Biology subjects

Combs-Giroir, R.

Publications and source records attributed to Combs-Giroir, R..

3 recordsLinked to original sources

bioRxiv2025

Population and adaptation history of 739 Thlaspi arvense natural accessions

Pennycress (Thlaspi arvense) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels--including aviation fuels. While domestication efforts are ongoing, a deeper understanding of the genetic architecture of traits is crucial for informing future breeding efforts. Here, we conducted the largest genomic and phenotypic survey of pennycress to date, analyzing 739 accessions collected across four continents. Leveraging whole-genome sequencing and field-collected phenotypes, we characterized the standing genetic variation underlying key agronomic traits and climate resilience. Our findings revealed multiple independent migration events to North America, with substantial genetic admixture. We identified homologs of Arabidopsis thaliana flowering-time genes that contribute to adaptation and demonstrated the agronomic benefits of winter-type pennycress. Furthermore, through multi-season field trials, we identified a genomic region containing a cluster of mTERF genes strongly associated with green canopy coverage, a critical trait for biomass retention and yield stability. These insights provide a genomic roadmap for accelerating pennycress domestication and improving its resilience to climate variability.

genomics↗

bioRxiv2024

Natural variation in physical responses to waterlogging across climate-diverse pennycress accessions

Fluctuations in flooding and differences in hydrological gradients affect the geographic distribution of plant species across ecosystems, resulting in the presence of adaptive traits in populations that confer enhanced fitness in flooded environments. Many winter annual crops, such as pennycress (Thlaspi arvense L.), are subjected to heavy precipitation events during their growing season, which are increasing in frequency due to climate change. Therefore, it is essential to identify pennycress accessions with natural variation in flooding resilience. In this study, we used climate modeling data to assess spring soil moisture levels in the geographic origins of 471 natural pennycress accessions. We selected 34 accessions with variations in predicted soil moisture to test survivability under prolonged waterlogging at the rosette stage. This identified variation in waterlogging tolerance, where six accessions had 0% survivability and nine accessions had 100% survivability. It took at least seven weeks for the first accessions to die under waterlogging, indicating that pennycress is hardy to prolonged waterlogging at the vegetative stage. Furthermore, we chose three "susceptible" and five "tolerant" accessions to waterlog for one week at the reproductive stage, the growth stage aligned with heavy spring rainfall. Six accessions had significantly reduced seed weight at maturity after recovery from waterlogging, and two accessions had minimal impacts on growth and seed yield after waterlogging. These two accessions can be used in future studies to explore adaptive traits, such as changes in root characteristics, as well as the genetic variation that contributes to pennycress waterlogging tolerance.

plant biology↗

bioRxiv2024

Morpho-physiological and transcriptomic responses of field pennycress to waterlogging

Field pennycress (Thlaspi arvense) is a new biofuel winter annual crop with extreme cold hardiness and a short life cycle, enabling off-season integration into corn and soybean rotations across the Midwest. Pennycress fields are susceptible to winter snow melt and spring rainfall, leading to waterlogged soils. The objective of this research was to determine if waterlogging during the reproductive stage had a significant effect on gene expression, morphology, physiology, recovery, and yield of two pennycress lines (SP32-10 and MN106). In a controlled environment, total pod number, shoot/root dry weight, and total seed count/weight were significantly reduced in SP32-10 in response to waterlogging, whereas primary branch number, shoot dry weight, and single seed weight were significantly reduced in MN106. This indicated waterlogging had a greater negative impact on seed yield in SP32-10 than MN106. The number of differentially expressed genes (DEGs) between waterlogged and control roots were doubled in MN106 (3,424) compared to SP32-10 (1,767). Functional enrichment analysis of upregulated DEGs revealed Gene Ontology (GO) terms associated with hypoxia and decreased oxygen, with genes in these categories involved in alcoholic fermentation and glycolysis. Interestingly, MN106 waterlogged roots exhibited significant stronger upregulation of these genes than SP32-10. Additionally, downregulated DEGs revealed GO terms associated with cell wall biogenesis and secondary metabolite biogenesis, indicating suppressed growth and energy conservation. Together, these results reveal the reconfiguration of cellular and metabolic processes in response to the severe energy crisis invoked by waterlogging in pennycress.

plant biology↗