Correction: Double triage to identify poorly annotated genes in maize: The missing link in community curation.

[This corrects the article DOI: 10.1371/journal.pone.

A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling.

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa).

Identification of the Teopod1, Teopod2, and Early Phase Change genes in maize.

Teopod1 (Tp1), Teopod2 (Tp2), and Early phase change (Epc) have profound effects on the timing of vegetative phase change in maize. Gain-of-function mutations in Tp1 and Tp2 delay all known phase-specific vegetative traits, whereas loss-of-function mutations in Epc accelerate vegetative phase change and cause shoot abortion in some genetic backgrounds. Here, we show that Tp1 and Tp2 likely represent cis-acting mutations that cause the overexpression of Zma-miR156j and Zma-miR156h, respectively.

Image-based assessment of plant disease progression identifies new genetic loci for resistance to Ralstonia solanacearum in tomato.

A major challenge in global crop production is mitigating yield loss due to plant diseases. One of the best strategies to control these losses is through breeding for disease resistance. One barrier to the identification of resistance genes is the quantification of disease severity, which is typically based on the determination of a subjective score by a human observer.

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

The maize gene is a mutant form of the gene that confers resistance to common rust. 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 in four different genetic backgrounds, were identified that had chimeric leaves with lesioned sectors showing HR abutting green nonlesioned sectors lacking HR.

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

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.

Maize brace roots provide stalk anchorage.

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.

Variation in Maize Chlorophyll Biosynthesis Alters Plant Architecture.

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.

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

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.

Double triage to identify poorly annotated genes in maize: The missing link in community curation.

The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer.

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

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.