Biology subjects

Hoefer, M.

Publications and source records attributed to Hoefer, M..

5 recordsLinked to original sources

bioRxiv2025

High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'

Malus baccata Jackii has been observed to exhibit multiple disease resistances, thus rendering it a promising source for breeding new disease-resistant apple cultivars. Here, we present the first haplotype-resolved genome assembly and annotation of this genotype, achieved by integrating PacBio HiFi sequencing, Hi-C, and mRNA sequencing data with a range of bioinformatic tools and databases. The genome assembly comprises 17 pseudochromosomes with total scaffold lengths of 654.6 Mb and 637.5 Mb for the two haplotypes, respectively. Both haplotypes have scaffold N50 values exceeding 30 Mb, with 42,441 and 46,507 predicted genes, of which 99.9% were successfully annotated. The high quality of this genome is supported by BUSCO analysis values exceeding 97.5% for both haplotypes. This comprehensive dataset is well suited for a wide range of future genomic analyses and is anticipated to benefit apple breeding, particularly in the context of enhancing disease resistance.

genomics↗

bioRxiv2024

Genome-Wide Association Study of Metabolic Traits in the Duckweed Spirodela polyrhiza

The exceptionally high growth rate and high contents of flavonoids make the giant duckweed Spirodela polyrhiza (L.) Schleid. (Arales: Lemnaceae) an ideal organism for food production and metabolic engineering. To facilitate this, identification of the genetic basis underlying growth and metabolic traits is essential. Here, we characterized the genetics underpinning the growth and contents of 42 metabolites in S. polyrhiza using a genome-wide association (GWA) approach. We found that biomass positively correlates with contents of many free amino acids, including L-Glutamine, L-Tryptophane and L-Serine, but negatively correlates with many specialized metabolites, such as flavonoids. GWA analysis showed that several candidate genes were simultaneously associated with several metabolic traits, qualifying them as targets for growth manipulation and metabolic engineering. Together, this study provides insights into the metabolic diversity of S. polyrhiza and its underlying genetic architecture, paving the way for industrial applications of this plant via targeted breeding or genetic engineering.

plant biology↗

bioRxiv2023

Occurrence of strawberry viruses in Fragaria germplasm and evaluation of cryotherapy as an eradication method for strawberry viruses

Strawberry plants are highly susceptible to viral infections, which pose significant threats to global strawberry production. This study aims to explore the efficacy of in vitro initiation and cryopreservation of shoot tips as a potential strategy for eradicating strawberry viruses. We tested plants for four important strawberry viruses namely: SMoV, SCV, SMEY and SVBV. The plants, which tested positive were either cultivated as in vitro cultures then returned to a green house or field collection cultivation, or treated by cryopreservation. After cryopreservation, the plants were cultivated again in vitro and then in the green house or field. The viruses were detected within each propagation step. Significant eradication effects were found for SMoV and SCV when plants were treated by in vitro initiation or with cryotherapy, but not for SMEY or SVBV. The results of this study show that cryotherapy or in vitro initiation can lead to the elimination of strawberry viruses, but the kind of therapy appears to depend on the type of virus.

plant biology↗

bioRxiv2021

Zooming into the genomic vicinity of the major locus for vicine and convicine in faba bean (Vicia faba L.)

The versatility of faba bean (Vicia faba L.) seed as valuable protein feed is hampered by its relatively high level of the compounds vicine and convicine (VC), which are antinutritive factors in poultry and further non-ruminant feed. The objective here was to develop the first-ever genetically low-VC winter faba bean. Hence, the low VC allele vc-, that should be the basis of a known, major locus for VC, need verification and molecular identification and be based on appropriately developed DNA-markers; the low VC feature awaited its transfer into the high-performing winter faba bean germplams. Based on bi-parental F2-families and isogenic lines, we thus developed highly useful SNP markers exploiting transcriptomic data. Furthermore, we fine-mapped and, based on synteny to Medicago truncatula and Cicer arietinum, we identified a candidate gene for the VC locus. A novel, genetically low VC winter faba bean population was bred. The path is now well-prepared for further marker-based breeding progress.

genetics↗

bioRxiv2021

A clonal fresh water plants acquires transgenerational stress resistance under recurring copper excess

Although non-genetic inheritance is thought to play an important role in plant ecology and evolution, evidence for adaptive transgenerational plasticity is scarce. Here, we investigated the consequences of copper excess on offspring defences and fitness in the giant duckweed (Spirodela polyrhiza) across multiple asexual generations. We found that exposing large monoclonal populations (>10,000 individuals) for 30 generations to copper excess decreased plant fitness during the first few generations but increased their fitness in consecutive generations under recurring stress when plants were grown for 5 generations under control conditions prior recurring conditions. Similarly, propagating individual plants as single descendants for 5 or 10 generations under copper excess decreased plant fitness when 5 generations and improved plant fitness when 10 generations passed between initial and recurring stress; thus, transgenerational stress responses likely contributed to the observed variations in offspring fitness of long-term copper exposed populations. Fitness benefits under recurring stress were partially associated with avoidance of excessive copper accumulation, which in turn correlated with transgenerationally modified flavonoid concentrations. Taken together, these data demonstrate time-dependent adaptive transgenerational responses under recurring stress, which highlights the importance of non-genetic inheritance for plant ecology and evolution.

ecology↗