Dataset Information

Responses to environmental variability by herbivorous insects and their natural enemies within a bioenergy crop, Miscanthus x giganteus.

ABSTRACT: Precision agriculture (PA) is the application of management decisions based on identifying, quantifying, and responding to space-time variability. However, knowledge of crop pest responses to within-field environmental variability, and the spatial distribution of their natural enemies, is limited. Quantitative methods providing insights on how pest-predator relationships vary within fields are potentially important tools. In this study, phloem feeders and their natural enemies, were observed over two years across 81 locations within a field of the perennial feedstock grass in Georgia, USA. Geographically weighted regression (GWR) was used to spatially correlate their abundance with environmental factors. Variables included distance to forest edge, Normalized Difference of Vegetation Index (NDVI), slope, aspect, elevation, soil particle size distribution, and weather values. GWR methods were compared with generalized linear regression methods that do not account for spatial information. Non-spatial models indicated positive relationships between phloem-feeder abundance and wind speed, but negative relationships between elevation, proportions of silt and sand, and NDVI. With data partitioned into three seasonal groups, terrain and soil variables remained significant, and natural enemies and spiders became relevant. Results from GWR indicated that magnitudes and directions of responses varied within the field, and that relationships differed among seasons. Strong negative relationships between response and explanatory factors occurred: with NDVI during mid-season; with percent silt, during mid-, and late seasons; and with spider abundance during early and late seasons. In GWR models, slope, elevation, and aspect were mostly positive indicating further that associations with elevation depended on whether models incorporated spatial information or not. By using spatially explicit models, the analysis provided a complex, nuanced understanding of within-field relationships between phloem feeders and environmental covariates. This approach provides an opportunity to learn about the variability within agricultural fields and, with further analysis, has potential to inform and improve PA and habitat management decisions.

SUBMITTER: Coffin AW

PROVIDER: S-EPMC7886118 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Responses to environmental variability by herbivorous insects and their natural enemies within a bioenergy crop, Miscanthus x giganteus.

Coffin Alisa W AW Olson Dawn M DM Seymour Lynne L Bosch David D DD Schmidt Jason M JM Strickland Timothy C TC

PloS one 20210216 2

Precision agriculture (PA) is the application of management decisions based on identifying, quantifying, and responding to space-time variability. However, knowledge of crop pest responses to within-field environmental variability, and the spatial distribution of their natural enemies, is limited. Quantitative methods providing insights on how pest-predator relationships vary within fields are potentially important tools. In this study, phloem feeders and their natural enemies, were observed ove ...[more]

PMID: 33592028

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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Miscanthus x giganteus tissues (including leaves, flowers, and rhizomes). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves, flowers and rhizomes of Miscanthus x giganteus. Each tissue represented a mixture of developmental stages, with a bias towards those from early, actively differentiating cells. For rhizomes, the apical tip portion was collected. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Steven Moose for providing the plant material and Kan Nobuta for assistance with the computational methods.

Project description:BackgroundMiscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.ResultsWe developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors.ConclusionsWe developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.

Dataset Information

Responses to environmental variability by herbivorous insects and their natural enemies within a bioenergy crop, Miscanthus x giganteus.

Publications

Responses to environmental variability by herbivorous insects and their natural enemies within a bioenergy crop, Miscanthus x giganteus.

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