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Climate change is projected to decrease maize yields due to warmer temperatures and their consequences. Studies using crop growth models (CGMs), however, have predicted that, through a combination of alterations to planting date, flowering time, and maturity, these yield losses can be mitigated or even reversed. Here, we examine three assumptions of such studies: (1) that climate has driven historical phenological trends, (2) that CGM ensembles provide unbiased estimates of yields under high temperatures, and (3) that the effects of temperature on yields are an emergent property of interactions between phenology and environment. We used data on maize phenology from the United States Department of Agriculture, a statistical model of maize hybrid heat tolerance derived from 80 years of public yield trial records across four US states, and outputs of an ensemble of CMIP6 climate models. While planting dates have advanced historically, we found a trend toward later planting dates after 2005 and no trend for silking or maturity, shifting more time into the reproductive period. We then projected maize yields using the historical model and crop calendars devised using three previously proposed adaptation strategies. In contrast to studies using CGMs, our statistical yield model projected severe yield losses under all three strategies. Finally, we projected maize yields accounting for historical genetic variability for heat tolerance, discovering that it was insufficient to overcome the negative effects of projected warming. These projections are driven by greater heat stress exposure under all crop calendars and climate scenarios. Combined with analysis of the internal sensitivities of CGMs to temperature, our results suggest that current projections do not adequately account for the effects of increasing temperatures on maize yields. Climate adaptation in the US Midwest must utilize a richer set of strategies than phenological adaptation, including improvements to heat tolerance and crop diversification. [ABSTRACT FROM AUTHOR]

Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples.Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area.PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any differences between the dyes can be adjusted out by standard methods of normalization, so that measures such as log ratios on the same slide are reliable measures of comparative expression. However, even after the normalization, there are still probe specific dye and slide variation among the data. We define a method to quantify the amount of the dye-by-probe and slide-by-probe interaction. This serves as a diagnostic, both visual and numeric, of the existence of probe-specific dye bias. We show how this improved the performance of two-color array analysis for arrays for genomic analysis of biological samples ranging from rice to human tissue.We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function), though numerical results are also obtained.We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor.

AIIRA seeks to transform agriculture by creating a new AI‐driven framework for modeling plants at various agronomically relevant scales. We accomplish this by designing and deploying AI‐driven predictive models that fuse diverse data with siloed domain knowledge. AIIRA's vision, illustrated in Figure 1, consists of four technical thrusts with cross‐cutting education, training, and outreach activities. Our activities are focused on theory, algorithms, and tools for the principled creation of goal‐oriented AI tools deployed at plant and field scales. Our use‐inspired AI developments are tightly integrated with USDA‐relevant challenges in crop improvement and sustainable crop production. Our strong social science focus ensures sustained AI adoption across the ag value chain. Our cyberinfrastructure (CI) efforts ensure cohesive, sustainable, and extensible CI to reproducibly share and manage data assets and analysis workflows to a diverse spectrum of the Ag community. Taken together, this will ensure long‐term payoffs in AI and agriculture. AIIRA has established a new field of Cyber Agricultural Systems at the intersection of plant science, agronomics, and AI. Our signature activities build the workforce for this new field through formal and informal educational activities. Through these activities, AIIRA creates accessible pathways for underrepresented groups, especially Native Americans and women. [ABSTRACT FROM AUTHOR]