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SUMMARY RNA‐Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA‐Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike‐ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike‐ins as a normalization control produces differences in RNA‐Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike‐ins with 3' RNA‐Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum. 

Many correlations exist between spectral reflectance or transmission with various phenotypic responses from plants. Of interest to us are metabolic characteristics, namely, how the various polarimetric components of plants may correlate to underlying environmental, metabolic, and genotypic differences among different varieties within a given species, as conducted during large field experimental trials. In this paper, we overview a portable Mueller matrix imaging spectropolarimeter, optimized for field use, by combining a temporal and spatial modulation scheme. Key aspects of the design include minimizing the measurement time while maximizing the signal-to-noise ratio by mitigating systematic error. This was achieved while maintaining an imaging capability across multiple measurement wavelengths, spanning the blue to near-infrared spectral region (405–730 nm). To this end, we present our optimization procedure, simulations, and calibration methods. Validation results, which were taken in redundant and non-redundant measurement configurations, indicated that the polarimeter provides average absolute errors of (5.3±2.2)×10⁻³and (7.1±3.1)×10⁻³, respectively. Finally, we provide preliminary field data (depolarization, retardance, and diattenuation) to establish baselines of barren and non-barrenZea maizehybrids (G90 variety), as captured from various leaf and canopy positions during our summer 2022 field experiments. Results indicate that subtle variations in retardance and diattenuation versus leaf canopy position may be present before they are clearly visible in the spectral transmission. 

Bidirectionality effects can be a significant confounding factor when measuring hyperspectral reflectance data. The bidirectional reflectance distribution function (BRDF) can effectively characterize the reflectivity of surfaces to correct remote sensing measurements. However, measuring BRDFs can be time-consuming, especially when collecting Mueller matrix BRDF (mmBRDF) measurements of a surface via conventional goniometric techniques. In this paper, we present a system for collecting mmBRDF measurements using static optical fiber detectors that sample the hemisphere surrounding an object. The entrance to each fiber contains a polarization state analyzer configuration, allowing for the simultaneous acquisition of the Stokes vector intensity components at many altitudinal and azimuthal viewing positions. We describe the setup, calibration, and data processing used for this system and present its performance as applied to mmBRDF measurements of a ground glass diffuser. 

Abstract Effective research, education, and outreach efforts by theArabidopsis thalianacommunity, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly‐shared resources. These resources include reference genome sequence data and an ever‐increasing number of diverse data sets and data types.TAIR(The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, theIAICheld another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community‐defined common standards for data and metadata, and accessible and user‐friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less‐established standards (e.g., phenomics, metabolomics). Community‐established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a “one‐stop shop” website, an Arabidopsis “Super‐Portal” to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy‐in and participation in its establishment and development to encourage adoption.