Niels A. Müller
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View article: Machine learning techniques for continuous genetic assignment of geographic origin of forest trees
Machine learning techniques for continuous genetic assignment of geographic origin of forest trees Open
Origin tracking is important to ensure use of the right seed source and trade with legally harvested timber. Additionally, it can help to reconstruct human-caused historical long-distance seed transfer and to spot mislabelling in forest fi…
View article: Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs
Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs Open
Common ash, Fraxinus excelsior , is threatened by the invasive pathogen Hymenoscyphus fraxineus , which causes ash dieback. The pathogen is rapidly spreading throughout Europe with severe ecological and economic consequences. Multiple stud…
View article: High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar Open
Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating adv…
View article: High-molecular-weight DNA extraction for broadleaved and conifer tree species
High-molecular-weight DNA extraction for broadleaved and conifer tree species Open
Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficien…
View article: A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs
A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs Open
Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughp…
View article: Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs
Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs Open
Common ash, Fraxinus excelsior , is threatened by the invasive pathogen Hymenoscyphus fraxineus , which causes ash dieback. The pathogen is rapidly spreading throughout Europe with severe ecological and economic consequences. Multiple stud…
View article: Advanced marker-assisted selection versus genomic selection in breeding programs
Advanced marker-assisted selection versus genomic selection in breeding programs Open
Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughp…
View article: <i>SNPscan breeder</i> – a computer program to test genomic tools in breeding programs
<i>SNPscan breeder</i> – a computer program to test genomic tools in breeding programs Open
SNPscan breeder is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria,…
View article: Sex determination and sex chromosome evolution in land plants
Sex determination and sex chromosome evolution in land plants Open
Linnaeus's very first opus, written when he was 22 years old, dealt with the analogy that exists between plants and animals in how they ‘propagate their species’, and a revised version with a plate depicting the union of male and female Me…
View article: ARR17 controls dioecy in <i>Populus</i> by repressing B-class MADS-box gene expression
ARR17 controls dioecy in <i>Populus</i> by repressing B-class MADS-box gene expression Open
The number of dioecious species for which the genetic basis of sex determination has been resolved is rapidly increasing. Nevertheless, the molecular mechanisms downstream of the sex determinants remain largely elusive. Here, by RNA-sequen…
View article: Supplementary Tables from ARR17 controls dioecy in <i>Populus</i> by repressing B-class MADS-box gene expression
Supplementary Tables from ARR17 controls dioecy in <i>Populus</i> by repressing B-class MADS-box gene expression Open
Supplementary Tables 1-7
View article: Whole‐genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility
Whole‐genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility Open
Whole‐genome sequencing of non‐model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological…
View article: Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription
Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription Open
Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA Polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA, and a divergent non-coding (DNC) transcript …
View article: The Diversity and Dynamics of Sex Determination in Dioecious Plants
The Diversity and Dynamics of Sex Determination in Dioecious Plants Open
The diversity of inflorescences among flowering plants is captivating. Such charm is not only due to the variety of sizes, shapes, colors, and flowers displayed, but also to the range of reproductive systems. For instance, hermaphrodites o…
View article: The genetic basis of sex determination in <i>Populus</i> provides molecular markers across the genus and indicates convergent evolution
The genetic basis of sex determination in <i>Populus</i> provides molecular markers across the genus and indicates convergent evolution Open
Many dioecious angiosperms are trees, which only flower after years of vegetative development and do not usually exhibit marked secondary sexual dimorphism. Nevertheless, if the genetic basis of sex determination is known, the sex of an in…
View article: Default Sex and Single Gene Sex Determination in Dioecious Plants
Default Sex and Single Gene Sex Determination in Dioecious Plants Open
A well-established hypothesis for the evolution of dioecy involves two genes linked at a sex-determining region (SDR). Recently there has been increased interest in possible single gene sex determination. Work in Populus has finally provid…
View article: <i>ENO</i> regulates tomato fruit size through the floral meristem development network
<i>ENO</i> regulates tomato fruit size through the floral meristem development network Open
A dramatic evolution of fruit size has accompanied the domestication and improvement of fruit-bearing crop species. In tomato ( Solanum lycopersicum ), naturally occurring cis-regulatory mutations in the genes of the CLAVATA-WUSCHEL signal…
View article: High Level of Conservation of Mitochondrial RNA Editing Sites Among Four <i>Populus</i> Species
High Level of Conservation of Mitochondrial RNA Editing Sites Among Four <i>Populus</i> Species Open
RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify th…
View article: Mutations in <i>EID1</i> and <i>LNK2</i> caused light-conditional clock deceleration during tomato domestication
Mutations in <i>EID1</i> and <i>LNK2</i> caused light-conditional clock deceleration during tomato domestication Open
Significance Internal timekeepers, called circadian clocks, are prevalent in all domains of life. Variation in circadian rhythms allows fine-tuning of an organism to its specific environment. Here we show that a mutation in LNK2 , in addit…
View article: Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions
Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions Open
Under field conditions, drought and heat stress typically happen simultaneously and their negative impact on the agricultural production is expected to increase worldwide under the climate change scenario. In this study, we performed RNA‐s…