Biology subjects

Frels, K.

Publications and source records attributed to Frels, K..

4 recordsLinked to original sources

bioRxiv2025

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

O_LIEukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. C_LIO_LIHere, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the speciess current genetic diversity to catalogue variation in genome structure and content. C_LIO_LIAcross this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. C_LIO_LIOur findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop. C_LI

genomics↗

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↗

bioRxiv2021

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation, and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe small RNAs, pseudogenes, and transposable elements, and highlight tissue specific expression and methylation patterns. Resequencing of forty wild accessions provides insights into genome-wide genetic variation as well as QTL regions for flowering time and a seedling color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

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↗