Biology subjects

Marks, M. D.

Publications and source records attributed to Marks, M. D..

6 recordsLinked to original sources

bioRxiv2026

Characterization of genetically effective cells and EMS mutagenesis on the novel winter oil seed Pennycress (Thlaspi arvense)

Pennycress (Thlaspi arvense L.) is an intermediate winter oilseed crop that has only recently been domesticated for agronomic use. Improving agronomic traits requires sources of genetic variation, and mutagenesis is frequently used to help overcome the limitations of natural populations. We investigate the impact of Ethyl methanesulfonate (EMS) on genetically effective cells (GECs) to characterize the intra-individual genetic variation of EMS mutagenesis in pennycress. We identified that pennycress contains at least 4 GECs which, when treated with EMS, create unique mutations across different branches within the same individual plant. We then propagated the M2 plants for whole genome sequencing, providing extensive characterization of the EMS mutation profile and developing a gene index as a resource for future reverse genetic screenings. Article SummaryPennycress is an emerging winter oil seed crop in the American Midwest. Domestication efforts have advanced rapidly through a combination of genetic techniques. One of the most successful methods has been the use of a mutant gene index, a large collection of pennycress seed where new genetic variation has been created through Ethyl methanesulfonate (EMS). EMS mutations are not uniform however, and a single treated seed can have wide genetic variation within the resulting plant. We investigate the role of genetically effective cells on EMS variation, and present the full EMS population as a resource for further pennycress domestication efforts.

genomics↗

bioRxiv2025

Acute EtOH enhances septohippocampal coordination but disrupts intrinsic hippocampal theta dynamics during foraging

Theta oscillations - rhythmic patterns of synchronous activity within discrete brain regions - are known to support memory, navigation, and behavioral coordination, and are sensitive to pharmacological manipulation. Acute ethanol (EtOH) exposure has been shown to alter theta oscillations, but its effects on transient theta bursts and cross- regional coordination during naturalistic behavior remain unclear. We recorded local field potentials (LFPs) from the medial septum (MS), hippocampal Cornu Ammonis 1 (CA1), and medial prefrontal cortex (mPFC) in freely foraging mice following intraperitoneal injection of EtOH (1.5 g/kg) or saline. We analyzed spectral power, theta burst dynamics, phase, and lag timing. Burst features from CA1 were used to train a machine learning classifier to predict session condition. EtOH impaired locomotion and reduced goal-directed behaviors, particularly early in the session. In CA1, theta power shifted toward lower frequencies and lagged coherence declined. EtOH increased the frequency but reduced the duration of theta bursts in CA1, and in MS, only burst count increased. EtOH enhanced the temporal alignment of MS-CA1 burst pairs. Phase- locking between CA1 and MS during coupled bursts remained present but showed altered structure. Our classifier achieved robust performance using burst features such as skew and entropy, and reliably distinguished treatment conditions. EtOH modulates septohippocampal dynamics by altering the timing and structure of theta bursts. These results suggest that burst-level features are sensitive markers of EtOHs circuit-level effects during naturalistic behavior.

neuroscience↗

bioRxiv2025

Creating a new oilseed crop, pennycress, by combining key domestication traits using CRISPR genome editing

Considerable offseason farmland lays fallow because there are few crops that can profitably fit between primary crops. To remedy, we employed CRISPR genome editing to the freeze-tolerant, rapid cycling wild Brassica, Thlaspi arvense L. (field pennycress). High-yielding domesticated pennycress varieties were created having seed compositions comparable to "double low" canola (low erucic acid and glucosinolate). Seed glucosinolate content was reduced 75 % by combining mutations in R2R3-MYB (MYB28) and bHLH MYC (MYC3) transcription factors. Pennycress weediness was greatly reduced by knockout of the bHLH transcription factor TRANSPARENT TESTA8 (TT8), lowering seed dormancy and seed coat protections thereby mitigating pennycress re-emergence in fields. Domesticated pennycress offers farmers a profitable, low-carbon-intensity intermediate crop that confers ecosystem benefits while producing grain for renewable fuels and enhanced food security.

genetics↗

bioRxiv2022

Facultative winter accession of Camelina sativa (L. Crantz) with early maturity contributes to understanding of the role of FLOWERING LOCUS C in camelina flowering

Camelina is being developed as a winter oilseed cover crop. Early flowering and maturity are desired traits in camelina to allow for relay planting or seeding of a summer annual following camelina harvest. Here we report that while all winter biotype accessions of camelina have a functional allele of FLOWERING LOCUS C (FLC) on chromosome 20, there are also at least 20 previously characterized spring biotype accessions that have a functional FLC allele at this locus. We observed this by analyzing 75 accessions (67 spring type, one facultative, and seven winter type) that were resequenced by Li et al., (2020) as well as 21 additional accessions for this analysis. This discovery will inform marker assisted selection efforts that are underway to increase genetic variation in the genetically narrow base of winter camelina germplasm. Furthermore, we optimized a KASP genotyping approach that effectively differentiates the presence of either the functional or subfunctional FLC allele on chromosome 20. These analyses identified a facultative winter biotype accession of camelina (PI650163-1, winter hardy with subfunctional chromosome 20 FLC allele) that has demonstrated two years of winter-hardiness and has flowered at least a week earlier than the common winter accession, Joelle. A bioinformatics approach to cytotype analysis in camelina also provided more precise categorizing of camelina accessions in the USDA-NPGS germplasm into 2n=38 and 2n=40 cytotypes. Early maturing winter-hardy camelina will reduce stress on a subsequent soybean crop and improve total cropping system yields when camelina and soybean are grown sequentially in the same season on the same land.

plant biology↗

bioRxiv2019

Progress toward the identification and stacking of crucial domestication traits in pennycress

The oilseed species Thlaspi arvense (pennycress) is being domesticated as a new crop that can provide both important ecosystem services and intensify farmland output. Through the use of high throughput sequencing and phenotyping, along with classical mutagenesis key traits needed for pennycress domestication have been identified. Domestication traits identified herein include reduced pod shatter, early maturity, reduced seed glucosinolate levels, and improved oil fatty acid content. By taking advantage of pennycress close genetic relationship with Arabidopsis thaliana, the causative mutations responsible for each of these traits have been identified. These mutations have been used to develop molecular markers to begin to stack the traits into individual lines.

plant biology↗

bioRxiv2017

Spring flowering habit in field pennycress (Thlaspi arvense) has arisen multiple independent times

- Pennycress (Thlaspi arvense L.) is currently being developed as a new cold-season oilseed crop. Like many Brassicaceae, pennycress can exhibit either a winter or spring annual phenotype. In Arabidopsis, mutations in negative regulators of flowering, including FLOWERING LOCUS C (FLC) and FRIGIDA can cause the transition to a spring annual habit. The genetics underlying the difference between spring and winter annual pennycress are currently unknown.\n\n- Using whole genome sequencing across wild spring annual pennycress accessions, co-segregation analyses, and comparative genomics approaches, we identify new alleles of TaFLC and explore their geographic distribution.\n\n- We report that loss of function mutations in TaFLC confer the spring annual phenotype in pennycress. We have also identified four natural alleles of TaFLC that confer a spring annual growth habit. The two spring annual FLC alleles present in European accessions were only identified in accessions collected in Montana, USA.\n\n- In pennycress, the spring annual habit has arisen several independent times. Accessions harboring the two European alleles were introduced to North America, likely after the species became a widespread on the continent. These findings provide new information on the natural history of the introduction and spread of the spring annual phenotype in pennycress.

plant biology↗