Biology subjects

Dockter, C.

Publications and source records attributed to Dockter, C..

6 recordsLinked to original sources

bioRxiv2026

Temporal genomic imprinting regulates grain filling in barley

In cereals, the persistent endosperm accumulates starch and storage proteins, making their grains a major source of food and feed. Early grain development is epigenetically controlled through the parent-of-origin-specific expression of imprinted genes in the endosperm that regulate endosperm proliferation, nutrient accumulation and embryo nourishment. Imprinted genes have been identified in several major cereals, and a few have been functionally characterized. However, it is unclear how imprinted genes regulate the accumulation of storage compounds in cereal grains. Through spatiotemporal transcriptome analysis of 255 imprinted genes in barley (Hordeum vulgare), we identify endosperm transfer cells in grains as a hotspot of expression of imprinted genes. Furthermore, we show that transcription factor LYS3 dynamically regulates grain filling in barley through early expression of the maternal allele, followed by partial activation of the paternal allele.

plant biology↗

bioRxiv2025

Environmental DNA Reveals Reykjavik's Human and Ecological History

Iceland was among the last large islands settled by humans, with colonization (Landnam) in the late 9th century CE (Common Era) and is often portrayed as an ecological disaster driven by the Norse settlers. Here, we revisit this narrative through environmental DNA (eDNA) and multiproxy analyses of sediment cores from Lake Tjornin in central Reykjavik, one of Icelands earliest and longest-occupied settlements. Originally a marine embayment, Tjornin became a freshwater lake around 660 CE. Our record reveals a human presence decades before the long-accepted arrival date of 877 CE, marked by the Landnam volcanic tephra. Early settlement brought livestock, barley cultivation, and other introduced taxa that enhanced nutrient cycling and unexpectedly increased local biodiversity. Contrary to the conventional view of rapid deforestation, eDNA shows that birch and willow expanded during the settlement period, likely supported by deliberate management. Pronounced ecological and land use shifts occurred after 1200 CE, but these were coeval with the Little Ice Age cooling, compounded by volcanic eruptions, storm surges, and plague, rather than anthropogenic degradation. Crop cultivation ceased, arboreal taxa retracted, and grazing pressure maintained open landscapes. Even more profound ecological changes came after c. 1750 CE with urbanization and industrialization, as wastewater discharge, heavy-metal pollution, and fossil fuel use reshaped Tjornins ecosystem. These findings challenge the prevailing model of Norse-induced environmental collapse, revealing instead a dynamic human-environment relationship shaped by both cultural practices and external stressors. By applying eDNA to a long-occupied urban catchment, we demonstrate the power of genomic methods to refine settlement chronologies, reassess ecological baselines and changes, and integrate natural and cultural histories. This approach offers a model for revisiting human-environment interactions in urban centers worldwide.

genomics↗

bioRxiv2025

Post-Domestication selection of MKK3 Shaped Seed Dormancy and End-Use Traits in Barley

Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crop plants (1). In cereals, shortening dormancy provides rapid and even post-harvest germination, but increases the risk of weather-induced pre-harvest sprouting (PHS) with harvest losses estimated at beyond 1 billion USD a year (2, 3, 4). Our understanding of how, why, when and where diversification of cereal dormancy arose is fragmentary. Here, we show in the founder cereal crop barley (Hordeum vulgare) that the Mitogen-Activated Protein Kinase (MAPK) pathway regulates dormancy primarily through a mosaic of locus haplotypes comprising copy-number variation and inherent kinase activity of Mitogen-activated protein kinase kinase 3 (MKK3). We provide evidence supporting the historical selection of specific MKK3 haplotypes that shape dormancy levels according to changing climatic pressures. Understanding the regulatory landscape of MKK3 provides a genetic framework to balance short grain dormancy and PHS-avoidance during a period of rapid climate change.

plant biology↗

bioRxiv2024

Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at [~]9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

genomics↗

bioRxiv2024

eProbe: a capture probe design toolkit for genetic diversity reconstructions from ancient environmental DNA

Ancient environmental DNA (aeDNA) is now commonly used in paleoecology and evolutionary ecology, yet due to difficulties in gaining sufficient genome coverage on individual species from metagenome data, its genetic perspectives remain largely uninvestigated. Hybridization capture has proven as an effective approach for enriching the DNA of target species, thus increasing the genome coverage of sequencing data and enabling population and evolutionary genetics analysis. However, to date there is no tool available for designing capture probe sets tailored for aeDNA based population genetics. Here we present eProbe, an efficient, flexible and easy-to-use program toolkit that provides a complete workflow for capture probe design, assessment and validation. By benchmarking a probe set for foxtail millet, an annual grass, made by the eProbe workflow, we demonstrate a remarkable increase of capturing efficiency, with the target taxa recovery rate improved by 577-fold, and the genome coverage achieved by soil capture-sequencing data even higher than data directly shotgun sequenced from the plant tissues. Probes that underwent our filtering panels show notably higher efficiency. The capture sequencing data enabled accurate population and evolutionary genetic analysis, by effectively inferring the fine-scale genetic structures and patterns, as well as the genotypes on functional genes.

bioinformatics↗

bioRxiv2021

FIND-IT: Ultrafast mining of genome diversity

Novel crop improvement methodologies, including the exploitation of natural genetic variation, are urgently required to feed our rapidly growing human population in the context of global climate change. Here we describe a Fast Identification of Nucleotide variants by DigITal PCR (FIND-IT) method for the rapid identification of pre-targeted genetic variants or rare alleles in large genomic populations. Libraries of 500,000 individuals can be screened and desired variants isolated within two weeks. FIND-IT is widely applicable for mining valuable diversity in any genomic population, including elite breeding and wild germplasm collections. The method provides single nucleotide resolution that has been validated by identifying and isolating knockout lines, non-synonymous codon changes and variants of miRNA and transcription factor binding sites in the agronomically important crop barley. In contrast to existing methods, FIND-IT does not require transformation, cloning or enzymatic steps, and is exempt from GMO regulations. Thus, FIND-IT can be applied immediately to elite crop cultivars and can be tailored to minimize or eliminate time-consuming backcrossing requirements.

genetics↗