Biology subjects

Dorn, K. M.

Publications and source records attributed to Dorn, K. M..

5 recordsLinked to original sources

bioRxiv2026

Genome and methylome of the root crop table beet (Beta vulgaris)

Table beet (Beta vulgaris subsp. vulgaris var. vulgaris), also known as red beet, garden beet, or beetroot, is an important crop with both nutritional and agricultural value, yet high-quality genomic resources for this taxon are limited. We present the chromosome-scale genome assembly RefTab-1 based on PacBio and Hi-C data of the inbred table beet genotype W357B. The assembly has a size of 668.6 Mbp and an N50 of 72 Mbp, with 96% of the assembly anchored to nine pseudo-chromosomes. We annotated 64% repetitive DNA, 24,863 protein-coding genes, and 10,405 non-coding RNA loci including a 5S rRNA cluster on chromosome 4. Genome-wide methylation profiling using EM-seq revealed high levels of cytosine methylation in repeats and context-specific methylation in gene bodies and promoters. We propose three terpene synthase candidate genes based on functional annotation and based on their location near a genetic marker on chromosome 8 previously associated with geosmin concentration, responsible for the earthy aroma of table beet. Comparative analysis with sugar beet indicated overall structural conservation and a 9 Mbp inversion on chromosome 9. These high-quality resources for table beet will enhance genetic, epigenetic, and comparative studies in Beta vulgaris, advancing beet biology and breeding programs.

genomics↗

bioRxiv2026

Evolutionary and Deep Learning Models Highlight Deleterious Mutations Behind the History of Sugar Beet Breeding

Sugar beet (Beta vulgaris ssp. vulgaris) is a major global source of sucrose. Domestication and a history of breeding have shaped the distribution of deleterious mutations across the genome. Accurately resolving these variants offers a compelling avenue to accelerate crop improvement through breeding or genetic engineering. We combine three scales of evolutionary time: protein conservation defined by conservation across all living organisms (SIFT), angiosperm-wide DNA language deep learning model (PlantCaduceus), and fine-scale evolutionary rates from Amaranthaceae plant family sequence alignments to define a high-confidence set of deleterious variants enriched for alleles under negative selection. We then evaluate these deleterious mutations across a multi-study panel of more than 1,900 whole-genome sequenced wild and cultivated beet accessions. We found that domesticated beet accessions exhibit higher deleterious load relative to wild maritima, yet sugar beet carries significantly fewer deleterious variants than other cultivated beet crops. Historical trends show a decline in genetic load across more than a century of sugar beet entries in the U.S. NPGS, reflecting sustained purging during modern breeding. This combinatorial method of leveraging evolutionary conservation reveals how deleterious mutations have shaped sugar beet breeding history and provides potential targets for future selection, causal-variant discovery, and precision genome engineering.

genomics↗

bioRxiv2020

Patterns of genetic variation in a prairie wildflower, Silphium integrifolium, suggest a non-prairie origin and untapped variation available for improved breeding.

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPremiseC_ST_ABSUnderstanding the relationship between genetic structure and geography provides information about a species evolutionary history and can be useful to breeders interested in de novo domestication. The North American prairie is especially interesting because of its relatively recent origin and subsequent dramatic fragmentation and degradation. Silphium integrifolium is an iconic perennial American prairie wildflower targeted for domestication as an oilseed crop. Germplasm in the existing breeding program is derived from accessions collected in restricted geographic regions. We present the first application of population genetic data in this species to address the following goals (1) improve breeding programs by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of selection during range expansion. MethodsWe developed a reference transcriptome as a genotyping reference for samples from throughout the species range. Population genetic analyses were used to describe the distribution of genetic variation and demographic modeling was used to characterize potential processes that shaped variation. Outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of selection. Key resultsGenetic variation partitions samples into three geographic clusters. Patterns of variation and demographic modeling suggest that the species origin is in the American southeast. Breeding program accessions are from the region with lowest observed genetic variation. ConclusionsThis iconic prairie species did not originate within the modern prairie. Breeding programs can be improved by including accessions from outside of the germplasm founding region, which has relatively little variation. The geographic structuring coupled with the identified targets and drivers of adaptation can guide collecting efforts towards populations with beneficial agronomic traits.

evolutionary biology↗

bioRxiv2018

Transcriptome assembly and annotation of johnsongrass (Sorghum halepense) rhizomes identifies candidate rhizome specific genes

Rhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum halepense (johnsongrass) is an aggressive perennial grass that relies on a robust rhizome system to persist through winters and reproduce asexually from its rootstock nodes. This study aimed to sequence and assemble expressed transcripts within the johnsongrass rhizome. A de novo transcriptome assembly was generated from a single johnsongrass rhizome meristem tissue sample. A total of 141,176 probable protein-coding sequences from the assembly were identified and assigned gene ontology terms using Blast2GO. The johnsongrass assembly was compared to Sorghum bicolor, a related non-rhizomatous species, along with an assembly of similar rhizome tissue from the perennial grain crop Thinopyrum intermedium. The presence/absence analysis yielded a set of 259 johnsongrass contigs that are likely associated with rhizome development.

genomics↗

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↗