Corrigendum: Proximal hyperspectral imaging detects diurnal and drought-induced changes in maize physiology.

[This corrects the article DOI: 10.3389/fpls.2021.640914.].

Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform.

BACKGROUND: Thermography is a popular tool to assess plant water-use behavior, as plant temperature is influenced by transpiration rate, and is commonly used in field experiments to detect plant water deficit. Its application in indoor automated phenotyping platforms is still limited and mainly focuses on differences in plant temperature between genotypes or treatments, instead of estimating stomatal conductance or transpiration rate. In this study, the transferability of commonly used thermography analysis protocols from the field to greenhouse phenotyping platforms was evaluated. In addition, the added value of combining thermal infrared (TIR) with hyperspectral imaging to monitor drought effects on plant transpiration rate (E) was evaluated. RESULTS: The sensitivity of commonly used TIR indices to detect drought-induced and genotypic differences in water status was investigated in eight maize inbred lines in the automated phenotyping platform PHENOVISION. Indices that normalized plant temperature for vapor pressure deficit and/or air temperature at the time of imaging were most sensitive to drought and could detect genotypic differences in the plants' water-use behavior. However, these indices were not strongly correlated to stomatal conductance and E. The canopy temperature depression index, the crop water stress index and the simplified stomatal conductance index were more suitable to monitor these traits, and were consequently used to develop empirical E prediction models by combining them with hyperspectral indices and/or environmental variables. Different modeling strategies were evaluated, including single index-based, machine learning and mechanistic models. Model comparison showed that combining multiple TIR indices in a random forest model can improve E prediction accuracy, and that the contribution of the hyperspectral data is limited when multiple indices are used. However, the empirical models trained on one genotype were not transferable to all eight inbred lines. CONCLUSION: Overall, this study demonstrates that existing TIR indices can be used to monitor drought stress and develop E prediction models in an indoor setup, as long as the indices normalize plant temperature for ambient air temperature or relative humidity.

Soybean Yield Formation Physiology - A Foundation for Precision Breeding Based Improvement.

The continued improvement of crop yield is a fundamental driver in agriculture and is the goal of both plant breeders and researchers. Plant breeders have been remarkably successful in improving crop yield, as demonstrated by the continued release of varieties with improved yield potential. This has largely been accomplished through performance-based selection, without specific knowledge of the molecular mechanisms underpinning these improvements. Insight into molecular mechanisms has been provided by plant molecular, genetic, and biochemical research through elucidation of the function of genes and pathways that underlie many of the physiological processes that contribute to yield potential. Despite this knowledge, the impact of most genes and pathways on yield components have not been tested in key crops or in a field environment for yield assessment. This gap is difficult to bridge, but field-based physiological knowledge offers a starting point for leveraging molecular targets to successfully apply precision breeding technologies such as genome editing. A better understanding of both the molecular mechanisms underlying crop yield physiology and yield limiting processes under field conditions is essential for elucidating which combinations of favorable alleles are required for yield improvement. Consequently, one goal in plant biology should be to more fully integrate crop physiology, breeding, genetics, and molecular knowledge to identify impactful precision breeding targets for relevant yield traits. The foundation for this is an understanding of yield formation physiology. Here, using soybean as an example, we provide a top-down review of yield physiology, starting with the fact that yield is derived from a population of plants growing together in a community. We review yield and yield-related components to provide a basic overview of yield physiology, synthesizing these concepts to highlight how such knowledge can be leveraged for soybean improvement. Using genome editing as an example, we discuss why multiple disciplines must be brought together to fully realize the promise of precision breeding-based crop improvement.

Proximal Hyperspectral Imaging Detects Diurnal and Drought-Induced Changes in Maize Physiology.

Hyperspectral imaging is a promising tool for non-destructive phenotyping of plant physiological traits, which has been transferred from remote to proximal sensing applications, and from manual laboratory setups to automated plant phenotyping platforms. Due to the higher resolution in proximal sensing, illumination variation and plant geometry result in increased non-biological variation in plant spectra that may mask subtle biological differences. Here, a better understanding of spectral measurements for proximal sensing and their application to study drought, developmental and diurnal responses was acquired in a drought case study of maize grown in a greenhouse phenotyping platform with a hyperspectral imaging setup. The use of brightness classification to reduce the illumination-induced non-biological variation is demonstrated, and allowed the detection of diurnal, developmental and early drought-induced changes in maize reflectance and physiology. Diurnal changes in transpiration rate and vapor pressure deficit were significantly correlated with red and red-edge reflectance. Drought-induced changes in effective quantum yield and water potential were accurately predicted using partial least squares regression and the newly developed Water Potential Index 2, respectively. The prediction accuracy of hyperspectral indices and partial least squares regression were similar, as long as a strong relationship between the physiological trait and reflectance was present. This demonstrates that current hyperspectral processing approaches can be used in automated plant phenotyping platforms to monitor physiological traits with a high temporal resolution.

Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid.

The key regulatory step in the biosynthesis of abscisic acid (ABA), a hormone central to the regulation of several important processes in plants, is the oxidative cleavage of the 11,12 double bond of a 9-cis-epoxycarotenoid. The enzyme viviparous14 (VP14) performs this cleavage in maize (Zea mays), making it a target for the rational design of novel chemical agents and genetic modifications that improve plant behavior through the modulation of ABA levels. The structure of VP14, determined to 3.2-Å resolution, provides both insight into the determinants of regio- and stereospecificity of this enzyme and suggests a possible mechanism for oxidative cleavage. Furthermore, mutagenesis of the distantly related CCD1 of maize shows how the VP14 structure represents a template for all plant carotenoid cleavage dioxygenases (CCDs). In addition, the structure suggests how VP14 associates with the membrane as a way of gaining access to its membrane soluble substrate.

Carotenoid content impacts flavor acceptability in tomato (Solanum lycopersicum).

BACKGROUND: Tomatoes contain high levels of several carotenoids including lycopene and ß-carotene. Beyond their functions as colorants and nutrients, carotenoids are precursors for important volatile flavor compounds. In order to assess the importance of apocarotenoid volatiles in flavor perception and acceptability, we conducted sensory evaluations of near-isogenic carotenoid biosynthetic mutants and their parent, Ailsa Craig. RESULTS: The carotenoid contents of these tomatoes were extremely low in the r mutant, increased in lycopene in old gold, and higher in tetra-cis-lycopene and ζ-carotene in tangerine. The volatiles derived from these carotenoids (ß-ionone, geranylacetone and 6-methyl-5-hepten-2-one) were proportionally altered relative to their precursors. Fruits were also analyzed for soluble solids, sugars, acids and flavor volatiles. Consumer panels rated the r mutant lowest for all sensory attributes, while Ailsa Craig was generally rated highest. Old gold and tangerine were rated intermediate in two of the three harvests. CONCLUSIONS: Several chemicals were negatively correlated with at least one of the hedonic scores while several others were positively correlated with tomato flavor acceptability. The results permitted identification of positive and negative interactions of volatiles with tomato flavor.

SlCCD7 controls strigolactone biosynthesis, shoot branching and mycorrhiza-induced apocarotenoid formation in tomato.

The regulation of shoot branching is an essential determinant of plant architecture, integrating multiple external and internal signals. One of the signaling pathways regulating branching involves the MAX (more axillary branches) genes. Two of the genes within this pathway, MAX3/CCD7 and MAX4/CCD8, encode carotenoid cleavage enzymes involved in generating a branch-inhibiting hormone, recently identified as strigolactone. Here, we report the cloning of SlCCD7 from tomato. As in other species, SlCCD7 encodes an enzyme capable of cleaving cyclic and acyclic carotenoids. However, the SlCCD7 protein has 30 additional amino acids of unknown function at its C terminus. Tomato plants expressing a SlCCD7 antisense construct display greatly increased branching. To reveal the underlying changes of this strong physiological phenotype, a metabolomic screen was conducted. With the exception of a reduction of stem amino acid content in the transgenic lines, no major changes were observed. In contrast, targeted analysis of the same plants revealed significantly decreased levels of strigolactone. There were no significant changes in root carotenoids, indicating that relatively little substrate is required to produce the bioactive strigolactones. The germination rate of Orobanche ramosa seeds was reduced by up to 90% on application of extract from the SlCCD7 antisense lines, compared with the wild type. Additionally, upon mycorrhizal colonization, C(13) cyclohexenone and C(14) mycorradicin apocarotenoid levels were greatly reduced in the roots of the antisense lines, implicating SlCCD7 in their biosynthesis. This work demonstrates the diverse roles of MAX3/CCD7 in strigolactone production, shoot branching, source-sink interactions and production of arbuscular mycorrhiza-induced apocarotenoids.

The carotenoid cleavage dioxygenase 1 enzyme has broad substrate specificity, cleaving multiple carotenoids at two different bond positions.

In many organisms, various enzymes mediate site-specific carotenoid cleavage to generate biologically active apocarotenoids. These carotenoid-derived products include provitamin A, hormones, and flavor and fragrance molecules. In plants, the CCD1 enzyme cleaves carotenoids at 9,10 (9',10') bonds to generate multiple apocarotenoid products. Here we systematically analyzed volatile apocarotenoids generated by maize CCD1 (ZmCCD1) from multiple carotenoid substrates. ZmCCD1 did not cleave geranylgeranyl diphosphate or phytoene but did cleave other linear and cyclic carotenoids, producing volatiles derived from 9,10 (9',10') bond cleavage. Additionally the Arabidopsis, maize, and tomato CCD1 enzymes all cleaved lycopene to generate 6-methyl-5-hepten-2-one. 6-Methyl-5-hepten-2-one, an important flavor volatile in tomato, was produced by cleavage of the 5,6 or 5',6' bond positions of lycopene but not geranylgeranyl diphosphate, zeta-carotene, or phytoene. In vitro, ZmCCD1 cleaved linear and cyclic carotenoids with equal efficiency. Based on the pattern of apocarotenoid volatiles produced, we propose that CCD1 recognizes its cleavage site based on the saturation status between carbons 7 and 8 (7' and 8') and carbons 11 and 12 (11' and 12') as well as the methyl groups on carbons 5, 9, and 13 (5', 9', and 13').

Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family.

Arabidopsis thaliana has nine genes that constitute a family of putative carotenoid cleavage dioxygenases (CCDs). While five members of the family are believed to be involved in synthesis of the phytohormone abscisic acid, the functions of the other four enzymes are less clear. Recently two of the enzymes, CCD7/MAX3 and CCD8/MAX4, have been implicated in synthesis of a novel apocarotenoid hormone that controls lateral shoot growth. Here, we report on the molecular and genetic interactions between CCD1, CCD7/MAX3 and CCD8/MAX4. CCD1 distinguishes itself from other reported CCDs as being the only member not targeted to the plastid. Unlike ccd7/max3 and ccd8/max4, both characterized as having highly branched phenotypes, ccd1 loss-of-function mutants are indistinguishable from wild-type plants. Thus, even though CCD1 has similar enzymatic activity to CCD7/MAX3, it does not have a role in synthesis of the lateral shoot growth inhibitor. Rather, it may have a role in synthesis of apocarotenoid flavor and aroma volatiles, especially in maturing seeds where loss of function leads to significantly higher carotenoid levels.

Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis.

Summary The CBF cold response pathway has a prominent role in cold acclimation. The pathway includes action of three transcription factors, CBF1, 2 and 3 (also known as DREB1b, c and a, respectively), that are rapidly induced in response to low temperature followed by expression of the CBF-targeted genes (the CBF regulon) that act in concert to increase plant-freezing tolerance. The results of transcriptome profiling and mutagenesis experiments, however, indicate that additional cold response pathways exist and may have important roles in life at low temperature. To further understand the roles that the CBF proteins play in configuring the low temperature transcriptome and to identify additional transcription factors with roles in cold acclimation, we used the Affymetrix GeneChip containing probe sets for approximately 24,000 Arabidopsis genes to define a core set of cold-responsive genes and to determine which genes were targets of CBF2 and 6 other transcription factors that appeared to be coordinately regulated with CBF2. A total of 514 genes were placed in the core set of cold-responsive genes, 302 of which were upregulated and 212 downregulated. Hierarchical clustering and bioinformatic analysis indicated that the 514 cold-responsive transcripts could be assigned to one of seven distinct expression classes and identified multiple potential novel cis-acting cold-regulatory elements. Eighty-five cold-induced genes and eight cold-repressed genes were assigned to the CBF2 regulon. An additional nine cold-induced genes and 15 cold-repressed genes were assigned to a regulon controlled by ZAT12. Of the 25 core cold-induced genes that were most highly upregulated (induced over 15-fold), 19 genes (84%) were induced by CBF2 and another two genes (8%) were regulated by both CBF2 and ZAT12. Thus, the large majority (92%) of the most highly induced genes belong to the CBF and ZAT12 regulons. Constitutive expression of ZAT12 in Arabidopsis caused a small, but reproducible, increase in freezing tolerance, indicating a role for the ZAT12 regulon in cold acclimation. In addition, ZAT12 downregulated the expression of the CBF genes indicating a role for ZAT12 in a negative regulatory circuit that dampens expression of the CBF cold response pathway.

AtPARN is an essential poly(A) ribonuclease in Arabidopsis.

Deadenylation is the first and rate-limiting step in the degradation of many mRNAs in a wide-range of organisms from yeast to higher eukaryotes. It can also play a regulatory role in early development. In this study, we examined the Arabidopsis homolog of poly(A) ribonuclease (PARN), a deadenylase first identified in mammals and absent from yeast. Consistent with the conservation of domains and residues important for catalytic activity, Arabidopsis PARN (AtPARN) expressed in Escherichia coli has poly(A) degradation activity in vitro. Protein localization experiments in plant cells indicate that AtPARN resides in both the nucleus and cytoplasm. To address the importance of the enzyme in vivo, we identified three independent T-DNA insertion mutants of AtPARN which interrupt the gene at different positions between the ATG and the stop codon. All three alleles cause lethality prior to seed germination, indicating that AtPARN is an essential gene first required during early development. Although homologous genes have yet to be inactivated in any other organism, our observations argue for the critical importance of PARN and suggest that it may be essential in many other multicellular eukaryotes.

Cold induction of Arabidopsis CBF genes involves multiple ICE (inducer of CBF expression) promoter elements and a cold-regulatory circuit that is desensitized by low temperature.

The Arabidopsis CBF1, 2, and 3 genes (also known as DREB1b, c, and a, respectively) encode transcriptional activators that have a central role in cold tolerance. CBF1-3 are rapidly induced upon exposing plants to low temperature, followed by expression of CBF-targeted genes, the CBF regulon, resulting in an increase in plant freezing tolerance. At present, little is known about the cold-sensing mechanism that controls CBF expression. Results presented here indicate that this mechanism does not require a cold shock to bring about the accumulation of CBF transcripts, but instead, absolute temperature is monitored with a greater degree of input, i.e. lower temperature, resulting in a greater output, i.e. higher levels of CBF transcripts. Temperature-shift experiments also indicate that the cold-sensing mechanism becomes desensitized to a given low temperature, such as 4 degrees C, and that resensitization to that temperature requires between 8 and 24 h at warm temperature. Gene fusion experiments identified a 125-bp section of the CBF2 promoter that is sufficient to impart cold-responsive gene expression. Mutational analysis of this cold-responsive region identified two promoter segments that work in concert to impart robust cold-regulated gene expression. These sequences, designated ICEr1 and ICEr2 (induction of CBF expression region 1 or 2), were also shown to stimulate transcription in response to mechanical agitation and the protein synthesis inhibitor, cycloheximide.