Biology subjects

Tost, M.

Publications and source records attributed to Tost, M..

5 recordsLinked to original sources

bioRxiv2025

Assessing the adaptative potential to temperature and precipitation along a steep environmental gradient in populations of European beech

Climate change poses a significant threat to European beech. These concerns highlight the need to assess the adaptive potential of European beech populations to climate change. Landscape genomics, also known as environmental association analysis, is a powerful tool for identifying gene loci that contribute to local adaptation to environmental pressures. Genotypic data was collected from [~]100 adult beech trees per stand in five locations in the South-Eastern Romanian Carpathians along an altitudinal gradient associated with precipitation and temperature. In total, 53 environmental variables, comprising frost frequency change, temperature and precipitation, were extracted from the climatology data base CHELSA. Based on these variables the Ellenberg-Quotient (EQ) was calculated. We performed environmental association analysis using LFMM (latent factor mixed models) to identify Single Nucleotide Polymorphism (SNP) markers associated with environmental variables and with the principal components calculated based on these. We identified 446 SNP markers significantly associated with the first principal component (PC). These were overlapping with the SNP markers significantly associated with all environmental variables except precipitation accumulated during the growing season. The first PC was correlated with all temperature-based variables and elevation at |r| [~]0.989 to [~]0.997 and with all precipitation-based and Ellenberg-Quotient variables at |r| [~]0.945 to 0.950, except precipitation accumulated during the growing season. A high peak region on chromosome 2 from [~]4.56 to [~]16.27 Mb appeared in all results. This region was [~]3.47 Mb downstream from a region for local adaptation identified by Lazic et al. (2024). In this peak, 273 markers located in the coding region of 22 genes were found. Ten out these 22 were described based on a literature review. Among these ten genes, two may be involved in local adaptation based on our literature review. These two genes are polygalacturonase QRT3-like and NRT1/PTR_FAMILY 5.4-like. The gene polygalacturonase QRT3-like plays a role in pollen development in Arabidopsis thaliana L. and Brassica rapa L. We observed at the corresponding SNP markers, a correlation of the minor allele frequency and temperature-based environmental variables.

genetics↗

bioRxiv2025

Genome-wide association study in European beech (Fagus sylvatica L.) for drought stress traits

Forest tree breeding is an extremely long and tedious process. To study the genetic architecture of polygenic traits in long-lived species such as forest trees, costly field experiments are implemented. Phenotypic data on traits, that are measured at maturity, are only available after a long time and juvenile-mature correlations are often unknown. Genome-wide association studies (GWAS) aim to identify loci associated with drought stress, tree physiology, growth or wood quality traits, which could be prioritized in breeding programs. Genotypic and phenotypic data were collected from approximately 100 adult beech trees per stand in five locations in the South-Eastern Romanian Carpathians along an altitudinal gradient associated with precipitation and temperature. We performed GWAS using PLINK to identify SNP markers associated with traits related to drought stress. A total of 121 markers on eight chromosomes were identified as being associated with stomatal density. Sixty-four markers are located on chromosome 10 in a region spreading from [~]4.89 to 13.67 Mb. There are five genes in this region that are thought to play a role in controlling stomatal density. All markers within this region exhibit similar allele frequencies, which are correlated with stomatal density and the altitudinal gradient of the stands. We assume this entire region is jointly involved in local adaptation to drought stress. We identified one interesting candidate SNP associated with leaf nitrogen content. Two SNP markers were identified as being significantly associated with {delta}13C as measure of intrinsic water use efficiency. Additionally, signals of significant polygenic selection for {delta}13C were observed.

genetics↗

bioRxiv2025

Optimization of a maize rapid cycle breeding scheme using the Modular Breeding Program Simulator (MoBPS)

In recent years, the turnover of plant breeding has substantially increased as the use of genomic information allows for earlier selection and the integration of controlled growing environments reduces time to reach a particular growing stage. However, high generation turnover and intensive selection of lines before own yield trials are performed come at the risk of a drastic reduction of genetic diversity paired with lower prediction accuracies. To this end, we investigate strategies to cope with these challenges in a maize rapid cycle breeding scheme using stochastic simulations using the software MoBPS. We find that genetic gains soon reach a plateau when only the original breeding material is phenotyped. Updating the training data set via additional phenotyping of crosses or doubled haploid lines ensures long-term progress with a gain of 6.80 / 6.95 genetic standard deviations for the performance as a cross / per se after 30 cycles of breeding compared to 3.40 / 4.28 without additional phenotyping. Adding genetic material with comparable genetic level and novel diversity from outside the breeding material led to a further increase to 9.34 / 7.89 genetic standard deviations. In particular, for the management of genetic diversity, further additions to the breeding scheme are analyzed to optimize the number of selected lines per cycle and to account for the relatedness of F2 plants in the selection using the software AlphaMate. Finding a balance between genetic gains and diversity is important for a given time frame. MoBPS provides a tool for the quantification of these effects and provides solutions specific to the respective breeding program.

genetics↗

bioRxiv2024

Experimental evolution in maize with replicated divergent selection identifies plant-height associated SNPs

Experimental evolution studies are common in agricultural research, where they are often deemed "long term selection". These are often used to perform selection mapping, which involves identifying markers which were putatively under selection based on finding signals of selection left in the genome. A challenge of previous selection mapping studies, especially in agricultural research, has been the specification of robust significance thresholds. This is in large part because long term selection studies in crops have rarely included replication. Usually, significance thresholds in long term selection experiments are based on outliers from an empirical distribution. This approach is prone to missing true positives or including false positives. Under laboratory conditions with model species, replicated selection has been shown to be a powerful tool, especially for the specification of significance thresholds. Another challenge is that commonly used single-marker based statistics may identify neutral linked loci which have hitchhiked along with regions that are actually under selection. In this study, we conducted divergent, replicated selection for short and tall plant-height in a random mating maize population under real field conditions. Selection of the 5% tallest and shortest plants was conducted for three generations. Significance thresholds were specified using the false discovery rate for selection (FDRfS) based on a window-based statistic applied on a statistic leveraging replicated selection (FSTSum). Overall, we found 3 significant regions putatively under selection. One region was located on chromosome 3 close to the plant-height genes Dwarf1 and iAA8. We applied a haplotype block analysis to further dissect the pattern of selection in significant regions of the genome. We observed patterns of strong selection in the subpopulations selected for short plant height on chromosome 3.

genetics↗

bioRxiv2022

New C3H KitN824K/WT cancer mouse model develops late-onset malignant mammary tumors with high penetrance

Gastro-intestinal stromal tumors and acute myeloid leukemia induced by activating stem cell factor receptor tyrosine kinase (KIT) mutations are highly malignant. Less clear is the role of KIT-mutations in the context of breast cancer. Treatment success of KIT-induced cancers is still unsatisfactory because of primary or secondary resistance to therapy. Mouse models offer essential platforms for studies on molecular disease mechanisms in basic cancer research. In the course of the Munich N-ethyl-N-nitrosourea (ENU) mutagenesis program a mouse line with inherited polycythemia was established. It carries a base-pair exchange in the Kit gene leading to an amino acid exchange at position 824 in the activation loop of KIT. This KIT-variant corresponds to the N822K mutation found in human cancers, which is associated with imatinib-resistance. C3H KitN824K/WT mice develop hyperplasia of interstitial cells of Cajal and retention of ingesta in the cecum. In contrast to previous KIT-mutant models, we observe a benign course of gastrointestinal pathology associated with prolonged survival. Female mutants develop mammary carcinomas at late onset and subsequent lung metastasis. The disease model complements existing oncology research platforms. It allows for addressing the role of KIT mutations in breast cancer and identifying genetic and environmental modifiers of disease progression.

cancer biology↗