Biology subjects

Nachappa, P.

Publications and source records attributed to Nachappa, P..

6 recordsLinked to original sources

bioRxiv2024

Plant responses to wheat curl mites and wheat streak mosaic virus (WSMV): first evidence of virus tolerance in wheat

Wheat curl mites (WCM) are arthropod pests that pose significant threats to wheat crops by causing direct damage by feeding, and transmitting viruses such as Wheat Streak Mosaic Virus (WSMV), Triticum Mosaic Virus (TriMV), and High Plains Wheat Mosaic Virus (HPWMoV), leading to substantial losses in wheat, barley, oats, and rye. Over three years of field screening, we found that the cultivar Hatcher consistently produced higher yields under high WSMV disease pressure, outperforming Mace and TAM112, which carry the Wsm1 gene and a QTL for curl mite resistance, respectively, indicating tolerance. To investigate the mechanisms underlying the tolerance phenotype in Hatcher, we compared its response to WCM and WSMV infection with a susceptible genotype, CO15D173R. Transcriptomic analysis revealed a nuanced interplay between plant defense and growth in Hatcher, with upregulation of genes related to jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) pathways, indicating a coordinated defense response. The activation of lignin biosynthesis genes points to a potential role of cell wall strengthening in deterring WCM and WSMV. Additionally, the regulation of genes involved in growth-related hormonal pathways such as gibberellic acid (GA), and brassinosteroids (BR) highlights Hatchers ability to maintain growth disease pressure. Our findings provide insight into the intricate network of phytohormones, growth-defense trade-offs, and cell wall modifications contributing to Hatchers tolerance to WCM and WSMV. This knowledge can inform the development of tolerant wheat varieties and enhance integrated pest management strategies, ultimately safeguarding wheat production.

plant biology↗

bioRxiv2023

HaploCatcher: An R Package for Prediction of Haplotypes

Wheat (Triticum aestivum L.) is crucial to global food security, but is often threatened by diseases, pests, and environmental stresses. Wheat stem sawfly (Cephus cinctus Norton) poeses a major threat to food security in the United States, and solid-stem varieties, which carry the stem-solidness locus (Sst1), are the main source of genetic resistance against sawfly. Marker-assisted selection uses molecular markers to identify lines possessing beneficial haplotypes, like that of the Sst1 locus. In this study, an R package titled "HaploCatcher" was developed to predict specific haplotypes of interest in genome-wide genotyped lines. A training population of 1,056 lines genotyped for the Sst1 locus, known to confer stem solidness, and genome-wide markers was curated to make predictions of the Sst1 haplotypes for 292 lines from the Colorado State University wheat breeding program. Predicted Sst1 haplotypes were compared to marker derived haplotypes. Our results indicated that the training set was substantially predictive, with kappa scores of 0.83 for k-nearest neighbors and 0.88 for random forest models. Forward validation on newly developed breeding lines demonstrated that a random forest model, trained on the total available training data, had comparable accuracy between forward and cross-validation. Estimated group means of lines classified by haplotypes from PCR-derived markers and predictive modeling did not significantly differ. The HaploCatcher package is freely available and may be utilized by breeding programs, using their own training populations, to predict haplotypes for whole genome sequenced early generation material. CORE IDEASO_LIIdentification, introgression, and frequency increase of large effect loci are important for cultivar development. C_LIO_LIThe Sst1 locus has a significant effect on cutting score in fields exposed to sawfly infestation. C_LIO_LIHistorical genetic information can be utilized to predict haplotypes for lines which have genome-wide genetic data. C_LIO_LIAn R package, HaploCatcher, has been developed to facilitate this analysis in other programs. C_LI

plant biology↗

bioRxiv2022

Genomic And Molecular Characterization Of The Wheat Streak Mosaic Virus Resistance Locus 2 (Wsm2) In Common Wheat (Triticum Aestivum. L)

Wheat streak mosaic virus is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains region of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in crops and aid the development of perfect markers for breeding. In this study, Wsm2 flanking markers were mapped to a 4.0 Mbp region of the wheat reference genome containing 142 candidate genes. Haplotype analysis in seventeen wheat genotypes collected from different agroecological zones indicated that Wsm2 lies in a dynamic region of the genome with extensive structural variation, and that it is likely absent from available genome assemblies of common wheat varieties. Exome sequencing of the variety Snowmass, which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in Snowmass compared to Antero, a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in Snowmass, three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.

pathology↗

bioRxiv2020

Tomato spotted wilt virus benefits its thrips vector by modulating metabolic and plant defense pathways in tomato

Several plant viruses modulate vector fitness and behavior in ways that may enhance virus transmission. Previous studies have documented indirect, plant-mediated effects of tomato spotted wilt virus (TSWV) infection on the fecundity, growth and survival of its principal thrips vector, Frankliniella occidentalis, the western flower thrips. In this study, we conducted thrips performance and preference experiments combined with plant gene expression, phytohormone and total free amino acid analyses to identify tomato host responses to single and dual challenge with TSWV and F. occidentalis, compared to F. occidentalis alone, to address the question: do systemically-infected, symptomatic tomato plants modulate primary metabolic (photosynthesis and related physiological functions) and defense-related pathways to culminate into a more favorable environment for the vector. In a greenhouse setting, we documented a significant increase in the number of offspring produced by F. occidentalis on TSWV-infected tomato plants compared to mock-inoculated plants, and in choice test assays, females exhibited enhanced settling on TSWV-infected leaves. Microarray analysis combined with phytohormone signaling pathway analysis revealed that TSWV infection, regardless of thrips activity, robustly upregulated salicylic acid (SA) synthesis and downstream defense signaling pathway genes typically known to be associated with execution of defense against pathogens. TSWV alone downregulated a few jasmonic acid (JA)-responsive, anti-herbivore defense genes, however these were limited to wound-induced proteinase inhibitors. While this may indicate a subtle SA-JA antagonistic cross-talk in response to the virus, abscisic acid (ABA, upregulated) and auxin pathways (downregulated) were also perturbed by TSWV infection, regardless of F. occidentalis colonization, and may play roles in coordinating and dampening defense against the vector on infected plants. Frankliniella occidentalis alone triggered JA and ET pathways, phytohormones that have been reported to work cooperatively to enhance induced resistance to microbes and herbivores; however, on infected plants, ET remained unperturbed by the thrips vector. TSWV infection, alone or in combination with thrips, suppressed genes associated with photosynthesis and chloroplast function thereby significantly impacting primary metabolism of the host plant, and hierarchical cluster analysis and network analysis revealed that many of these genes were co-regulated with phytohormone defense signaling genes. Virus infection also altered genes related to cell wall organization which may render plants more susceptible to the penetration of thrips mouthparts. Lastly, TSWV infection increased expression of genes related to protein synthesis and degradation which is reflected in the increased total free amino acid content in virus-infected plants that harbored higher thrips populations. These results suggest coordinated gene networks that regulate plant primary metabolism and defense responses rendering virus-infected plants more conducive host for vectors, a relationship that is beneficial to the vector and the virus when considered within the context of the complex transmission biology of TSWV. To our knowledge this is the first study to identify global transcriptional networks that underlie the TSWV-thrips interaction as compared to a single mechanistic approach. Findings of this study increase our fundamental knowledge of host plant-virus-vector interactions and identifies underlying mechanisms of induced host susceptibility to the insect vector.

plant biology↗

bioRxiv2020

Location, location, location: Feeding site affects aphid performance by altering access and quality of nutrients

Feeding location on a plant can affect aphid reproduction and survival, however little is known about factors that influence aphid performance on specific plant parts. We determined performance and feeding behavior of soybean aphid (Aphis glycines) on stem, adaxial (upper) and abaxial (lower) leaf surfaces during early vegetative growth of soybean plants and analyzed the associated phloem sap composition. Stems harbored greater aphid populations and aphids had shorter development time on stems compared to adaxial and abaxial leaf surfaces. While aphids feeding on the stem took the longest time to begin probing, potentially due to higher density and length of trichomes, this did not impact aphid population growth. Once aphids began probing, the sieve elements were more conducive to feeding as evidenced by less salivation from the stem as compared to either leaf surface. Moreover, vascular sap-enriched exudates from stems had higher sugars and amino acids, which supported higher aphid populations in artificial diet feeding assays. The high quality of stems as a food source may in part explain the shorter development time and overall greater population of aphids observed on stems. In summary, our findings suggest that the choice of feeding location and performance of aphids on a specific plant is driven largely by accessibility to and the quality of nutrients rather than morphological factors.

ecology↗

bioRxiv2020

Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in Colorado and Insights into the Wheat Virome

The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.

pathology↗