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Unoccupied aerial systems (UAS) based high throughput phenotyping studies require further investigation to combine different environments and planting times into one model. Here 100 elite breeding hybrids of maize ( Zea mays L.) were evaluated in two environment trials–one with optimal planting and irrigation (IHOT), and one dryland with delayed planting (DHOT). RGB (Red-Green-Blue) based canopy height measurement (CHM) and vegetation indices (VIs) were estimated from a UAS platform. Time series and cumulative VIs, by both summation (ΣVI-SUMs) and area under the curve (ΣVI-AUCs), were fit via machine learning regression modeling (random forest, linear, ridge, lasso, elastic net regressions) to estimate grain yield. VIs were more valuable predictors of yield to combine different environments than CHM. Time series VIs and CHM produced high accuracies (~68–72%), but inconsistent models. A little sacrifice in accuracy (~60–65%) produced consistent models using ΣVI-SUMs and CHM during pre-reproductive vegetative growth. Absence of VIs produced poorer accuracies (by about ~5–10%). Normalized difference type VIs produced maximum accuracies, and flowering times were the best times for UAS data acquisition. This study suggests that the best yielding varieties can be accurately predicted in new environments at or before flowering when combining multiple temporal flights and predictors.

Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1-the summer 2015 and winter 2016 growing seasons-of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project's goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and most comprehensive project of its kind to date, these lessons are particularly salient to researchers embarking on agricultural research with UAVs.

With a changing climate and a growing population, the world increasingly needs more-productive and resilient crops. But improving them requires a knowledge of what actually works in the field. With a changing climate and a growing population, the world increasingly needs more-productive and resilient crops. But improving them requires a knowledge of what actually works in the field. Aerial view of green corn fields on a farm in Brazil on a cloudy day

The whiskey industry is dominated by whiskey styles with recipes that contain corn as the primary grain. However, little research has been conducted to investigate whiskey specific distinctions arising from different corn varieties and growing environments (i.e. terroir). Further, no studies have investigated the aroma or flavor impacts of different varieties and terroirs. Here, three different commodity yellow dent hybrid corn varieties were grown on different farms in Texas, spanning from the Texas Panhandle to the Mexico-United States border. Using novel small-batch mashing techniques, a newly developed new-make (i.e. unaged whiskey,immediate by-product of distillation) bourbon sensory lexicon, a trained sensory panel, high-performance liquid chromatography, and gas chromatography-mass spectrometry/olfactometry (GC-MS/O), we report for the first time a method for evaluating sample effects on alcohol yield and flavor in new-make bourbon whiskey. We discover that variety, terroir and their interactions, previously ignored, can substantially affect valuable sensory aspects of whiskey, suggesting the importance of scientifically evaluating corn genetics and agronomy for developing better whiskey. Excitingly, our data suggest milled corn with higher levels of benzadehyde, readily measured by GC-MS/O, correlates with improved sensory aspects of distillate, which must be expensively evaluated using a trained human sensory panel.

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides ) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736  C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma’s D , suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

Lodging has been recognized as one of the major destructive factors for crop quality and yield, resulting in an increasing need to develop cost-efficient and accurate methods for detecting crop lodging in a routine manner. Using structure-from-motion (SfM) and novel geospatial computing algorithms, this study investigated the potential of high resolution imaging with unmanned aircraft system (UAS) technology for detecting and assessing lodging severity over an experimental maize field at the Texas A&M AgriLife Research and Extension Center in Corpus Christi, Texas, during the 2016 growing season. The method was proposed to not only detect the occurrence of lodging at the field scale, but also to quantitatively estimate the number of lodged plants and the lodging rate within individual rows. Nadir-view images of the field trial were taken by multiple UAS platforms equipped with consumer grade red, green, and blue (RGB), and near-infrared (NIR) cameras on a routine basis, enabling a timely observation of the plant growth until harvesting. Models of canopy structure were reconstructed via an SfM photogrammetric workflow. The UAS-estimated maize height was characterized by polygons developed and expanded from individual row centerlines, and produced reliable accuracy when compared against field measures of height obtained from multiple dates. The proposed method then segmented the individual maize rows into multiple grid cells and determined the lodging severity based on the height percentiles against preset thresholds within individual grid cells. From the analysis derived from this method, the UAS-based lodging results were generally comparable in accuracy to those measured by a human data collector on the ground, measuring the number of lodging plants (R2 = 0.48) and the lodging rate (R2 = 0.50) on a per-row basis. The results also displayed a negative relationship of ground-measured yield with UAS-estimated and ground-measured lodging rate.

Genomic and phenotypic screening of the A. E. Watkins landrace wheat collection identifies beneficial novel haplotypes demonstrated to improve modern wheat without negative linkage drag or pleiotropy.

A major challenge of genetic improvement and selection is to accurately predict individuals with the highest fitness in a population without direct measurement. Over the last decade, genomic predictions (GP) based on genome-wide markers have become reliable and routine. Now phenotyping technologies, including unoccupied aerial systems (UAS also known as drones), can characterize individuals with a data depth comparable to genomics when used throughout growth. This study, for the first time, demonstrated that the prediction power of temporal UAS phenomic data can achieve or exceed that of genomic data. UAS data containing red–green–blue (RGB) bands over 15 growth time points and multispectral (RGB, red-edge and near infrared) bands over 12 time points were compared across 280 unique maize hybrids. Through cross-validation of untested genotypes in tested environments (CV2), temporal phenomic prediction (TPP), outperformed GP (0.80 vs 0.71); TPP and GP performed similarly in 3 other cross-validation scenarios. Genome-wide association mapping using area under temporal curves of vegetation indices (VIs) revealed 24.5% of a total of 241 discovered loci (59 loci) had associations with multiple VIs, explaining up to 51% of grain yield variation, less than GP and TPP predicted. This suggests TPP, like GP, integrates small effect loci well improving plant fitness predictions. More importantly, TPP appeared to work successfully on unrelated individuals unlike GP.

Agricultural researchers are embracing remote sensing tools to phenotype and monitor agriculture crops. Specifically, large quantities of data are now being collected on small plot research studies using Unoccupied Aerial Systems (UAS, aka drones), ground systems, or other technologies but data processing and analysis lags behind. One major contributor to current data processing bottlenecks has been the lack of publicly available software tools tailored towards remote sensing of small plots and usability for researchers inexperienced in remote sensing. To address these needs we created plot shapefile maker (R/UAS::plotshpcreate): an open source R function which rapidly creates ESRI polygon shapefiles to the desired dimensions of individual agriculture research plots areas of interest and associates plot specific information. Plotshpcreate was developed to utilize inputs containing experimental design, field orientation, and plot dimensions for easily creating a multi-polygon shapefile of an entire small plot experiment. Output shapefiles are based on the user inputs geolocation of the research field ensuring accurate overlay of polygons often without manual user adjustment. The output shapefile is useful in GIS software to extract plot level data tracing back to the unique IDs of the experimental plots. Plotshpcreate is available on GitHub (https://github.com/andersst91/UAStools).

Current methods in measuring maize ( Zea mays L.) southern rust ( Puccinia polyspora Underw.) and subsequent crop senescence require expert observation and are resource-intensive and prone to subjectivity. In this study, unoccupied aerial system (UAS) field-based high-throughput phenotyping (HTP) was employed to collect high-resolution aerial imagery of elite maize hybrids planted in the 2020 and 2021 growing seasons, with 13 UAS flights obtained from 2020 and 17 from 2021. In total, 36 vegetation indices (VIs) were extracted from mosaicked aerial images that served as temporal phenomic predictors for southern rust scored in the field and senescence as scored using UAS-acquired mosaic images. Temporal best linear unbiased predictors (TBLUPs) were calculated using a nested model that treated hybrid performance as nested within flights in terms of rust and senescence. All eight machine learning regressions tested (ridge, lasso, elastic net, random forest, support vector machine with radial and linear kernels, partial least squares, and k-nearest neighbors) outperformed a general linear model with both higher prediction accuracies (92–98%) and lower root mean squared error (RMSE) for rust and senescence scores (linear model RMSE ranged from 65.8 to 2396.5 across all traits, machine learning regressions RMSE ranged from 0.3 to 17.0). UAS-acquired VIs enabled the discovery of novel early quantitative phenotypic indicators of maize senescence and southern rust before being detectable by expert annotation and revealed positive correlations between grain filling time and yield (0.22 and 0.44 in 2020 and 2021), with practical implications for precision agricultural practices.