Patch Track Software for Measuring Kinematic Phenotypes of Arabidopsis Roots Demonstrated on Auxin Transport Mutants

Plant roots elongate when cells produced in the apical meristem enter a transient period of rapid expansion. To measure the dynamic process of root cell expansion in the elongation zone, we captured digital images of growing Arabidopsis roots with horizontal microscopes and analyzed them with a custom image analysis program (PatchTrack) designed to track the growth-driven displacement of many closely spaced image patches. Fitting a flexible logistics equation to patch velocities plotted versus position along the root axis produced the length of the elongation zone (mm), peak relative elemental growth rate (% h-1), the axial position of the peak (mm from the tip), and average root elongation rate (mm h-1). For a wild-type root, the average values of these kinematic traits were 0.52 mm, 23.7% h-1, 0.35 mm, and 0.1 mm h-1, respectively. We used the platform to determine the kinematic phenotypes of auxin transport mutants. The results support a model in which the PIN2 auxin transporter creates an area of expansion-suppressing, supraoptimal auxin concentration that ends 0.1 mm from the quiescent center (QC), and that ABCB4 and ABCB19 auxin transporters maintain expansion-limiting suboptimal auxin levels beginning approximately 0.5 mm from the QC. This study shows that PatchTrack can quantify dynamic root phenotypes in kinematic terms.

Evaluating relationships between seed morphological traits and seed dormancy in Chenopodium quinoa Willd

Introduction

Quinoa is a high-value, nutritious crop that performs well in variable environments, marginal soils, and in diverse crop rotations. Quinoa's many attributes make it an ideal crop for supporting human health in global communities and economies. To date, quinoa research has largely focused on traits in adult plants important for enhancing plant phenotypic plasticity, abiotic stress, disease resistance, and yield. Fewer studies have evaluated quinoa seed dormancy and suggest that most modern quinoa varieties have weak or no seed dormancy, and a narrow window of seed viability post-harvest. In other crops, diminished seed dormancy is a major risk factor for preharvest sprouting (PHS; germination on the panicle due to rain prior to harvest) and may also pose a similar risk for quinoa.

Methods

This study (1) developed a dormancy screening assay to characterize seed dormancy strength in a large collection of quinoa varieties, (2) investigated if morphological variables including seed coat color, seed coat thickness, seed shape including eccentricity which evaluates the roundness or flatness of a seed, and other agronomic traits like crude protein content and seed moisture, contribute to quinoa seed dormancy, and (3) evaluated the use of a phenetic modeling approach to explore relationships between seed morphology and seed dormancy.

Results

Dormancy screening indicated seed dormancy ranges in quinoa varieties from none to strong dormancy. Further, phenetic modeling approaches indicate that seed coat thickness and eccentricity are important morphological variables that impact quinoa seed dormancy strength.

Conclusions

While dormancy screening and phenetic modeling approaches do not provide a direct solution to preventing PHS in quinoa, they do provide new tools for identifying dormant varieties as well as morphological variables contributing to seed dormancy.

A comprehensive characterization of agronomic and end-use quality phenotypes across a quinoa world core collection

Quinoa (Chenopodium quinoa Willd.), a pseudocereal with high protein quality originating from the Andean region of South America, has broad genetic variation and adaptability to diverse agroecological conditions, contributing to the potential to serve as a global keystone protein crop in a changing climate. However, the germplasm resources currently available to facilitate quinoa expansion worldwide are restricted to a small portion of quinoa's total genetic diversity, in part because of day-length sensitivity and issues related to seed sovereignty. This study aimed to characterize phenotypic relationships and variation within a quinoa world core collection. The 360 accessions were planted in a randomized complete block design with four replicates in each of two greenhouses in Pullman, WA during the summer of 2018. Phenological stages, plant height, and inflorescence characteristics were recorded. Seed yield, composition, thousand seed weight, nutritional composition, shape, size, and color were measured using a high-throughput phenotyping pipeline. Considerable variation existed among the germplasm. Crude protein content ranged from 11.24% to 17.81% (fixed at 14% moisture). We found that protein content was negatively correlated with yield and positively correlated with total amino acid content and days to harvest. Mean essential amino acids values met adult daily requirements but not leucine and lysine infant requirements. Yield was positively correlated with thousand seed weight and seed area, and negatively correlated with ash content and days to harvest. The accessions clustered into four groups, with one-group representing useful accessions for long-day breeding programs. The results of this study establish a practical resource for plant breeders to leverage as they strategically develop germplasm in support of the global expansion of quinoa.

BRXL4-LAZY1 interaction at the plasma membrane controls Arabidopsis branch angle and gravitropism

Gravitropism guides growth to shape plant architecture above and below ground. Mutations in LAZY1 impair stem gravitropism and cause less upright inflorescence branches (wider angles). The LAZY1 protein resides at the plasma membrane and in the nucleus. The plasma membrane pool is necessary and sufficient for setting branch angles. To investigate the molecular mechanism of LAZY1 function, we screened for LAZY1-interacting proteins in yeast. We identified BRXL4, a shoot-specific protein related to BREVIS RADIX. The BRXL4-LAZY1 interaction occurred at the plasma membrane in plant cells, and not detectably in the nucleus. Mutations in the C-terminus of LAZY1, but not other conserved regions, prevented the interaction. Opposite to lazy1, brxl4 mutants displayed faster gravitropism and more upright branches. Overexpressing BRXL4 produced strong lazy1 phenotypes. The apparent negative regulation of LAZY1 function is consistent with BRXL4 reducing LAZY1 expression or the amount of LAZY1 at the plasma membrane. Measurements indicated that both are true. LAZY1 mRNA was three-fold more abundant in brxl4 mutants and almost undetectable in BRXL4 overexpressors. Plasma membrane LAZY1 was higher and nuclear LAZY1 lower in brxl4 mutants compared with the wild type. To explain these results, we suggest that BRXL4 reduces the amount of LAZY1 at the plasma membrane where it functions in gravity signaling and promotes LAZY1 accumulation in the nucleus where it reduces LAZY1 expression, possibly by suppressing its own transcription. This explanation of how BRXL4 negatively regulates LAZY1 suggests ways to modify shoot system architecture for practical purposes.

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

Characterizing introgression-by-environment interactions using maize near isogenic lines

Significant introgression-by-environment interactions are observed for traits throughout development from small introgressed segments of the genome. Relatively small genomic introgressions containing quantitative trait loci can have significant impacts on the phenotype of an individual plant. However, the magnitude of phenotypic effects for the same introgression can vary quite substantially in different environments due to introgression-by-environment interactions. To study potential patterns of introgression-by-environment interactions, fifteen near-isogenic lines (NILs) with > 90% B73 genetic background and multiple Mo17 introgressions were grown in 16 different environments. These environments included five geographical locations with multiple planting dates and multiple planting densities. The phenotypic impact of the introgressions was evaluated for up to 26 traits that span different growth stages in each environment to assess introgression-by-environment interactions. Results from this study showed that small portions of the genome can drive significant genotype-by-environment interaction across a wide range of vegetative and reproductive traits, and the magnitude of the introgression-by-environment interaction varies across traits. Some introgressed segments were more prone to introgression-by-environment interaction than others when evaluating the interaction on a whole plant basis throughout developmental time, indicating variation in phenotypic plasticity throughout the genome. Understanding the profile of introgression-by-environment interaction in NILs is useful in consideration of how small introgressions of QTL or transgene containing regions might be expected to impact traits in diverse environments.

The complex response of free and bound amino acids to water stress during the seed setting stage in Arabidopsis

Free amino acids (FAAs) and protein-bound amino acids (PBAAs) in seeds play an important role in seed desiccation, longevity, and germination. However, the effect that water stress has on these two functional pools, especially when imposed during the crucial seed setting stage is unclear. To better understand these effects, we exposed Arabidopsis plants at the seed setting stage to a range of water limitation and water deprivation conditions and then evaluated physiological, metabolic, and proteomic parameters, with special focus on FAAs and PBAAs. We found that in response to severe water limitation, seed yield decreased, while seed weight, FAA, and PBAA content per seed increased. Nevertheless, the composition of FAAs and PBAAs remained unaltered. In response to severe water deprivation, however, both seed yield and weight were reduced. In addition, major alterations were observed in both FAA and proteome compositions, which indicated that both osmotic adjustment and proteomic reprogramming occurred in these naturally desiccation-tolerant organs. However, despite the major proteomic alteration, the PBAA composition did not change, suggesting that the proteomic reprogramming was followed by a proteomic rebalancing. Proteomic rebalancing has not been observed previously in response to stress, but its occurrence under stress strongly suggests its natural function. Together, our data show that the dry seed PBAA composition plays a key role in seed fitness and therefore is rigorously maintained even under severe water stress, while the FAA composition is more plastic and adaptable to changing environments, and that both functional pools are distinctly regulated.

Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

OBJECTIVES

Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017.

DATA DESCRIPTION

Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.

Predicting Zea mays Flowering Time, Yield, and Kernel Dimensions by Analyzing Aerial Images

Image analysis methods for measuring crop phenotypes may replace traditional measurements if they more efficiently and reliably capture similar or superior information. This study used a recreational-grade unmanned aerial vehicle carrying a spectrally-modified consumer-grade camera to collect images in which each pixel value is a vegetation index based on the normalized difference between the blue and near infrared wavelength bands (BNDVI). The subjects of the study were Zea mays hybrids with good yield potential grown in 4-row plots. Flights were conducted at least once per week during three successive growing seasons in south-central Wisconsin. Average BNDVI for each plot (genotype) rose steadily through June, peaked in July, and then declined as plants matured. BNDVI histograms changed shape over the season as the canopy concealed soil, became more uniformly green, then senesced. Principal Components Analysis (PCA) captured the change in histogram shape. PC1 represented canopy closure. PC2 represented the mean of the BNDVI distribution. PC3 represented the spread of the distribution. Correlation analysis showed that flowering time correlated with PC2 and PC3 best (r ≈ 0.5) a few days before the event (day in which 50% of the plants exhibited tassels). Three ears were picked from each plot to quantify kernel dimensions by image analysis before each plot was mechanically harvested to determine grain weight per plot. Correlations between this measurement of yield and PC2 were low in June but exceeded 0.4 within 10 days after flowering. Kernel length correlated similarly with PC2. The correlation between PC2 and kernel thickness displayed a similar but inverted time course. These results indicate that greater mid-season BNDVI values correlate positively with yield comprised of tall, thin kernels. Partial least squares regression performed on the BNDVI time courses predicted flowering time (r = 0.54-0.79) and yield (r = 0.4-0.69). This three-year experiment demonstrated that readily available hardware and software can create a phenotyping platform capable of predicting maize flowering time, yield, and kernel dimensions to a useful degree.

Classifying cold-stress responses of inbred maize seedlings using RGB imaging

Increasing the tolerance of maize seedlings to low-temperature episodes could mitigate the effects of increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting seedlings of 40 maize inbred genotypes to a defined, temporary cold stress while collecting digital profile images over a 9-daytime course. Image analysis performed with PlantCV software quantified shoot height, shoot area, 14 other morphological traits, and necrosis identified by color analysis. Hierarchical clustering of changes in growth rates of morphological traits and quantification of leaf necrosis over two time intervals resulted in three clusters of genotypes, which are characterized by unique responses to cold stress. For any given genotype, the set of traits with similar growth rates is unique. However, the patterns among traits are different between genotypes. Cold sensitivity was not correlated with the latitude where the inbred varieties were released suggesting potential further improvement for this trait. This work will serve as the basis for future experiments investigating the genetic basis of recovery to cold stress in maize seedlings.

A machine vision platform for measuring imbibition of maize kernels: quantification of genetic effects and correlations with germination

BACKGROUND

Imbibition (uptake of water by a dry seed) initiates the germination process. An automated method for quantifying imbibition would enable research on the genetic elements that influence the underlying hydraulic and biochemical processes. In the case of crop research, a high throughput imbibition assay could be used to investigate seed quality topics or to improve yield by selecting varieties with superior germination characteristics.

RESULTS

An electronic force transducer measured imbibition of single maize kernels with very high resolution but low throughput. An image analysis method was devised to achieve high throughput and sufficient resolution. A transparent fixture held 90 maize kernels in contact with water on the imaging window of a flatbed document scanner that produced an image of the kernels automatically every 10 min for 22 h. Custom image analysis software measured the area A of each indexed kernel in each image to produce imbibition time courses. The ultimate change in area (ΔA) ranged from 19.3 to 23.4% in a population of 72 hybrids derived from 9 inbred parents. Kernel area as a function of time was fit well by A t = A f 1 - e - k t where A _f is the final kernel area. The swelling coefficient, k, ranged from 0.098 to 0.159 h^-1 across the genotypes. The full diallel structure of the population enabled maternal genotype effects to be assessed. In a separate experiment, measurements of kernels of the same 25 inbreds produced in three different years demonstrated that production and storage variables affected imbibition much less than genotype. In a third experiment, measurements of 30 diverse inbred lines showed that k varied inversely with germination time (r = - 0.7) and directly with germination percentage (r = 0.7).

CONCLUSIONS

Nonspecialized imaging hardware and custom analysis software running on public cyber infrastructure form a low-cost platform for measuring seed imbibition with high resolution and throughput. We measured imbibition of thousands of kernels to determine that genotype influenced imbibition of maize kernels much more than seed production and storage environments. In some hybrids, k depended on which inbred parent was maternal. Quantitative relationships between k and germination traits were discovered.

An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot (Daucus carota L.)

Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

OBJECTIVES

Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available.

DATA DESCRIPTION

Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are released as comma separated value spreadsheets accompanied by extensive README text descriptions. For genotypic and phenotypic data, both raw data and a version with outliers removed are reported. For weather data, two versions are reported: a full dataset calibrated against nearby National Weather Service sites and a second calibrated set with outliers and apparent artifacts removed.

Genotype-by-environment interactions affecting heterosis in maize

The environment can influence heterosis, the phenomena in which the offspring of two inbred parents exhibits phenotypic performance beyond the inbred parents for specific traits. In this study we measured 25 traits in a set of 47 maize hybrids and their inbred parents grown in 16 different environments with varying levels of average productivity. By quantifying 25 vegetative and reproductive traits across the life cycle we were able to analyze interactions between the environment and multiple distinct instances of heterosis. The magnitude and rank among hybrids for better-parent heterosis (BPH) varied for the different traits and environments. Across the traits, a higher within plot variance was observed for inbred lines compared to hybrids. However, for most traits, variance across environments was not significantly different for inbred lines compared to hybrids. Further, for many traits the correlations of BPH to hybrid performance and BPH to better parent performance were of comparable magnitude. These results indicate that inbred lines and hybrids show similar trends in environmental response and both are contributing to observed genotype-by-environment interactions for heterosis. This study highlights the degree of heterosis is not an inherent trait of a specific hybrid, but varies depending on the trait measured and the environment where that trait is measured. Studies that attempt to correlate molecular processes with heterosis are hindered by the fact that heterosis is not a consistent attribute of a specific hybrid.

Distribution of Endogenous NO Regulates Early Gravitropic Response and PIN2 Localization in Arabidopsis Roots

High-resolution and automated image analysis of individual roots demonstrated that endogenous nitric oxide (NO) contribute significantly to gravitropism of Arabidopsis roots. Lowering of endogenous NO concentrations strongly reduced and even reversed gravitropism, resulting in upward bending, without affecting root growth rate. Notably, the asymmetric accumulation of NO along the upper and lower sides of roots correlated with a positive gravitropic response. Detection of NO by the specific DAF-FM DA fluorescent probe revealed that NO was higher at the lower side of horizontally-oriented roots returning to initial values 2 h after the onset of gravistimulation. We demonstrate that NO promotes plasma membrane re-localization of PIN2 in epidermal cells, which is required during the early root gravitropic response. The dynamic and asymmetric localization of both auxin and NO is critical to regulate auxin polar transport during gravitropism. Our results collectively suggest that, although auxin and NO crosstalk occurs at different levels of regulation, they converge in the regulation of PIN2 membrane trafficking in gravistimulated roots, supporting the notion that a temporally and spatially coordinated network of signal molecules could participate in the early phases of auxin polar transport during gravitropism.

Spontaneous polyploidization in cucumber

This is the first quantitative estimation of spontaneous polyploidy in cucumber and we detected 2.2% polyploids in a greenhouse study. We provide evidence that polyploidization is consistent with endoreduplication and is an on-going process during plant growth. Cucumber occasionally produces polyploid plants, which are problematic for growers because these plants produce misshaped fruits with non-viable seeds. In this study, we undertook the first quantitative study to estimate the relative frequency of spontaneous polyploids in cucumber. Seeds of recombinant inbred lines were produced in different environments, plants were grown in the field and greenhouse, and flow cytometry was used to establish ploidies. From 1422 greenhouse-grown plants, the overall relative frequency of spontaneous polyploidy was 2.2%. Plants possessed nuclei of different ploidies in the same leaves (mosaic) and on different parts of the same plant (chimeric). Our results provide evidence of endoreduplication and polysomaty in cucumber, and that it is an on-going and dynamic process. There was a significant effect (p = 0.018) of seed production environment on the occurrence of polyploid plants. Seed and seedling traits were not accurate predictors of eventual polyploids, and we recommend that cucumber producers rogue plants based on stature and leaf serration to remove potential polyploids.

Constitutive Expression of Arabidopsis SMALL AUXIN UP RNA19 (SAUR19) in Tomato Confers Auxin-Independent Hypocotyl Elongation

The plant hormone indole-3-acetic acid (IAA or auxin) mediates the elongation growth of shoot tissues by promoting cell expansion. According to the acid growth theory proposed in the 1970s, auxin activates plasma membrane H⁺-ATPases (PM H⁺-ATPases) to facilitate cell expansion by both loosening the cell wall through acidification and promoting solute uptake. Mechanistically, however, this process is poorly understood. Recent findings in Arabidopsis (Arabidopsis thaliana) have demonstrated that auxin-induced SMALL AUXIN UP RNA (SAUR) genes promote elongation growth and play a key role in PM H⁺-ATPase activation by inhibiting PP2C.D family protein phosphatases. Here, we extend these findings by demonstrating that SAUR proteins also inhibit tomato PP2C.D family phosphatases and that AtSAUR19 overexpression in tomato (Solanum lycopersicum) confers the same suite of phenotypes as previously reported for Arabidopsis. Furthermore, we employ a custom image-based method for measuring hypocotyl segment elongation with high resolution and a method for measuring cell wall mechanical properties, to add mechanistic details to the emerging description of auxin-mediated cell expansion. We find that constitutive expression of GFP-AtSAUR19 bypasses the normal requirement of auxin for elongation growth by increasing the mechanical extensibility of excised hypocotyl segments. In contrast, hypocotyl segments overexpressing a PP2C.D phosphatase are specifically impaired in auxin-mediated elongation. The time courses of auxin-induced SAUR expression and auxin-dependent elongation growth were closely correlated. These findings indicate that induction of SAUR expression is sufficient to elicit auxin-mediated expansion growth by activating PM H⁺-ATPases to facilitate apoplast acidification and mechanical wall loosening.

A robust, high-throughput method for computing maize ear, cob, and kernel attributes automatically from images

Grain yield of the maize plant depends on the sizes, shapes, and numbers of ears and the kernels they bear. An automated pipeline that can measure these components of yield from easily-obtained digital images is needed to advance our understanding of this globally important crop. Here we present three custom algorithms designed to compute such yield components automatically from digital images acquired by a low-cost platform. One algorithm determines the average space each kernel occupies along the cob axis using a sliding-window Fourier transform analysis of image intensity features. A second counts individual kernels removed from ears, including those in clusters. A third measures each kernel's major and minor axis after a Bayesian analysis of contour points identifies the kernel tip. Dimensionless ear and kernel shape traits that may interrelate yield components are measured by principal components analysis of contour point sets. Increased objectivity and speed compared to typical manual methods are achieved without loss of accuracy as evidenced by high correlations with ground truth measurements and simulated data. Millimeter-scale differences among ear, cob, and kernel traits that ranged more than 2.5-fold across a diverse group of inbred maize lines were resolved. This system for measuring maize ear, cob, and kernel attributes is being used by multiple research groups as an automated Web service running on community high-throughput computing and distributed data storage infrastructure. Users may create their own workflow using the source code that is staged for download on a public repository.

TIPS: a system for automated image-based phenotyping of maize tassels

BACKGROUND

The maize male inflorescence (tassel) produces pollen necessary for reproduction and commercial grain production of maize. The size of the tassel has been linked to factors affecting grain yield, so understanding the genetic control of tassel architecture is an important goal. Tassels are fragile and deform easily after removal from the plant, necessitating rapid measurement of any shape characteristics that cannot be retained during storage. Some morphological characteristics of tassels such as curvature and compactness are difficult to quantify using traditional methods, but can be quantified by image-based phenotyping tools. These constraints necessitate the development of an efficient method for capturing natural-state tassel morphology and complementary automated analytical methods that can quickly and reproducibly quantify traits of interest such as height, spread, and branch number.

RESULTS

This paper presents the Tassel Image-based Phenotyping System (TIPS), which provides a platform for imaging tassels in the field immediately following removal from the plant. TIPS consists of custom methods that can quantify morphological traits from profile images of freshly harvested tassels acquired with a standard digital camera in a field-deployable light shelter. Correlations between manually measured traits (tassel weight, tassel length, spike length, and branch number) and image-based measurements ranged from 0.66 to 0.89. Additional tassel characteristics quantified by image analysis included some that cannot be quantified manually, such as curvature, compactness, fractal dimension, skeleton length, and perimeter. TIPS was used to measure tassel phenotypes of 3530 individual tassels from 749 diverse inbred lines that represent the diversity of tassel morphology found in modern breeding and academic research programs. Repeatability ranged from 0.85 to 0.92 for manually measured phenotypes, from 0.77 to 0.83 for the same traits measured by image-based methods, and from 0.49 to 0.81 for traits that can only be measured by image analysis.

CONCLUSIONS

TIPS allows morphological features of maize tassels to be quantified automatically, with minimal disturbance, at a scale that supports population-level studies. TIPS is expected to accelerate the discovery of associations between genetic loci and tassel morphology characteristics, and can be applied to maize breeding programs to increase productivity with lower resource commitment.

Role of SKD1 Regulators LIP5 and IST1-LIKE1 in Endosomal Sorting and Plant Development

SKD1 is a core component of the mechanism that degrades plasma membrane proteins via the Endosomal Sorting Complex Required for Transport (ESCRT) pathway. Its ATPase activity and endosomal recruitment are regulated by the ESCRT components LIP5 and IST1. How LIP5 and IST1 affect ESCRT-mediated endosomal trafficking and development in plants is not known. Here we use Arabidopsis mutants to demonstrate that LIP5 controls the constitutive degradation of plasma membrane proteins and the formation of endosomal intraluminal vesicles. Although lip5 mutants were able to polarize the auxin efflux facilitators PIN2 and PIN3, both proteins were mis-sorted to the tonoplast in lip5 root cells. In addition, lip5 root cells over-accumulated PIN2 at the plasma membrane. Consistently with the trafficking defects of PIN proteins, the lip5 roots showed abnormal gravitropism with an enhanced response within the first 4 h after gravistimulation. LIP5 physically interacts with IST1-LIKE1 (ISTL1), a protein predicted to be the Arabidopsis homolog of yeast IST1. However, we found that Arabidopsis contains 12 genes coding for predicted IST1-domain containing proteins (ISTL1-12). Within the ISTL1-6 group, ISTL1 showed the strongest interaction with LIP5, SKD1, and the ESCRT-III-related proteins CHMP1A in yeast two hybrid assays. Through the analysis of single and double mutants, we found that the synthetic interaction of LIP5 with ISTL1, but not with ISTL2, 3, or 6, is essential for normal plant growth, repression of spontaneous cell death, and post-embryonic lethality.

The receptor-like kinase FERONIA is required for mechanical signal transduction in Arabidopsis seedlings

Among the myriad cues that constantly inform plant growth and development, mechanical forces are unique in that they are an intrinsic result of cellular turgor pressure and also imposed by the environment. Although the key role of mechanical forces in shaping plant architecture from the cellular level to the level of organ formation is well established, the components of the early mechanical signal transduction machinery remain to be defined at the molecular level. Here, we show that an Arabidopsis mutant lacking the receptor-like kinase FERONIA (FER) shows severely altered Ca(2+) signaling and growth responses to different forms of mechanical perturbation. Ca(2+) signals are either abolished or exhibit qualitatively different signatures in feronia (fer) mutants exposed to local touch or bending stimulation. Furthermore, mechanically induced upregulation of known touch-responsive genes is significantly decreased in fer mutants. In addition to these defects in mechanical signaling, fer mutants also exhibit growth phenotypes consistent with impaired mechanical development, including biased root skewing, an inability to penetrate hard agar layers, and abnormal growth responses to impenetrable obstacles. Finally, high-resolution kinematic analysis of root growth revealed that fer mutants show pronounced spatiotemporal fluctuations in root cell expansion profiles with a timescale of minutes. Based on these results, we propose that FER is a key regulator of mechanical Ca(2+) signaling and that FER-dependent mechanical signaling functions to regulate growth in response to external or intrinsic mechanical forces.

Image analysis is driving a renaissance in growth measurement

The domain of machine vision, in which digital images are acquired automatically in a highly structured environment for the purpose of computationally measuring features in the scene, is applicable to the measurement of plant growth. This article reviews the quickly growing collection of reports in which digital image-processing has been used to measure plant growth, with emphasis on the methodology and adaptations required for high-throughput studies of populations.

AUXIN UP-REGULATED F-BOX PROTEIN1 regulates the cross talk between auxin transport and cytokinin signaling during plant root growth

Plant root development is mediated by the concerted action of the auxin and cytokinin phytohormones, with cytokinin serving as an antagonist of auxin transport. Here, we identify the AUXIN UP-REGULATED F-BOX PROTEIN1 (AUF1) and its potential paralog AUF2 as important positive modifiers of root elongation that tether auxin movements to cytokinin signaling in Arabidopsis (Arabidopsis thaliana). The AUF1 mRNA level in roots is strongly up-regulated by auxin but not by other phytohormones. Whereas the auf1 single and auf1 auf2 double mutant roots grow normally without exogenous auxin and respond similarly to the wild type upon auxin application, their growth is hypersensitive to auxin transport inhibitors, with the mutant roots also having reduced basipetal and acropetal auxin transport. The effects of auf1 on auxin movements may be mediated in part by the misexpression of several PIN-FORMED (PIN) auxin efflux proteins, which for PIN2 reduces its abundance on the plasma membrane of root cells. auf1 roots are also hypersensitive to cytokinin and have increased expression of several components of cytokinin signaling. Kinematic analyses of root growth and localization of the cyclin B mitotic marker showed that AUF1 does not affect root cell division but promotes cytokinin-mediated cell expansion in the elongation/differentiation zone. Epistasis analyses implicate the cytokinin regulator ARR1 or its effector(s) as the target of the SKP1-Cullin1-F Box (SCF) ubiquitin ligases assembled with AUF1/2. Given the wide distribution of AUF1/2-type proteins among land plants, we propose that SCF(AUF1/2) provides additional cross talk between auxin and cytokinin, which modifies auxin distribution and ultimately root elongation.

Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks

Auxin and ethylene are key regulators of plant growth and development, and thus the transcriptional networks that mediate responses to these hormones have been the subject of intense research. This study dissected the hormonal cross talk regulating the synthesis of flavonols and examined their impact on root growth and development. We analyzed the effects of auxin and an ethylene precursor on roots of wild-type and hormone-insensitive Arabidopsis (Arabidopsis thaliana) mutants at the transcript, protein, and metabolite levels at high spatial and temporal resolution. Indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) differentially increased flavonol pathway transcripts and flavonol accumulation, altering the relative abundance of quercetin and kaempferol. The IAA, but not ACC, response is lost in the transport inhibitor response1 (tir1) auxin receptor mutant, while ACC responses, but not IAA responses, are lost in ethylene insensitive2 (ein2) and ethylene resistant1 (etr1) ethylene signaling mutants. A kinetic analysis identified increases in transcripts encoding the transcriptional regulators MYB12, Transparent Testa Glabra1, and Production of Anthocyanin Pigment after hormone treatments, which preceded increases in transcripts encoding flavonoid biosynthetic enzymes. In addition, myb12 mutants were insensitive to the effects of auxin and ethylene on flavonol metabolism. The equivalent phenotypes for transparent testa4 (tt4), which makes no flavonols, and tt7, which makes kaempferol but not quercetin, showed that quercetin derivatives are the inhibitors of basipetal root auxin transport, gravitropism, and elongation growth. Collectively, these experiments demonstrate that auxin and ethylene regulate flavonol biosynthesis through distinct signaling networks involving TIR1 and EIN2/ETR1, respectively, both of which converge on MYB12. This study also provides new evidence that quercetin is the flavonol that modulates basipetal auxin transport.

Separating parental environment from seed size effects on next generation growth and development in Arabidopsis

Plant growth and development is profoundly influenced by environmental conditions that laboratory experimentation typically attempts to control. However, growth conditions are not uniform between or even within laboratories and the extent to which these differences influence plant growth and development is unknown. Experiments with wild-type Arabidopsis thaliana were designed to quantify the influences of parental environment and seed size on growth and development in the next generation. A single lot of seed was planted in six environmental chambers and grown to maturity. The seed produced was mechanically sieved into small and large size classes then grown in a common environment and subjected to a set of assays spanning the life cycle. Analysis of variance demonstrated that seed size effects were particularly significant early in development, affecting primary root growth and gravitropism, but also flowering time. Parental environment affected progeny germination time, flowering and weight of seed the progeny produced. In some cases, the parental environment affected the magnitude of (interacted with) the observed seed size effects. These data indicate that life history circumstances of the parental generation can affect growth and development throughout the life cycle of the next generation to an extent that should be considered when performing genetic studies.

Dynamics of auxin-dependent Ca2+ and pH signaling in root growth revealed by integrating high-resolution imaging with automated computer vision-based analysis

Plants adapt to a changing environment by entraining their growth and development to prevailing conditions. Such 'plastic' development requires a highly dynamic integration of growth phenomena with signal perception and transduction systems, such as occurs during tropic growth. The plant hormone auxin has been shown to play a key role in regulating these directional growth responses of plant organs to environmental cues. However, we are still lacking a cellular and molecular understanding of how auxin-dependent signaling cascades link stimulus perception to the rapid modulation of growth patterns. Here, we report that in root gravitropism of Arabidopsis thaliana, auxin regulates root curvature and associated apoplastic, growth-related pH changes through a Ca2+-dependent signaling pathway. Using an approach that integrates confocal microscopy and automated computer vision-based image analysis, we demonstrate highly dynamic root surface pH patterns during vertical growth and after gravistimulation. These pH dynamics are shown to be dependent on auxin, and specifically on auxin transport mediated by the auxin influx carrier AUX1 in cells of the lateral root cap and root epidermis. Our results further indicate that these pH responses require auxin-dependent changes in cytosolic Ca2+ levels that operate independently of the TIR1 auxin perception system. These results demonstrate a methodology that can be used to visualize vectorial auxin responses in a manner that can be integrated with the rapid plant growth responses to environmental stimuli.

Real-time reverse-transcriptase--polymerase chain reaction for Salmonella enterica detection from jalapeño and serrano peppers

Outbreaks of Salmonella linked to fresh produce emphasize the need for rapid detection methods to curb the spread of foodborne pathogens. Reverse-transcriptase-polymerase chain reaction (RT-PCR) detects the presence of mRNA (shorter half-life than DNA), with greater potential of detecting viable pathogens. Real-time RT-PCR eliminates the need for gel electrophoresis and significantly enhances the speed of detection (<1 day) compared with traditional methods (>5 days). The objectives of this research were to apply real-time SYBR Green I-based RT-PCR to detect Salmonella from jalapeño and serrano peppers spiked with low and high inocula of Salmonella. Inoculated and uninoculated peppers were rinsed with water and dried under ultraviolet light for 10 min. Approximately 25 g peppers was inoculated with 10(8) to 10(1) colony forming units (CFU) of Salmonella enterica serovar Typhimurium in a stomacher bag and hand massaged in sterile 0.05 M glycine-0.14 M saline buffer (0.05% Tween, 3% beef extract) for optimal recovery of bacteria. A short preenrichment step of 6 h in buffered peptone water was needed for the detection of low inocula (10(4) CFU/25 g). One-milliliter portions of the extracts were serially diluted, plated on XLT4 agar, and used for RNA extraction with the Qiagen RNeasy Mini Kit. RT-PCR was carried out using SYBR Green I one-step RT-PCR with previously described invA gene primers and an internal amplification control. Detection limits were 10(4) CFU/25 g (approximately 10(2) CFU/g) and 10(7) CFU/25 g (approximately 10(5) CFU/g) Salmonella from enriched and unenriched inoculated peppers, respectively. Even though this method included a 6-h incubation period, the results were still obtainable in 1 day. This method shows promise for applications in routine surveillance and during outbreaks.

Plasticity of Arabidopsis root gravitropism throughout a multidimensional condition space quantified by automated image analysis

Plant development is genetically determined but it is also plastic, a fundamental duality that can be investigated provided large number of measurements can be made in various conditions. Plasticity of gravitropism in wild-type Arabidopsis (Arabidopsis thaliana) seedling roots was investigated using automated image acquisition and analysis. A bank of computer-controlled charge-coupled device cameras acquired images with high spatiotemporal resolution. Custom image analysis algorithms extracted time course measurements of tip angle and growth rate. Twenty-two discrete conditions defined by seedling age (2, 3, or 4 d), seed size (extra small, small, medium, or large), and growth medium composition (simple or rich) formed the condition space sampled with 1,216 trials. Computational analyses including dimension reduction by principal components analysis, classification by k-means clustering, and differentiation by wavelet convolution showed distinct response patterns within the condition space, i.e. response plasticity. For example, 2-d-old roots (regardless of seed size) displayed a response time course similar to those of roots from large seeds (regardless of age). Enriching the growth medium with nutrients suppressed response plasticity along the seed size and age axes, possibly by ameliorating a mineral deficiency, although analysis of seeds did not identify any elements with low levels on a per weight basis. Characterizing relationships between growth rate and tip swing rate as a function of condition cast gravitropism in a multidimensional response space that provides new mechanistic insights as well as conceptually setting the stage for mutational analysis of plasticity in general and root gravitropism in particular.

Computer-vision analysis of seedling responses to light and gravity

Measuring the effects of mutation, natural variation or treatment on the development of plant form is often complicated by the shapes, dynamics or small size of the organismal structures under study. This limits accuracy and throughput of measurement and thereby limits progress toward understanding the underlying gene networks and signaling systems. A computer-vision platform based on electronic image capture and shape-analysis algorithms was developed as an alternative to the mostly manual methods of measuring seedling development currently in use. The spatial and temporal resolution of the method is in the range of microns and minutes, respectively. The algorithm simultaneously quantifies apical hook opening and inhibition of hypocotyl elongation during photomorphogenesis of Arabidopsis thaliana seedlings. It can determine when and where gravitropic curvature develops along the root axis in A. thaliana and Medicago truncatula seedlings. Novel features of gravitropic curvature development were discovered as a result of the high resolution. The computer-vision algorithms developed and demonstrated here could be used to study mutant phenotypes in detail, to form the basis of a high-throughput screening platform, or to quantify natural variation in a population of plants.

Separating the roles of acropetal and basipetal auxin transport on gravitropism with mutations in two Arabidopsis multidrug resistance-like ABC transporter genes

Two Arabidopsis thaliana ABC transporter genes linked to auxin transport by various previous results were studied in a reverse-genetic fashion. Mutations in Multidrug Resistance-Like1 (MDR1) reduced acropetal auxin transport in roots by 80% without affecting basipetal transport. Conversely, mutations in MDR4 blocked 50% of basipetal transport without affecting acropetal transport. Developmental and auxin distribution phenotypes associated with these altered auxin flows were studied with a high-resolution morphometric system and confocal microscopy, respectively. Vertically grown mdr1 roots produced positive and negative curvatures threefold greater than the wild type, possibly due to abnormal auxin distribution observed in the elongation zone. However, upon 90 degrees reorientation, mdr1 gravitropism was inseparable from the wild type. Thus, acropetal auxin transport maintains straight growth but contributes surprisingly little to gravitropism. Conversely, vertically maintained mdr4 roots grew as straight as the wild type, but their gravitropism was enhanced. Upon reorientation, curvature in this mutant developed faster, was distributed more basally, and produced a greater total angle than the wild type. An amplified auxin asymmetry may explain the mdr4 hypertropism. Double mutant analysis indicated that the two auxin transport streams are more independent than interdependent. The hypothesis that flavanols regulate MDR-dependent auxin transport was supported by the epistatic relationship of mdr4 to the tt4 phenylpropanoid pathway mutation.

Structure-activity relationship investigations of a potent and selective benzodiazepine oxytocin antagonist

We have investigated the structure-activity relationships of the 1- and 3-substituents and replacements of the 5-phenyl group of GW405212X 1, a potent selective oxytocin antagonist. The effect of these modifications on oxytocin binding antagonism and on pharmacokinetic parameters is reported.

Clinical issues relating to the diagnosis of mild dementia in a British community survey

Many epidemiologists base their diagnoses of dementia on scores on brief cognitive tests, but the border between normal aging and mild dementia is so poorly understood that simple demarcations cannot adequately encapsulate the wealth of clinical material that needs to be taken into account in assigning diagnostic labels. Data from a British study of the prevalence and natural history of dementia, in which diagnoses of dementia were made by clinicians using a new, standardized interview schedule, are presented to demonstrate the effects of physical disability, psychiatric illness, and other factors on memory impairment and performance in everyday life. Our purpose is not to insist that clinicians are always correct but rather to highlight the complexities involved and the need for investigators to be more open about the way in which they distinguish between physical, psychiatric, and cognitive infirmities.

The progression of mild idiopathic dementia in a community population

Thirty-one subjects aged 75 years and over who were identified as suffering from mild, idiopathic dementia in a large community survey were reviewed at annual intervals for 2 years. Diagnoses and severity ratings were based on defined criteria following a mental state examination, a medical and psychiatric history, detailed cognitive testing, and an interview with relatives or other key informants. Fourteen subjects became more severely demented within 2 years. The initial cognitive test battery failed to reveal any differences between respondents whose dementia advanced and those whose condition remained unchanged, but, in the former group, subjects' symptoms had been present for longer, and a greater proportion had been recognised as demented, or possibly demented, by their general practitioners. We suggest that subjects whose dementia progressed had actually been more severely disabled at the time of identification.

Continued clinical validation of dementia diagnosed in the community using the Cambridge Mental Disorders of the Elderly Examination

We describe the outcome 2 years later of elderly Cambridge residents who had been diagnosed as demented using the Cambridge Mental Disorders of the Elderly Examination. Mortality rates were high but diagnoses were confirmed for all of the 43 moderate and severe cases who survived for this period, and for 51 of the 56 subjects who had been rated initially as mildly demented; 28 of the 56 mildly demented subjects progressed to more severe levels of impairment. As many as 12 of the 24 original minimally demented cases showed evidence of intellectual deterioration, which lends weight to the validity of this experimental category.

A follow-up study of dementia diagnosed in the community using the Cambridge Mental Disorders of the Elderly Examination

Elderly Cambridge residents diagnosed as demented using the Cambridge Mental Disorders of the Elderly Examination (CAMDEX) were reviewed approximately 12 months later. Diagnoses were confirmed in 133 of 137 surviving cases (97%). Subjects said to have minimal dementia (cognitive impairment insufficient to warrant a diagnosis of dementia proper) had a varied outcome. Only 6 out of 29 survivors showed progressive intellectual deterioration and 13 were reclassified as normal. Subjects passed as normal in the first year of the study were reviewed using the Mini-Mental State Examination. We cannot be certain how many were actually dementing, but our findings suggest that only a small number of false negative diagnoses were made in the first year of the study.

The prevalence of dementia as measured by the Cambridge Mental Disorders of the Elderly Examination

General practice patients aged 75 years and over were screened for cognitive impairment using the Mini-Mental State Examination. Those scoring 23 or below and a sample of those scoring 24 or 25 were assessed using the Cambridge Mental Disorders of the Elderly Examination (CAMDEX), a structured interview schedule specifically designed to detect mild dementia. The CAMDEX includes a mental state examination, a psychiatric history, detailed cognitive testing and an information interview. The prevalence of dementia in 2311 patients was found to be 10.5%, about half that found in most earlier studies. Possible reasons for this low rate are discussed.

The reliability and validity of the Mini-Mental State in a British community survey

The Mini-Mental State (MMSE) was administered to 2302 general practice patients aged 75 yr and over. Those scoring 23 or less and a sample of those scoring 24 or 25 were selected for further investigation using the Cambridge Mental Disorders of the Elderly Examination. Inter-observer reliability was high with a mean kappa value of 0.97. Eighty-six per cent of respondents judged to have organic mental disorders scored 23 or less on the MMSE and 92% of those judged to be cognitively intact scored 24 or more. However, only 55% of respondents who scored 23 or less were demented or delirious while a number of relatively well educated, mildly demented subjects scored 24 and 25. The customary cut-off point of 23/24 may need to be revised in future community studies. MMSE scores cannot be used to make even tentative psychiatric diagnoses; more detailed investigation of low scorers is essential.

On the biodegradation of poly-beta-hydroxybutyrate (PHB) homopolymer and poly-beta-hydroxybutyrate-hydroxyvalerate copolymers

The known biodegradability of PHB in certain biological environments has led to its proposed use as a 'biodegradable' implant material. Monofilaments of PHB homopolymer and two PHV-PHB copolymers have been studied in vivo and in vitro and assessed for changes in mechanical properties and topography. In vivo biodegradation was only observed with PHB when pre-degraded by 10.0 Mrad of gamma-irradiation before implantation. High temperature in vitro hydrolysis suggested that PHV copolymer additions retarded the rate of degradation of PHB. Hydration reactions had most effect on the ultimate tensile properties of the materials. In contrast, the elastic properties appeared to be relatively unaffected.

The in vivo and in vitro degradation of poly(glycolic acid) suture material as a function of applied strain

The in vivo and in vitro stability of a degradable suture material, poly(glycolic acid) has been shown to be dependent on the magnitude of a pre-imposed strain. The degradation, monitored by changes in the tensile load at break, was considerably enhanced by pre-straining the material to one half of the normal extension at break, using a novel implantable device.