Publications by authors named "Rajdeep S Khangura"

7 Publications

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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

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

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

PLoS One 2019 28;14(10):e0224086. Epub 2019 Oct 28.

DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

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. All of the triaged models had significant errors-including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224086PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816542PMC
March 2020

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