants is not trivial; partly because the mechanisms by which DNA polymorphisms in the intergenic regions affect gene regulation are poorly understood. Here we utilized a dominant genetic reporter to investigate the effect of cis and -acting regulatory variation. We performed a forward genetic screen for natural variation that suppressed or enhanced the semi-dominant mutant allele , encoding the magnesium chelatase subunit I of maize. This mutant permits rapid phenotyping of leaf color as a reporter for chlorophyll accumulation, and mapping of natural variation in maize affecting chlorophyll metabolism. We identified a single modifier locus segregating between B73 and Mo17 that was linked to the reporter gene itself, which we call (). Based on the variation in OY1 transcript abundance and genome-wide association data, is predicted to consist of multiple -acting regulatory sequence polymorphisms encoded at the wild-type alleles. The locus appears to be a common polymorphism in the maize germplasm that alters the expression level of a key gene in chlorophyll biosynthesis. These alleles have no discernable impact on leaf chlorophyll in the absence of the reporter. Thus, the use of a mutant as a reporter for magnesium chelatase activity resulted in the detection of expression-level polymorphisms not readily visible in the laboratory.
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http://dx.doi.org/10.1534/g3.118.200798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385977PMC
February 2019

Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize.

Plant Cell 2018 12 9;30(12):2922-2942. Epub 2018 Nov 9.

Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455

Genome-wide association studies (GWAS) have identified loci linked to hundreds of traits in many different species. Yet, because linkage equilibrium implicates a broad region surrounding each identified locus, the causal genes often remain unknown. This problem is especially pronounced in nonhuman, nonmodel species, where functional annotations are sparse and there is frequently little information available for prioritizing candidate genes. We developed a computational approach, Camoco, that integrates loci identified by GWAS with functional information derived from gene coexpression networks. Using Camoco, we prioritized candidate genes from a large-scale GWAS examining the accumulation of 17 different elements in maize () seeds. Strikingly, we observed a strong dependence in the performance of our approach based on the type of coexpression network used: expression variation across genetically diverse individuals in a relevant tissue context (in our case, roots that are the primary elemental uptake and delivery system) outperformed other alternative networks. Two candidate genes identified by our approach were validated using mutants. Our study demonstrates that coexpression networks provide a powerful basis for prioritizing candidate causal genes from GWAS loci but suggests that the success of such strategies can highly depend on the gene expression data context. Both the software and the lessons on integrating GWAS data with coexpression networks generalize to species beyond maize.
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http://dx.doi.org/10.1105/tpc.18.00299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354270PMC
December 2018

Adult plant resistance in maize to northern leaf spot is a feature of partial loss-of-function alleles of Hm1.

PLoS Pathog 2018 10 17;14(10):e1007356. Epub 2018 Oct 17.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America.

Adult plant resistance (APR) is an enigmatic phenomenon in which resistance genes are ineffective in protecting seedlings from disease but confer robust resistance at maturity. Maize has multiple cases in which genes confer APR to northern leaf spot, a lethal disease caused by Cochliobolus carbonum race 1 (CCR1). The first identified case of APR in maize is encoded by a hypomorphic allele, Hm1A, at the hm1 locus. In contrast, wild-type alleles of hm1 provide complete protection at all developmental stages and in every part of the maize plant. Hm1 encodes an NADPH-dependent reductase, which inactivates HC-toxin, a key virulence effector of CCR1. Cloning and characterization of Hm1A ruled out differential transcription or translation for its APR phenotype and identified an amino acid substitution that reduced HC-toxin reductase (HCTR) activity. The possibility of a causal relationship between the weak nature of Hm1A and its APR phenotype was confirmed by the generation of two new APR alleles of Hm1 by mutagenesis. The HCTRs encoded by these new APR alleles had undergone relatively conservative missense changes that partially reduced their enzymatic activity similar to HM1A. No difference in accumulation of HCTR was observed between adult and juvenile plants, suggesting that the susceptibility of seedlings derives from a greater need for HCTR activity, not reduced accumulation of the gene product. Conditions and treatments that altered the photosynthetic output of the host had a dramatic effect on resistance imparted by the APR alleles, demonstrating a link between the energetic or metabolic status of the host and disease resistance affected by HC-toxin catabolism by the APR alleles of HCTR.
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http://dx.doi.org/10.1371/journal.ppat.1007356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205646PMC
October 2018

Propagation of cell death in dropdead1, a sorghum ortholog of the maize lls1 mutant.

PLoS One 2018 10;13(9):e0201359. Epub 2018 Sep 10.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America.

We describe dropdead1-1 (ded1), an EMS-induced recessive lesion mimic mutant of sorghum. It is characterized by the formation of spreading necrotic lesions that share many attributes with those associated with the maize lethal leaf spot1 (lls1) and Arabidopsis accelerated cell death1 (acd1) mutation. We show that as in lls1, ded1 lesions are initiated by wounding and require light for continued propagation, and that loss of chloroplast integrity is responsible for ded1 cell death. Consistent with these parallels, we demonstrate that ded1 is an ortholog of lls1 and encodes pheophorbide a oxidase (PaO) with 93% identity at the protein level. The mutant ded1 allele resulted from a stop codon-inducing single base pair change in exon 6 of the sorghum ortholog of lls1. The ded1 transcript was rapidly and transiently induced after wounding and substantially elevated in leaves containing ded1 lesions. Given that PaO is a key enzyme of the chlorophyll degradation pathway, its dysfunction would result in the accumulation of pheophorbide, a potent photosensitizer that results in the production of singlet oxygen. Consistent with this, cell death associated with ded1 lesions is most likely caused by singlet oxygen as our results exclude superoxide and H2O2 from this role. We explore the signal responsible for the propagation of lesions affecting both ded1 and lls1 lesions and find that both developmental age and ethylene increase the rate of lesion expansion in both mutants.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201359PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6130852PMC
February 2019

Dark period transcriptomic and metabolic profiling of two diverse accessions.

Plant Direct 2018 Feb 22;2(2):e00032. Epub 2018 Feb 22.

Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN USA.

is a model species for the study of plant adaptation to abiotic stresses. Two accessions of , Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profiling and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome, and 65 of which were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long-chain fatty acid derivatives as compared to SH, whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F hybrids than the mid-parent averages and the accumulation of 17% of the metabolites in F plants transgressed the level in both parents. Concentrations of several metabolites in F hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the genome and newly identified high-quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.
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http://dx.doi.org/10.1002/pld3.32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508522PMC
February 2018

Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum.

G3 (Bethesda) 2018 03 2;8(3):1079-1094. Epub 2018 Mar 2.

Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907

The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS)-treated BTx623 individuals, that using replication to detect false positive-induced variants in next-generation sequencing (NGS) data permits higher throughput variant detection with greater accuracy. We used a lower sequence coverage depth (average of 7×) from 586 independently mutagenized individuals and detected 5,399,493 homozygous single nucleotide polymorphisms (SNPs). Of these, 76% originated from only 57,872 genomic positions prone to false positive variant calling. These positions are characterized by high copy number paralogs where the error-prone SNP positions are at copies containing a variant at the SNP position. The ability of short stretches of homology to generate these error-prone positions suggests that incompletely assembled or poorly mapped repeated sequences are one driver of these error-prone positions. Removal of these false positives left 1,275,872 homozygous and 477,531 heterozygous EMS-induced SNPs, which, congruent with the mutagenic mechanism of EMS, were >98% G:C to A:T transitions. Through this analysis, we generated a collection of sequence indexed mutants of sorghum. This collection contains 4035 high-impact homozygous mutations in 3637 genes and 56,514 homozygous missense mutations in 23,227 genes. Each line contains, on average, 2177 annotated homozygous SNPs per genome, including seven likely gene knockouts and 96 missense mutations. The number of mutations in a transcript was linearly correlated with the transcript length and also the G+C count, but not with the GC/AT ratio. Analysis of the detected mutagenized positions identified CG-rich patches, and flanking sequences strongly influenced EMS-induced mutation rates. This method for detecting false positive-induced mutations is generally applicable to any organism, is independent of the choice of variant-calling algorithm, and is most valuable when the true mutation rate is likely to be low, such as in laboratory-induced mutations or somatic mutation detection in medicine.
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http://dx.doi.org/10.1534/g3.117.300301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844295PMC
March 2018

Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in .

Plant Cell 2018 01 20;30(1):48-66. Epub 2017 Dec 20.

Donald Danforth Plant Science Center, Saint Louis, Missouri 63132

Inflorescence architecture is a key determinant of yield potential in many crops and is patterned by the organization and developmental fate of axillary meristems. In cereals, flowers and grain are borne from spikelets, which differentiate in the final iteration of axillary meristem branching. In spp, inflorescence branches terminate in either a spikelet or a sterile bristle, and these structures appear to be paired. In this work, we leverage to investigate a role for the phytohormones brassinosteroids (BRs) in specifying bristle identity and maintaining spikelet meristem determinacy. We report the molecular identification and characterization of the () locus in , which encodes a rate-limiting enzyme in BR biosynthesis. Loss-of-function mutants fail to initiate a bristle identity program, resulting in homeotic conversion of bristles to spikelets. In addition, spikelet meristem determinacy is altered in the mutants, which produce two florets per spikelet instead of one. Both of these phenotypes provide avenues for enhanced grain production in cereal crops. Our results indicate that the spatiotemporal restriction of BR biosynthesis at boundary domains influences meristem fate decisions during inflorescence development. The mutants provide insight into the molecular basis underlying morphological variation in inflorescence architecture.
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http://dx.doi.org/10.1105/tpc.17.00816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5810575PMC
January 2018

Mediator Complex Subunits MED2, MED5, MED16, and MED23 Genetically Interact in the Regulation of Phenylpropanoid Biosynthesis.

Plant Cell 2017 12 4;29(12):3269-3285. Epub 2017 Dec 4.

Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907

The phenylpropanoid pathway is a major global carbon sink and is important for plant fitness and the engineering of bioenergy feedstocks. In , disruption of two subunits of the transcriptional regulatory Mediator complex, MED5a and MED5b, results in an increase in phenylpropanoid accumulation. By contrast, the semidominant mutation () results in dwarfism and constitutively repressed phenylpropanoid accumulation. Here, we report the results of a forward genetic screen for suppressors of We identified 13 independent lines that restore growth and/or phenylpropanoid accumulation in the background. Two of the suppressors restore growth without restoring soluble phenylpropanoid accumulation, indicating that the growth and metabolic phenotypes of the mutant can be genetically disentangled. Whole-genome sequencing revealed that all but one of the suppressors carry mutations in or other Mediator subunits. RNA-seq analysis showed that the mutation causes widespread changes in gene expression, including the upregulation of negative regulators of the phenylpropanoid pathway, and that the suppressors reverse many of these changes. Together, our data highlight the interdependence of individual Mediator subunits and provide greater insight into the transcriptional regulation of phenylpropanoid biosynthesis by the Mediator complex.
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http://dx.doi.org/10.1105/tpc.17.00282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5757269PMC
December 2017

Phytohormone inhibitor treatments phenocopy brassinosteroid-gibberellin dwarf mutant interactions in maize.

Plant Direct 2017 Jul 12;1(2). Epub 2017 Jul 12.

Department of Biochemistry Purdue University West Lafayette IN USA.

Phytohormone biosynthesis produces metabolites with profound effects on plant growth and development. Modulation of hormone levels during developmental events, in response to the environment, by genetic polymorphism, or by chemical application, can reveal the plant processes most responsive to a phytohormone. Applications of chemical inhibitors and subsequent measurements of specific phytohormones can determine whether, and which, phytohormone is affected by a molecule. In many cases, the sensitivity of biochemical testing has determined multiple pathways affected by a single inhibitor. Genetic studies are not subject to this problem, and a wealth of data about the morphological impacts of hormone biosynthetic inhibition have accumulated through the study of enzyme mutants. In this work, we sought to assess the specificity of three triazole inhibitors of cytochrome P450s by determining their abilities to recapitulate the phenotypes of single and double mutants affected in the production of brassinosteroid (BR) and gibberellin (GA) biosynthesis. The GA biosynthetic inhibitors uniconazole (UCZ) and paclobutrazol (PAC) were applied to the BR biosynthetic mutant (), and all double-mutant phenotypes were recovered in the UCZ treatment. PAC was unable to suppress the retention of pistils in the tassels of mutant plants. The BR biosynthetic inhibitor propiconazole (PCZ) suppressed tiller outgrowth in the GA biosynthetic mutant (). All treatments were additive with genetic mutants for effects on plant height. Due to additional measurements performed here but not in previous studies of the double mutants, we detected new interactions between GA and BR biosynthesis affecting the days to tassel emergence and tassel branching. These experiments, a refinement of our previous model, and a discussion of the extension of this type of work are presented.
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http://dx.doi.org/10.1002/pld3.9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508556PMC
July 2017

Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines.

G3 (Bethesda) 2017 02 9;7(2):413-425. Epub 2017 Feb 9.

Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907

In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS)-mutagenized , including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the ortholog encoding the gibberellic acid (GA) biosynthetic enzyme -kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
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http://dx.doi.org/10.1534/g3.116.029660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295590PMC
February 2017

A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation.

Cell Res 2017 Feb 9;27(2):226-240. Epub 2016 Dec 9.

Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China.

Transposons are generally kept silent by epigenetic mechanisms including DNA methylation. Here, we identified a pair of Harbinger transposon-derived proteins (HDPs), HDP1 and HDP2, as anti-silencing factors in Arabidopsis. hdp1 and hdp2 mutants displayed an enhanced silencing of transgenes and some transposons. Phylogenetic analyses revealed that HDP1 and HDP2 were co-domesticated from the Harbinger transposon-encoded transposase and DNA-binding protein, respectively. HDP1 interacts with HDP2 in the nucleus, analogous to their transposon counterparts. Moreover, HDP1 and HDP2 are associated with IDM1, IDM2, IDM3 and MBD7 that constitute a histone acetyltransferase complex functioning in DNA demethylation. HDP2 and the methyl-DNA-binding protein MBD7 share a large set of common genomic binding sites, indicating that they jointly determine the target specificity of the histone acetyltransferase complex. Thus, our data revealed that HDP1 and HDP2 constitute a functional module that has been recruited to a histone acetyltransferase complex to prevent DNA hypermethylation and epigenetic silencing.
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http://dx.doi.org/10.1038/cr.2016.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339849PMC
February 2017

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

G3 (Bethesda) 2016 12 7;6(12):4175-4183. Epub 2016 Dec 7.

United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132

Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts 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 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 × 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 (QTL) controlling seed elemental accumulation. While a set of these QTL was 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.
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http://dx.doi.org/10.1534/g3.116.034827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5144985PMC
December 2016

Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana.

PLoS Genet 2016 09 13;12(9):e1006298. Epub 2016 Sep 13.

Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.

Sulphur (S) is an essential element for all living organisms. The uptake, assimilation and metabolism of S in plants are well studied. However, the regulation of S homeostasis remains largely unknown. Here, we report on the identification and characterisation of the more sulphur accumulation1 (msa1-1) mutant. The MSA1 protein is localized to the nucleus and is required for both S-adenosylmethionine (SAM) production and DNA methylation. Loss of function of the nuclear localised MSA1 leads to a reduction in SAM in roots and a strong S-deficiency response even at ample S supply, causing an over-accumulation of sulphate, sulphite, cysteine and glutathione. Supplementation with SAM suppresses this high S phenotype. Furthermore, mutation of MSA1 affects genome-wide DNA methylation, including the methylation of S-deficiency responsive genes. Elevated S accumulation in msa1-1 requires the increased expression of the sulphate transporter genes SULTR1;1 and SULTR1;2 which are also differentially methylated in msa1-1. Our results suggest a novel function for MSA1 in the nucleus in regulating SAM biosynthesis and maintaining S homeostasis epigenetically via DNA methylation.
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http://dx.doi.org/10.1371/journal.pgen.1006298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021336PMC
September 2016

Re-Evaluation of Reportedly Metal Tolerant Arabidopsis thaliana Accessions.

PLoS One 2016 28;11(7):e0130679. Epub 2016 Jul 28.

Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America.

Santa Clara, Limeport, and Berkeley are Arabidopsis thaliana accessions previously identified as diversely metal resistant. Yet these same accessions were determined to be genetically indistinguishable from the metal sensitive Col-0. We robustly tested tolerance for Zn, Ni and Cu, and genetic relatedness by growing these accessions under a range of Ni, Zn and Cu concentrations for three durations in multiple replicates. Neither metal resistance nor variance in growth were detected between them and Col-0. We re-sequenced the genomes of these accessions and all stocks available for each accession. In all cases they were nearly indistinguishable from the standard laboratory accession Col-0. As Santa Clara was allegedly collected from the Jasper Ridge serpentine outcrop in California, USA we investigated the possibility of extant A. thaliana populations adapted to serpentine soils. Botanically vouchered Arabidopsis accessions in the Jepson database were overlaid with soil maps of California. This provided no evidence of A. thaliana collections from serpentine sites in California. Thus, our work demonstrates that the Santa Clara, Berkeley and Limeport accessions are not metal tolerant, not genetically distinct from Col-0, and that there are no known serpentine adapted populations or accessions of A. thaliana.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130679PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965157PMC
July 2017

Maternal Gametophyte Effects on Seed Development in Maize.

Genetics 2016 09 27;204(1):233-48. Epub 2016 Jul 27.

Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305

Flowering plants, like placental mammals, have an extensive maternal contribution toward progeny development. Plants are distinguished from animals by a genetically active haploid phase of growth and development between meiosis and fertilization, called the gametophyte. Flowering plants are further distinguished by the process of double fertilization that produces sister progeny, the endosperm and the embryo, of the seed. Because of this, there is substantial gene expression in the female gametophyte that contributes to the regulation of growth and development of the seed. A primary function of the endosperm is to provide growth support to its sister embryo. Several mutations in Zea mays subsp. mays have been identified that affect the contribution of the mother gametophyte to the seed. The majority affect both the endosperm and the embryo, although some embryo-specific effects have been observed. Many alter the pattern of expression of a marker for the basal endosperm transfer layer, a tissue that transports nutrients from the mother plant to the developing seed. Many of them cause abnormal development of the female gametophyte prior to fertilization, revealing potential cellular mechanisms of maternal control of seed development. These effects include reduced central cell size, abnormal architecture of the central cell, abnormal numbers and morphology of the antipodal cells, and abnormal egg cell morphology. These mutants provide insight into the logic of seed development, including necessary features of the gametes and supporting cells prior to fertilization, and set up future studies on the mechanisms regulating maternal contributions to the seed.
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http://dx.doi.org/10.1534/genetics.116.191833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012389PMC
September 2016

nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins.

Plant Physiol 2016 08 10;171(4):2633-47. Epub 2016 Jun 10.

Department of Horticulture and Landscape Architecture (N.B.B., T.H., J.B., B.S.), Department of Biochemistry (N.B.B., B.P.D.), and Department of Botany and Plant Pathology (G.J.), Purdue University, West Lafayette, Indiana 47907; and RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan (S.F.)

A small number of phytohormones dictate the pattern of plant form affecting fitness via reproductive architecture and the plant's ability to forage for light, water, and nutrients. Individual phytohormone contributions to plant architecture have been studied extensively, often following a single component of plant architecture, such as plant height or branching. Both brassinosteroid (BR) and gibberellin (GA) affect plant height, branching, and sexual organ development in maize (Zea mays). We identified the molecular basis of the nana plant2 (na2) phenotype as a loss-of-function mutation in one of the two maize paralogs of the Arabidopsis (Arabidopsis thaliana) BR biosynthetic gene DWARF1 (DWF1). These mutants accumulate the DWF1 substrate 24-methylenecholesterol and exhibit decreased levels of downstream BR metabolites. We utilized this mutant and known GA biosynthetic mutants to investigate the genetic interactions between BR and GA. Double mutants exhibited additivity for some phenotypes and epistasis for others with no unifying pattern, indicating that BR and GA interact to affect development but in a context-dependent manner. Similar results were observed in double mutant analyses using additional BR and GA biosynthetic mutant loci. Thus, the BR and GA interactions were neither locus nor allele specific. Exogenous application of GA3 to na2 and d5, a GA biosynthetic mutant, also resulted in a diverse pattern of growth responses, including BR-dependent GA responses. These findings demonstrate that BR and GA do not interact via a single inclusive pathway in maize but rather suggest that differential signal transduction and downstream responses are affected dependent upon the developmental context.
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http://dx.doi.org/10.1104/pp.16.00399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972271PMC
August 2016

Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana.

Genetics 2016 06 13;203(2):817-29. Epub 2016 Apr 13.

Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907

Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers in Arabidopsis thaliana reproductive development. Plants lacking the CHD3 remodeler, PICKLE, exhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube, as well as delayed progression of ovule and embryo development. Genetic analyses demonstrate that these phenotypes result from loss of PICKLE in the maternal sporophyte. The paralogous gene PICKLE RELATED 2 is preferentially expressed in the endosperm and acts antagonistically with respect to PICKLE in the seed: loss of PICKLE RELATED 2 suppresses the large seed phenotype of pickle seeds. Surprisingly, the alteration of seed size in pickle plants is sufficient to determine the expression of embryonic traits in the seedling primary root. These findings establish an important role for CHD3 remodelers in plant reproduction and highlight how the epigenetic status of one tissue can impact the development of genetically distinct tissues.
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http://dx.doi.org/10.1534/genetics.115.180141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896196PMC
June 2016

Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition.

Plant Physiol 2016 04 19;170(4):1989-98. Epub 2016 Feb 19.

Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.)

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.
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http://dx.doi.org/10.1104/pp.15.01971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825124PMC
April 2016

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana.

Proc Natl Acad Sci U S A 2015 Sep 31;112(37):11726-31. Epub 2015 Aug 31.

Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695;

Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. As an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite-gene associations led to the identification of N-malonyl-D-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5'-phosphate for its activity. This study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. It also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.
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http://dx.doi.org/10.1073/pnas.1503272112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577208PMC
September 2015

Natural variation at sympathy for the ligule controls penetrance of the semidominant Liguleless narrow-R mutation in Zea mays.

G3 (Bethesda) 2014 Oct 24;4(12):2297-306. Epub 2014 Oct 24.

Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907

Leaf architecture determines plant structural integrity, light harvesting, and economic considerations such as plant density. Ligules, junctions at the leaf sheath and blade in grasses, protect stalks from environmental stresses and, in conjunction with auricles, controls leaf angle. Previous studies in mutants have recessive liguleless mutants (lg1 and lg2) and dominant mutations in knotted1-like homeobox genes (Lg3-O, Lg4, and Kn1) involved in ligule development. Recently, a new semidominant liguleless mutant, Liguleless narrow (Lgn-R), has been characterized in maize that affects ligule and auricle development and results in a narrow leaf phenotype. We show that quantitative genetic variation affects penetrance of Lgn-R. To examine the genetic architecture underlying Lgn-R expressivity, crosses between Lgn-R/+ mutants in a B73 background and intermated B73 x Mo17 recombinant inbred lines were evaluated in multiple years and locations. A single main-effect quantitative trait locus (QTL) on chromosome 1 (sympathy for the ligule; sol) was discovered with a Mo17-contributed allele that suppressed Lgn-R mutant phenotypes. This QTL has a genetic-interaction with a locus on chromosome 7 (lucifer; lcf) for which the B73-contributed allele increases the ability of the sol(Mo17) allele to suppress Lgn-R. Neither of the genetic intervals likely to contain sol or lcf overlap with any current liguleless genes nor with previously identified genome-wide association QTL connected to leaf architecture. Analysis of phenotypes across environments further identified a genotype by enviroment interaction determining the strength of the sol x lcf interaction.
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http://dx.doi.org/10.1534/g3.114.014183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267926PMC
October 2014

Arabidopsis gulliver1/SUPERROOT2-7 identifies a metabolic basis for auxin and brassinosteroid synergy.

Plant J 2014 Dec;80(5):797-808

School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 151-747, Korea.

Phytohormone homeostasis is essential for proper growth and development of plants. To understand the growth mechanisms mediated by hormonal levels, we isolated a gulliver1 (gul1) mutant that had tall stature in the presence of both brassinazole and the light. The gul1 phenotype depended on functional BR biosynthesis; the genetic introduction of dwarf4, a BR biosynthetic mutation, masked the long hypocotyl phenotype of gul1. Furthermore, BR biosynthesis was dramatically enhanced, such that the level of 22-hydroxy campesterol was 5.8-fold greater in gul1. Molecular cloning revealed that gul1 was a missense mutation, resulting in a glycine to arginine change at amino acid 116 in SUPERROOT2 (CYP83B1), which converts indole acetaldoxime to an S-alkyl thiohydroximate adduct in the indole glucosinolate pathway. Auxin metabolite profiling coupled with quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis of auxin biosynthetic genes revealed that gul1/sur2-7 activated multiple alternative branches of tryptophan-dependent auxin biosynthetic pathways. Furthermore, exogenous treatment of gul1/sur2-7 with BRs caused adventitious roots from hypocotyls, indicative of an increased response to BRs relative to wild-type. Different from severe alleles of sur2, gul1/sur2-7 lacked 'high-auxin' phenotypes that include stunted growth and callus-like disintegration of hypocotyl tissues. The auxin level in gul1/sur2-7 was only 1.6-fold greater than in the wild-type, whereas it was 4.2-fold in a severe allele like sur2-8. Differences in auxin content may account for the range of phenotypes observed among the sur2 alleles. This unusual allele provides long-sought evidence for a synergistic interaction between auxin and BRs in promoting growth in Arabidopsis at the level of their biosynthetic enzymes.
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http://dx.doi.org/10.1111/tpj.12678DOI Listing
December 2014

Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis species range.

Plant Physiol 2014 Nov 22;166(3):1593-608. Epub 2014 Sep 22.

Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom (D.-Y.C., J.D., D.E.S.);Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., A.K., S.K.); andDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (B.L., H.L., E.Y., B.D.)

Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.
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http://dx.doi.org/10.1104/pp.114.247825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226352PMC
November 2014