Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration

Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.

Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems

BACKGROUND

Small RNAs (sRNA) are potent regulators of gene expression that can diffuse short distances between cells and move long distances through plant vasculature. However, the degree to which sRNA silencing signals can move from the phloem to the shoot apical meristem (SAM) remains unclear.

RESULTS

Two independent transgenic approaches were used to examine whether phloem sRNA silencing can reach different domains of the SAM and silence SAM-expressed genes. First, the phloem companion-cell specific SUCROSE-PROTON SYMPORTER2 (SUC2) promoter was used to drive expression of an inverted repeat to target the FD gene, an exclusively SAM-localized floral regulator. Second, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) transgene in SAM stem cells. Both phloem silencing signals phenocopied the loss of function of their targets and altered target gene expression suggesting that a phloem-to-SAM silencing communication axis exists, connecting distal regions of the plant to SAM stem cells.

CONCLUSIONS

Demonstration of phloem-to-SAM silencing reveals a regulatory link between somatic sRNA expressed in distal regions of the plant and the growing shoot. Since the SAM stem cells ultimately produce the gametes, we discuss the intriguing possibility that phloem-to-SAM sRNA trafficking could allow transient somatic sRNA expression to manifest stable, transgenerational epigenetic changes.

Quantitative dissection of color patterning in the foliar ornamental coleus

Coleus (Coleus scutellarioides) is a popular ornamental plant that exhibits a diverse array of foliar color patterns. New cultivars are currently hand selected by both amateur and experienced plant breeders. In this study, we reimagine breeding for color patterning using a quantitative color analysis framework. Despite impressive advances in high-throughput data collection and processing, complex color patterns remain challenging to extract from image datasets. Using a phenotyping approach called "ColourQuant," we extract and analyze pigmentation patterns from one of the largest coleus breeding populations in the world. Working with this massive dataset, we can analyze quantitative relationships between maternal plants and their progeny, identify features that underlie breeder-selections, and collect and compare public input on trait preferences. This study is one of the most comprehensive explorations into complex color patterning in plant biology and provides insights and tools for exploring the color pallet of the plant kingdom.

Sterile Spikelets Contribute to Yield in Sorghum and Related Grasses

Sorghum (Sorghum bicolor) and its relatives in the grass tribe Andropogoneae bear their flowers in pairs of spikelets in which one spikelet (seed-bearing or sessile spikelet [SS]) of the pair produces a seed and the other is sterile or male (staminate). This division of function does not occur in other major cereals such as wheat (Triticum aestivum) or rice (Oryza sativa). Additionally, one bract of the SS spikelet often produces a long extension, the awn, that is in the same position as, but independently derived from, that of wheat and rice. The function of the sterile spikelet is unknown and that of the awn has not been tested in Andropogoneae. We used radioactive and stable isotopes of carbon, RNA sequencing of metabolically important enzymes, and immunolocalization of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to show that the sterile spikelet assimilates carbon, which is translocated to the largely heterotrophic SS. The awn shows no evidence of photosynthesis. These results apply to distantly related species of Andropogoneae. Removal of sterile spikelets in sorghum significantly decreases seed weight (yield) by ∼9%. Thus, the sterile spikelet, but not the awn, affects yield in the cultivated species and fitness in the wild species.

The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology

Efforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (Solanum pennellii). We find that compared with some commonly used conventional traits, (1) persistent-homology-based methods can more comprehensively capture morphological variation; (2) these techniques discriminate between genotypes with a larger normalized effect size and detect a greater number of unique quantitative trait loci (QTLs); (3) multivariate traits, whether statistically derived from univariate or persistent-homology-based traits, improve our ability to understand the genetic basis of phenotype; and (4) persistent-homology-based techniques detect unique QTLs compared to conventional traits or their multivariate derivatives, indicating that previously unmeasured aspects of morphology are now detectable. The QTL results further imply that genetic contributions to morphology can affect both the shoot and root, revealing a pleiotropic basis to natural variation in tomato. Persistent homology is a versatile framework to quantify plant morphology and developmental processes that complements and extends existing methods.

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.

Genetic and Developmental Basis for Increased Leaf Thickness in the Arabidopsis Cvi Ecotype

Leaf thickness is a quantitative trait that is associated with the ability of plants to occupy dry, high irradiance environments. Despite its importance, leaf thickness has been difficult to measure reproducibly, which has impeded progress in understanding its genetic basis, and the associated anatomical mechanisms that pattern it. Here, we used a custom-built dual confocal profilometer device to measure leaf thickness in the Arabidopsis Ler × Cvi recombinant inbred line population and found statistical support for four quantitative trait loci (QTL) associated with this trait. We used publically available data for a suite of traits relating to flowering time and growth responses to light quality and show that three of the four leaf thickness QTL coincide with QTL for at least one of these traits. Using time course photography, we quantified the relative growth rate and the pace of rosette leaf initiation in the Ler and Cvi ecotypes. We found that Cvi rosettes grow slower than Ler, both in terms of the rate of leaf initiation and the overall rate of biomass accumulation. Collectively, these data suggest that leaf thickness is tightly linked with physiological status and may present a tradeoff between the ability to withstand stress and rapid vegetative growth. To understand the anatomical basis of leaf thickness, we compared cross-sections of Cvi and Ler leaves and show that Cvi palisade mesophyll cells elongate anisotropically contributing to leaf thickness. Flow cytometry of whole leaves show that endopolyploidy accompanies thicker leaves in Cvi. Overall, our data suggest that mechanistically, an altered schedule of cellular events affecting endopolyploidy and increasing palisade mesophyll cell length contribute to increase of leaf thickness in Cvi. Ultimately, knowledge of the genetic basis and developmental trajectory leaf thickness will inform the mechanisms by which natural selection acts to produce variation in this adaptive trait.

Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii

Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato Solanum pennellii and identified quantitative trait loci. We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors. Several ILs with thick leaves have dramatically elongated palisade mesophyll cells and, in some cases, increased leaf ploidy. We characterized the thick IL2-5 and IL4-3 in detail and found increased mesophyll cell size and leaf ploidy levels, suggesting that endoreduplication underpins leaf thickness in tomato. Next, we queried the transcriptomes and inferred dynamic Bayesian networks of gene expression across early leaf ontogeny in these lines to compare the molecular networks that pattern leaf thickness. We show that thick ILs share S. pennellii-like expression profiles for putative regulators of cell shape and meristem determinacy as well as a general signature of cell cycle-related gene expression. However, our network data suggest that leaf thickness in these two lines is patterned at least partially by distinct mechanisms. Consistent with this hypothesis, double homozygote lines combining introgression segments from these two ILs show additive phenotypes, including thick leaves, higher ploidy levels, and larger palisade mesophyll cells. Collectively, these data establish a framework of genetic, anatomical, and molecular mechanisms that pattern leaf thickness in desert-adapted tomato.

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.

OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution

Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier-like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed-setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) -localized protein that participates in auxin homeostasis, transport and distribution in vivo. This work describes an example of an auxin-related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits.

Plant architecture without multicellularity: quandaries over patterning and the soma-germline divide in siphonous algae

Multicellularity has independently evolved numerous times throughout the major lineages of life. Often, multicellularity can enable complex, macroscopic organismal architectures but it is not required for the elaboration of morphology. Several alternative cellular strategies have arisen as solutions permitting exquisite forms. The green algae class Ulvophyceae, for example, contains truly multicellular organisms, as well as macroscopic siphonous cells harboring one or multiple nuclei, and siphonocladous species, which are multinucleate and multicellular. These diverse cellular organizations raise a number of questions about the evolutionary and molecular mechanisms underlying complex organismal morphology in the green plants. Importantly, how does morphological patterning arise in giant coenocytes, and do nuclei, analogous to cells in multicellular organisms, take on distinct somatic and germline identities? Here, we comparatively explore examples of patterning and differentiation in diverse coenocytic and single-cell organisms and discuss possible mechanisms of development and nuclear differentiation in the siphonous algae.

Metabolic and co-expression network-based analyses associated with nitrate response in rice

BACKGROUND

Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions.

RESULTS

A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. limiting N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation.

CONCLUSIONS

The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops.

The challenges of commercializing second-generation transgenic crop traits necessitate the development of international public sector research infrastructure

It has been 30 years since the first transformation of a gene into a plant species, and since that time a number of biotechnology products have been developed, with the most important being insect- and herbicide-resistant crops. The development of second-generation products, including nutrient use efficiency and tolerance to important environmental stressors such as drought, has, up to this time, been less successful. This is in part due to the inherent complexities of these traits and in part due to limitations in research infrastructure necessary for public sector researchers to test their best ideas. Here we discuss lessons from previous work in the generation of the first-generation traits, as well as work from our labs and others on identifying genes for nitrogen use efficiency. We then describe some of the issues that have impeded rapid progress in this area. Finally, we propose the type of public sector organization that we feel is necessary to make advances in important second-generation traits such as nitrogen use efficiency.

Transcript and metabolite signature of maize source leaves suggests a link between transitory starch to sucrose balance and the autonomous floral transition

Little is known about the nature of floral inductive cues in day-neutral plants that are insensitive to photoperiod variations and, therefore, rely on endogenous signals to initiate reproductive growth. The INDETERMINATE1 (ID1) transcription factor is a key regulator of the transition to flowering in day-neutral maize. The ID1 gene is expressed exclusively in developing leaves, where it controls the production or transmission of leaf-derived florigenic signals. Florigen-producing source leaves were compared with mature leaves of late-flowering id1 plants, and metabolite and gene expression differences associated with the floral transition in maize were observed. While id1 mutants have a similar capacity for photosynthesis to wild-type siblings, id1 source leaves show quantitative differences in carbohydrate allocation prior to the floral transition stage, with a marked increase in sucrose and other soluble sugars, accompanied by a decrease in tricarboxylic acid (TCA) cycle organic acids. Importantly, source leaves of autonomous-flowering maize are typified by a higher transitory starch to sucrose ratio and a transcript profile enriched for sucrose synthesis and starch metabolism-related gene function. Finally, similar changes in transitory starch and sucrose are not observed in teosinte, the tropical progenitor of maize that requires short-day photoperiods to induce flowering. Together, these data define a transcript and metabolite signature associated with the autonomous floral transition in temperate maize leaves.

ZCN8 encodes a potential orthologue of Arabidopsis FT florigen that integrates both endogenous and photoperiod flowering signals in maize

Higher plants use multiple perceptive measures to coordinate flowering time with environmental and endogenous cues. Physiological studies show that florigen is a mobile factor that transmits floral inductive signals from the leaf to the shoot apex. Arabidopsis FT protein is widely regarded as the archetype florigen found in diverse plant species, particularly in plants that use inductive photoperiods to flower. Recently, a large family of FT homologues in maize, the Zea CENTRORADIALIS (ZCN) genes, was described, suggesting that maize also contains FT-related proteins that act as a florigen. The product of one member of this large family, ZCN8, has several attributes that make it a good candidate as a maize florigen. Mechanisms underlying the floral transition in maize are less well understood than those of other species, partly because flowering in temperate maize is dependent largely on endogenous signals. The maize indeterminate1 (id1) gene is an important regulator of maize autonomous flowering that acts in leaves to mediate the transmission or production of florigenic signals. This study finds that id1 acts upstream of ZCN8 to control its expression, suggesting a possible new link to flowering in day-neutral maize. Moreover, in teosinte, a tropical progenitor of maize that requires short-day photoperiods to induce flowering, ZCN8 is highly up-regulated in leaves under inductive photoperiods. Finally, vascular-specific expression of ZCN8 in Arabidopsis complements the ft-1 mutation, demonstrating that leaf-specific expression of ZCN8 can induce flowering. These results suggest that ZCN8 may encode a florigen that integrates both endogenous and environmental signals in maize.

Expression differences between normal and indeterminate1 maize suggest downstream targets of ID1, a floral transition regulator in maize

The INDETERMINATE1 (ID1) transcription factor is a key regulator of the transition to flowering in maize. ID1 is expressed in immature leaves where it controls the production or transmission of leaf-derived florigenic signals. Loss-of-function id1 mutants make many more leaves than normal plants and produce aberrant flowers; however, they exhibit no obvious developmental defects in early growth stages. A maize oligonucleotide microarray was used to assess the molecular differences between immature leaves of wild-type and id1 mutant plants prior to the floral transition. This analysis revealed 55 genes with a significant 2-fold difference in expression; 22 are down-regulated and 33 are up-regulated in id1 mutants. Most prominent is a novel family of three beta-glucosidase genes that are most closely related to sorghum dhurrinases. These genes, termed Zmdhr1, Zmdhr2, and Zmdhr3, are undetectable in immature leaves of id1 mutants and are expressed exclusively in normal immature leaves in a pattern identical to the ID1 gene. Other down-regulated genes include a group of four zinc finger protein-encoding genes that are unrelated to ID1. A significant number of genes up-regulated in id1 mutant immature leaves have potential roles in photosynthesis and carbon fixation, substantiating a possible connection between floral induction and assimilate partitioning. Finally, expression of these genes was compared in florally induced versus uninduced teosinte, a photoperiod-sensitive progenitor of day-neutral maize. Only a few genes showed expression differences, suggesting that ID1 acts in a novel autonomous floral induction pathway that is distinct from the photoperiod induction pathway.

The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants

BACKGROUND

The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation.

RESULTS

Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only.

CONCLUSION

Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein orthologs from rice and sorghum. These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.