Biology subjects

Lutz, U.

Publications and source records attributed to Lutz, U..

4 recordsLinked to original sources

bioRxiv2024

Cryptic Variation in Adaptive Phenotypes Revealed by Panspecific flc Mutants

The study of mutants is one of the best tools for understanding the genetic basis of phenotypes that contribute to adaptation. Oddly, mutant analyses are almost always restricted to single genetic backgrounds and findings therefore can not be easily generalized. A case in point is the key regulator of flowering, FLOWERING LOCUS C (FLC), which has been inferred to explain much of the flowering time variation in Arabidopsis thaliana, yet mutants have been examined in very few backgrounds. We have previously established a set of panspecific flc mutants in 62 accessions of A. thaliana (Ruffley et al. 2024). Here, we investigate how genetic background modulates mutant effects on flowering and vegetative traits, as well as on physiology and transcriptomes. Time to onset of flowering in the genome-edited flc lines was reduced by up to 83%, but considerable variation remained. Genetic mapping showed that extremely early flowering in the absence of FLC was mostly explained by natural variation at the known FLC target FT, with additional contribution from loci colocalizing with FLC. Prognostic sequence analyses of accessions did not suggest that extremely-early combinations of engineered flc and natural FT alleles would be deleterious, yet extremely early flowering accessions are not represented in the commonly used collections of A. thaliana accessions. To test whether this discrepancy could be due to sampling bias, we undertook a focused collection effort of wild populations in Southern Italy, which confirmed that extremely early flowering accessions exist in natural populations. Apart from its specific role in flowering time regulation, FLC has pleiotropic effects on other ecophysiological traits such as growth, and these were also dependent on the genetic background, which was further supported by transcriptomic comparisons. Together we conclude that the various roles of FLC have greatly diversified in different genetic backgrounds. Our study provides a proof-of-concept on how analysis of panspecific mutants can reveal the true extent of genetic networks in which a focal gene participates in.

plant biology↗

bioRxiv2021

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

evolutionary biology↗

bioRxiv2021

Small peptides modulate the immune function of the ion channel-like protein ACD6 in Arabidopsis thaliana

ACCELERATED CELL DEATH 6 (ACD6) mediates a trade-off between growth and defense in Arabidopsis thaliana. However, the precise biochemical mechanism by which ACD6 and related proteins in plants act remains enigmatic. Here, we identified two loci, MODULATOR OF HYPERACTIVE ACD6 1 (MHA1) and its paralog MHA1-LIKE (MHA1L), that code for [~]7 kDa proteins that differentially interact with specific ACD6 variants. MHA1L enhances accumulation of an ACD6 complex, thereby increasing activity of the ACD6 standard allele for regulating plant growth and defenses. ACD6 is a multipass transmembrane protein with intracellular ankyrin repeats that are structurally similar to those found in mammalian ion channels. Several lines of evidence link increased ACD6 activity to enhanced calcium influx, likely mediated by ACD6 itself and with MHA1L as a direct regulator of ACD6.

plant biology↗

bioRxiv2017

A set of Columbia-0-specific single nucleotide polymorphism markers for the genetic analysis of natural variation in Arabidopsis thaliana

Genetic markers are important tools for the study of natural and induced genetic variation. Due to the strong increase in the number of genome sequences, an overview of the genomic diversity of many natural strains from individual species could be gained. This allows for the design of markers for flexible use and cost-efficient small scale genetic studies requiring minimal laboratory and bioinformatics effort. Here, we describe 140 single nucleotide polymorphism (SNP) markers with genome-wide distribution that discriminate between the genotype of the common Arabidopsis thaliana reference accession Columbia-0 (Col-0) and the majority of Arabidopsis thaliana accessions that have been sequenced to date. We designed, generated and validated the markers using the kompetitive allele-specific PCR (KASP) technology and made all 140SNPvCol marker assays publicly available through a service provider. Through the integration of available genomic SNP allele information of 1,135 accessions, we found that 120 of these 140 markers could detect non-reference alleles in 647 accessions and more than 100 markers showed non-reference alleles in 1,094 accessions. We further show that the marker set can be used for the verification or identification of accessions of unknown identity. As the KASP methodology is very flexible, an optimal marker subset can be easily selected among the available 140SNPvCol markers presented here to analyze genetic combinations of Col-0 with any other accession.

genetics↗