Biology subjects

Dardick, C.

Publications and source records attributed to Dardick, C..

8 recordsLinked to original sources

bioRxiv2026

Spatially resolved transcriptomics of poplar reveals tissue organization across shoot-associated organs

Poplar (Populus spp.) is a model for tree biology and a platform for engineering woody biomass, biofuels, biomaterials, and bioproducts. Many relevant traits depend on tissue position, developmental stage, and cell type, yet these spatial relationships are difficult to recover from bulk or single-cell transcriptomes. Here, we generated a spatial transcriptome atlas of Populus tremula x P. alba INRA 717-1B4 across the shoot apex, axillary bud, stem, and petiole. After quality control, the atlas retained 29,687 spatial spots from 45 tissue sections and detected 58,748 genes. Histology-guided clustering and marker analysis resolved meristematic, epidermal, cortical, vascular, and organ-specific domains. Cross-organ comparisons assessed whether published markers retained tissue-associated expression across different anatomical contexts and developmental stages, while de novo analysis identified additional domain-enriched candidates. As case studies of the utility of the atlas, we examined the emergence of trichome-associated programs in the shoot apex and adaxial - abaxial expression differences in petioles. A trichome identity score based on poplar markers from the single-cell shoot atlas peaked along the inferred meristem-to-primordium trajectory, revealing spatially localized expression of trichome-associated programs during early leaf development. Petiole expression differences were concentrated in the epidermis and cortex and involved polarity-associated, auxin-responsive, and cell-wall-remodeling genes, with distinct expression profiles across leaf positions. Together, these data provide a spatial reference for investigating tissue differentiation and developmental patterning in a transformable poplar genotype.

plant biology↗

bioRxiv2026

Benchmarking SNP-Calling Accuracy Against Known Citrus Pedigrees Reveals Pangenome Advantages Over Linear References

BackgroundPangenomes are a promising new approach to genomics that can reduce reference bias in genotyping, but the reliability of such a data model remains unclear in tracking variation across species. To test the utility of graph-based pangenomes for interspecific breeding, we developed a Minigraph-Cactus super-pangenome representing four Citrus species derived from the founder lines of a citrus breeding program. To benchmark SNP calling accuracy using graph and linear-based approaches, we performed whole genome short read sequencing for two sets of pedigreed progeny: 30 F1 hybrids and 244 advanced hybrids from an F1 crossed with a parent not included in the pangenome. ResultsThe linear approach yielded more SNP calls than the graph-based approach, however, both methods exhibited similar Mendelian Inheritance Error Rates (MIER) in a tool-dependent manner. Reconstruction of parental haplotype blocks in the advanced hybrids revealed a striking improvement in performance in the pangenome graph-based calls, suggesting MIER is vulnerable to error when reference bias influences both parental and progeny genotype calls. Masking of regions diverged from the reference path improved MIER accuracy metrics and haplotype block reconstruction in both the linear and graph-based SNP calls. ConclusionsIn non-model systems, inheritance patterns observed from pedigreed hybrids provide a framework for benchmarking variant-calling accuracy using pangenomes. SNP miscalls originating from diverged regions can falsely satisfy MIER filters, thus we recommend haplotype blocks. The inherent structure of the pangenome graph has promising applications for removing regions of unreliable mapping quality, which cannot otherwise be reliably removed using traditional filtering metrics.

genomics↗

bioRxiv2025

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

Oxford Nanopore Technologies (ONT) sequencing platforms have enabled scientists to generate sequence reads of 20 kilobase or more, which has facilitated the assembly of complete genomes. Nanopore sequencing involves recording the change in electrical signals as the DNA molecule transverses the pore. Converting this signal information into bases - a process called basecalling - is challenging and require the implementation of machine learning. The models developed for ONT basecallers have continually improved. However, the mean quality of the reads generated fall below a Phred score of 20 (99% accuracy), the target quality for high-quality genome assembly, when used on challenging plant samples. These low-quality base calls limit the ability to conduct de novo genome assembly, accurate phasing of haplotypes, and long-read genotyping. To overcome these shortcomings, we fine-tuned ONTs high accuracy basecalling model using Bonito, an AI-based deep learning basecaller, to develop crop-specific models for five important species in the Rosaceae family. These species include highly valuable tree crops such as apple, peach, pear, plum, and sweet cherry. Through the development of an automated training pipeline, we were able to achieve [~]14% higher mean and median basecall quality, and a [~]20% increase in total reads with Phred scores >15. These results were achieved without significantly affecting the read length N50s and total reads called. As a result, these new crop-specific models will enable members of the Rosaceae genomics community to produce higher quality ONT sequencing data. Furthermore, we are releasing our automated pipeline to facilitate others to train their own organism or crop-specific models.

genomics↗

bioRxiv2025

Improved genome assembly of double haploid Prunus persica siblings Lovell 2D and Lovell 5D and the peach NLRome

Prunus persica (peach) has long served as a model fruit tree for studying phenological events. It has a relatively small genome and exhibits tremendous plasticity in climate tolerances due to the high variation of chill requirements, bloom times, and fruit ripening times. The peach variety Lovell 2D was used to generate one of the first high-quality genome assemblies for a tree species, using Sanger sequencing of genetic-map ordered BAC clones. A key to the high quality of this early assembly was the use of a doubled haploid variety, which eliminates the challenges posed by mixed haplotypes. Here, we re-sequenced and assembled the Lovell 2D genome along with a doubled haploid sibling Lovell 5D using 3rd generation technologies. The resulting genomes were significantly more contiguous than the current Lovell 2D reference genome (ver2.0 updated in 2017) and are closer to the estimated total genome size for peach (265Mb). In addition, new gene, transposable element (TE), and Nucleotide-binding domain and Leucine-rich repeat receptor (NLR) annotations were performed to enhance the integrity and utility of the genome. These updated peach doubled-haploid reference assemblies will provide the research community with an improved reference genome for genomics-guided studies and breeding efforts.

genomics↗

bioRxiv2024

Working smarter, not harder: silencing LAZY1 in Prunus domestica causes outward, wandering branch orientations with commercial and ornamental applications.

Controlling branch orientation is a central challenge in tree fruit production, as it impacts factors as diverse as light interception, pesticide use, fruit quality, yield, and labor costs. In an attempt to modify branch orientation, growers use many different management practices, including tying branches to wires or applying growth regulator sprays. However, these practices are often costly and ineffective. In contrast, altering the expression of genes that control branch angles and orientations would permanently optimize tree architecture with minimal management inputs. One gene implicated in branch angle control is LAZY1, which promotes upward branch growth in response to gravity. We used an antisense vector to silence LAZY1 in plum (Prunus domestica). We found that these LAZY1-silenced lines have significantly increased branch and petiole angles. In addition, they lack apical dominance and display a "wandering" or weeping branch trajectory. Given these phenotypes, we assessed whether the strength or stiffness of the branches were compromised. No differences were observed in new growth. While the wood of first-year LAZY1-silenced branches was more flexible and weaker than the control, the strength and stiffness of the branches were not decreased because branch diameter is increased. Finally, we evaluated the utility of LAZY1-silenced trees for two planar orchard systems, training them in super slender axe and espalier. LAZY1-silenced trees had more open canopies and were easier to constrain to the trellis height. This work illustrates the power of manipulating gene expression to optimize plant architecture for each horticultural application.

plant biology↗

bioRxiv2021

Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

plant biology↗

bioRxiv2020

IGT/LAZY family genes are differentially influenced by light signals and collectively required for light-induced changes to branch angle

Plants adjust their growth orientations in response to environmental signals such as light and gravity in order to optimize photosynthesis and access to nutrients. However, given the fixed nature of gravity, understanding how light and gravity signals are integrated is challenging. Branch orientation, or gravitropic set point angle, is a key aspect of plant architecture, set with respect to gravity and shown to be altered by changes in light conditions. The IGT gene family, also known as the LAZY family, contains important components for branch angle and gravity responses, including three gene clades: LAZY, DEEPER ROOTING (DRO), and TILLER ANGLE CONTROL (TAC). LAZY and DRO genes promote upward branch orientations downstream of amyloplast sedimentation, and upstream of auxin redistribution in response to gravity. In contrast, TAC1 promotes downward branch angles in response to photosynthetic signals. Here, we investigated the influence of different light signaling pathways on LAZY and DRO gene expression, and their role in light regulation of branch angle responses. We found differential effects of continuous light and dark, circadian clock, photoreceptor-mediated signaling, and photosynthetic signals on LAZY and DRO gene expression. Phenotypic analysis revealed that LAZY and DRO genes are collectively required for branch angle responses to light. HighlightLAZY and DRO gene expression responds differentially to changes in light regime and signaling. Loss of multiple LAZY and DRO genes leads to loss of branch angle response to light.

plant biology↗

bioRxiv2018

Branch angle responses to photosynthesis are partially dependent on TILLER ANGLE CONTROL 1

Light serves as an important environmental cue in regulating plant architecture. Previous work had demonstrated that both photoreceptor-mediated signaling and photosynthesis play a role in determining the orientation of plant organs. TILLER ANGLE CONTROL 1 (TAC1) was recently shown to function in setting the orientation of lateral branches in diverse plant species, but the degree to which it plays a role in light-mediated phenotypes is unknown. Here, we demonstrated that TAC1 expression was light dependent, as expression was lost under dark or far-red growth conditions, but did not display any clear diurnal rhythm. Loss of TAC1 in the dark was gradual, and experiments with photoreceptor mutants indicated this was not dependent upon Red/Far-Red or Blue light signaling, but partially required the signaling integrator CONSTITUTIVE PHOTOMORPHGENESIS 1 (COP1). Over-expression of TAC1 partially prevented the narrowing of branch angles in the dark or under Far-Red light. Treatment with the carotenoid biosynthesis inhibitor Norflurazon or the PSII inhibitor DCMU led to loss of TAC1 expression similar to dark or far-red conditions, but surprisingly expression increased in response to the PSI inhibitor Paraquat. Our results indicate that TAC1 plays an important role in modulating plant architecture in response to photosynthetic signals.\n\nHIGHLIGHTBranch angles narrow in darkness or under far-red light. This response is partially mediated by TAC1 which responds to photosynthetic signals, providing a key link between photosynthesis and plant architecture.

plant biology↗