Biology subjects

Studer, B.

Publications and source records attributed to Studer, B..

30 records · Page 2Linked to original sources

bioRxiv2023

ChromaX: a fast and scalable breeding program simulator

SummaryChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes. Availability and ImplementationThe documentation is available at https://chromax.readthedocs.io The code is available at https://github.com/kora-labs/chromax Contactomargallalaly.younis@inf.ethz.ch, luca.corinzia@inf.ethz.ch, matteo.turchetta@inf.ethz.ch

bioinformatics↗

bioRxiv2022

Fine-mapping and comparative genomic analysis reveal the gene composition at the S and Z self-incompatibility loci in grasses

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.

plant biology↗

bioRxiv2022

Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover

Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide, once validated, a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover. Key messageHigh variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding.

plant biology↗

bioRxiv2021

Genetic architecture and genomic prediction accuracy of apple quantitative traits across environments

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. The apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic prediction accuracy, and studying genotype by environment interactions (GxE). Here we show contrasting genetic architecture and genomic prediction accuracies for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic prediction accuracies of 0.18-0.88 were estimated using single-environment univariate, single-environment multivariate, multi-environment univariate, and multi-environment multivariate models. The GxE accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.

genomics↗

bioRxiv2021

GBSmode: a pipeline for haplotype-aware analysis of genotyping-by-sequencing data

2AO_SCPLOWBSTRACTC_SCPLOW2.1 BO_SCPLOWACKGROUNDC_SCPLOWGenotyping-by-sequencing (GBS) has revolutionised molecular genetic analysis. It enables simultaneous genotyping of thousands of DNA markers in the genome of any species. In contrast to whole-genome shotgun sequencing, GBS exploits a restriction enzyme to reduce genome complexity and directs the sequencing to begin at fixed digestion sites. However, currently used tools for the analysis of GBS data, such as SAMtools, often neglect the fundamental technical differences between GBS and shotgun sequencing. 2.2 RO_SCPLOWESULTSC_SCPLOWHere we present GBSmode, a dedicated pipeline to call DNA sequence variants using whole-read information from GBS data. It removes false positives by incorporating biological features such as the ploidy level and the number of possible alleles in the population under investigation. Comparison of GBSmode with SAMtools in an F2 population of rice (Oryza sativa L.) showed both identified a similar number of polymorphisms (13,449 and 14,445, respectively) with a high overlap (8,143). However, differences were found in the number of read misalignments (8.0% and 14.3% for GBSmode and SAMtools, respectively) and genotyping errors (5.0% and 8.3% for GBSmode and SAMtools, respectively). Further tests in a bi-parental F1 population of cassava (Manihot esculenta Crantz) showed GBSmode found 31,489 polymorphic loci, whereas the number was higher with SAMtools (43,860). However, this difference was mainly attributable to GBSmode rejecting 11,695 loci that were biologically not possible. 2.3 CO_SCPLOWONCLUSIONSC_SCPLOWThis study shows that GBSmode is a versatile tool for the analysis of GBS data. Moreover, GBSmode was able to reduce genotyping errors arising from read misalignments by combining haplotype data with biological information. Whilst other tools may find more markers, GBSmode is designed for accuracy.

bioinformatics↗

bioRxiv2021

A multispecies amplicon sequencing approach for genetic diversity assessment in grassland plant species

Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within-species diversity) is related to many beneficial effects to the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large-scale assessment. However, the continuous advancement of high-throughput DNA sequencing approaches have improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost-effective method. Here we report a set of twelve multispecies primer pairs that can be used for high-throughput PGD assessment in multiple grassland plant species. The loci targeted by the amplicons were selected and tested in two phases: a "discovery phase" based on a sequence capture assay (611 target nuclear loci assessed in 16 grassland plant species), which resulted in the selection of eleven loci; and a "validation phase", in which the selected loci were targeted and sequenced using twelve multispecies primers in test populations of Dactylis glomerata L., Lolium perenne L., Festuca pratensis Huds., Trifolium pratense L. and T. repens L. The resulting multispecies amplicons had overall nucleotide diversities per species ranging from 5.19 x 10-3 to 1.29 x 10-2, which is in the range of flowering-related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the amplicon-specific primer pairs reported in this study provide the basis for large-scale, multispecies PGD monitoring in grassland plants.

ecology↗

bioRxiv2021

Evidence for high intergenic sequence variation in heterozygous Italian ryegrass (Lolium multiflorum Lam.) genome revealed by a high-quality draft diploid genome assembly

BackgroundOver the last decade, progress in DNA sequencing technologies and assembly methods allowed plant scientists to move beyond the use of model organisms and work directly on the genomes of the major crops. Forage grass research can also benefit from this revolution, enabling progress in population genetic studies, functional biology, and genomics-assisted breeding. Due to its large genome size and high repeat content, so far only incomplete and fragmented assemblies are available for the grasses of the Lolium and Festuca species complex. FindingsHere, we report a highly contiguous draft assembly of Italian ryegrass (L. multiflorum Lam.), spanning 4.5 Gb and with a N50 of 3 Mb, containing ~70,000 gene models. Thanks to its relatedness to barley, 78% of the assembly was anchored on seven pseudomolecules. The high heterozygosity of the plant allowed obtaining a diploid assembly - i.e. across 95% of the assembly, both alleles were assembled on separate sequences. This feature allowed unraveling a very high amount of intergenic sequence variation between allelic sequences. ConclusionsWe present a nearly complete genome assembly of a genotype used in contemporary Swiss forage grass breeding programs. This work shows how genomic research has improved, allowing to decode the genetic code of large, complex, and heterozygous plants. It also allows the functional characterization of the ryegrass gene repertoire and the large-scale development of molecular markers. Furthermore, it paves the road for a reference-based characterization and exploitation of the genetic variation within the Lolium and Festuca species complex.

genomics↗

bioRxiv2021

Identification of candidate genes for self-compatibility in perennial ryegrass (Lolium perenne L.)

Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in approximately 40% of plant species. Two multiallelic loci, called S and Z, control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass (Lolium perenne L.) was previously mapped on linkage group (LG) 5 in a F2 population segregating for SC. Using a subset of the same population (n=68), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 cM using additional 2,056 plants and 23 novel sequence-based markers. Using an Italian ryegrass (Lolium multiflorum Lam.) genome assembly as reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our work is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm. Key messageA previously reported QTL conferring self-compatibility to perennial ryegrass was fine mapped to a 0.26 cM locus, corresponding to an estimated ~ 3 Mb physical region containing 57 predicted protein-encoding genes.

plant biology↗

bioRxiv2021

Temporal differentiation of resource capture and biomass accumulation as a driver of yield increase in intercropping

- Intercropping, i.e. the simultaneous cultivation of different crops on the same field, has demonstrated yield advantages compared to monoculture cropping. These yield advantages have often been attributed to complementary resource use, but few studies quantified the temporal complementarity of nutrient acquisition and biomass production. Our understanding of how nutrient uptake rates of nitrogen (N) and phosphorous (P) and biomass accumulation change throughout the growing season and between different neighbors is limited. - We conducted weekly destructive harvests to measure temporal trajectories of N and P uptake and biomass production in three crop species (oat, lupin and camelina) growing either as isolated single plants, in monocultures or as intercrops. Additionally, we quantified organic acid exudation in the rhizosphere and biological N2-fixation of lupin throughout the growing season. Logistic models were fitted to characterize nutrient acquisition and biomass accumulation trajectories. - Nutrient uptake and biomass accumulation trajectories were curtailed by competitive interactions, resulting in earlier peak rates and lower total accumulated nutrients and biomass compared to cultivation as isolated single plants. Different pathways led to overyielding in the two mixtures. The oat-camelina mixture was characterized by a shift from belowground temporal niche partitioning of resource uptake to aboveground competition for light during the growing season. The oat-lupin mixture showed strong competitive interactions, where lupin eventually overyielded due to reliance on atmospheric N and stronger competitiveness for soil P. - Synthesis: This study demonstrates temporal shifts to earlier peak rates of plants growing with neighbors compared to those growing alone, suggesting that the observed temporal shifts in our experiment are driven by competitive interactions rather than active plant behavior to reduce competition. The two differing pathways to overyielding in the two mixtures highlight the importance of examining temporal dynamics in intercropping systems to understand the underlying mechanisms of overyielding.

ecology↗

bioRxiv2020

Chromosome-scale de novo diploid assembly of the apple cultivar 'Gala Galaxy'

Apple (Malus x domestica) is one of the most important fruit crops in terms of worldwide production. Due to its self-incompatibility system and the long juvenile period, breeding of new apple cultivars combining traits desired by growers (e.g. yield, pest and disease resistance) and consumers (e.g. fruit size, color, and flavor) is a long and complex process. Genomics-assisted breeding strategies can facilitate the selection of germplasm leading to new cultivars. While the most complete apple genome assemblies available to date are from anther-derived homozygous lines, de novo assembly of apple genomes encompassing the natural heterozygosity remains challenging. Using long- and short-read sequencing technologies in combination with optical mapping, we de novo assembled a diploid and heterozygous genome of the apple cultivar Gala Galaxy. This approach resulted in 154 hybrid scaffolds (N50 = 34.3 Mb) spanning 999.9 Mb and in 414.7 Mb of unscaffolded sequences. Anchoring 31 scaffolds with a genetic map was sufficient to represent an entire haploid genome of 17 pseudomolecules (719.4 Mb). The remaining sequences were assembled in a second set of 17 pseudomolecules, which spanned 601 Mb, leaving 80.6 Mb of unplaced sequences. A total of 41,264 genes were annotated using 74,900 transcripts derived from RNA sequencing of pooled leaf tissue samples. This study provides a high-quality diploid reference genome sequence encompassing the natural heterozygosity of the widely popular cultivar Gala Galaxy. The DNA sequence resources and the assembly described here will serve as a solid foundation for fundamental and applied apple breeding research.

genomics↗

bioRxiv2018

Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch in European winter wheat

O_LIAccurate, high-throughput phenotyping for quantitative traits is the limiting factor for progress in plant breeding. We developed automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance.\nC_LIO_LI335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform a GWAS.\nC_LIO_LIWe identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four resistance traits. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance.\nC_LIO_LIOur experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.\nC_LI

plant biology↗

bioRxiv2018

Genetic determination of stomatal patterning in winter wheat (Triticum aestivum L.)

Leaf stomata are microscopic pores mediating plant-environment interactions. Their role in carbon uptake and transpiration make them prime candidates for improving water use efficiency (WUE). Stomatal density (SD), the number of stomata per unit area, has been shown to be negatively correlated with WUE. However, little is known about the genetic basis of SD in wheat (Triticum aestivum L.), and to what extant genetic variation exists in contemporary wheat germplasm. Here, we evaluated stomatal patterning over two growing seasons in a set of 333 wheat lines, representing the European winter wheat germplasm. Stomatal patterning was mainly determined by two underlying traits, the distance between files of stomata and the distance between stomata within a file. By haplotype association mapping, quantitative trait loci for SD were consistently detected in both seasons on wheat chromosomes (CHR) 2A, 3A and 7B. The single nucleotide polymorphism markers most significantly associated with SD coincided with the genes INDUCER OF CBF EXPRESSION 1 (ICE1) and STOMATAL CYTOKINESIS-DEFECTIVE 1 (SCD1) on CHR 3A, and genes involved in ethylene and auxin signaling on CHR 2A and 7B, respectively. Our study unlocks the phenotypic and genotypic variation for stomatal patterning traits in contemporary wheat germplasm. It provides gene targets for functional validation and practical tools to manipulate SD using marker-assisted selection for crop improvement.

plant biology↗