Biology subjects

Stich, B.

Publications and source records attributed to Stich, B..

23 records · Page 2Linked to original sources

bioRxiv2022

Brassicaceae display diverse photorespiratory carbon recapturing mechanisms

Carbon concentrating mechanisms enhance the carboxylase efficiency of the central photosynthetic enzyme rubisco by providing supra-atmospheric concentrations of CO2 in its surrounding. In the C4 photosynthesis pathway, this is achieved by combinatory changes to leaf biochemistry and anatomy. Carbon concentration by the photorespiratory glycine shuttle requires fewer and less complex modifications. It could represent an early step during evolution from C3 to C4 photosynthesis and an inspiration for engineering approaches. Plants displaying CO2 compensation points between 10 to 40 ppm are therefore often termed C3-C4 intermediates. In the present study, we perform a physiological, biochemical and anatomical survey of a large number of Brassicaceae species to better understand the C3-C4 intermediate phenotype. Our phylogenetic analysis suggested that C3-C4 metabolism evolved up to five times independently in the Brassicaceae. The efficiency of the pathways showed considerable variation between the species but also within species. Centripetal accumulation of organelles in the bundle sheath was consistently observed in all C3-C4 classified accessions indicating a crucial role of anatomical features for CO2 concentrating pathways. Leaf metabolite patterns were strongly influenced by the individual plant accessions, but accumulation of photorespiratory shuttle metabolites glycine and serine was generally observed. Analysis of PEPC activities suggests that C4-like shuttles have not evolve in the investigated Brassicaceae. HighlightOur physiological, biochemical and anatomical survey of Brassicaceae revels multiple evolution of C3-C4 intermediacy connected to variation in photorespiratory carbon recapturing efficiency and a distinct C3-C4 bundle sheath anatomy.

plant biology↗

bioRxiv2022

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: I. Effect of selection strategy, implementation stage, and selection intensity on short-term genetic gain

Genomic selection (GS) is used in many animal and plant breeding programs to enhance genetic gain for complex traits. However, its optimal integration in clone breeding programs that up to now relied on phenotypic selection (PS) requires further research. The objectives of this study were to (i) investigate under a fixed budget how the weight of GS relative to PS, the stage of implementing GS, the correlation between an auxiliary trait assessed in early generations and the target trait, the variance components, and the prediction accuracy affect the genetic gain of the target trait of GS compared to PS, (ii) determine the optimal allocation of resources maximizing the genetic gain of the target trait in each selection strategy and for varying cost scenarios, and (iii) make recommendations to breeders how to implement GS in clone and especially potato breeding programs. In our simulation results, any selection strategy involving GS had a higher short-term genetic gain for the target trait than Standard-PS. In addition, we show that implementing GS in consecutive selection stages can largely enhance short-term genetic gain and recommend the breeders to implement GS at single hills and A clone stages. Furthermore, we observed for selection strategies involving GS that the optimal allocation of resources maximizing the genetic gain of the target trait differed considerably from those typically used in potato breeding programs. Therefore, our study provides new insight for breeders regarding how to optimally implement GS in a commercial potato breeding program to improve the short-term genetic gain for their target trait.

genetics↗

bioRxiv2022

The double round-robin population unravels the genetic architecture of grain size in barley

Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characters and observed 84 % or higher heritability across four environments. The results of the quantitative trait locus (QTL) detection indicate that the genetic architecture of grain size is more complex than reported previously. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley. HighlightMulti parent population uncovered the natural allelic series across quantitative loci associated with grain size and weight that will contribute to identifying causal genes and yield improvement in barley.

plant biology↗

bioRxiv2022

Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation

In human genetics, several studies have shown that phenotypic variation is more likely to be caused by structural variants (SV) than by single nucleotide variants (SNV). However, accurate while cost-efficient discovery of SV in complex genomes remains challenging. The objectives of our study were to (i) facilitate SV discovery studies by benchmarking SV callers and their combinations with respect to their sensitivity and precision to detect SV in the barley genome, (ii) characterize the occurrence and distribution of SV clusters in the genomes of 23 barley inbreds that are the parents of a unique resource for mapping quantitative traits, the double round robin population, (iii) quantify the association of SV clusters with transcript abundance, and (iv) evaluate the use of SV clusters for the prediction of phenotypic traits. In our computer simulations based on a sequencing coverage of 25x, a sensitivity >70% and precision >95% was observed for all combinations of SV types and SV length categories if the best combination of SV callers was used. We observed a significant (P < 0.05) association of gene-associated SV clusters with global gene-specific gene expression. Furthermore, about 9% of all SV clusters that were within 5kb of a gene were significantly (P < 0.05) associated with the gene expression of the corresponding gene. The prediction ability of SV clusters was higher compared to that of single nucleotide polymorphisms from an array across the seven studied phenotypic traits. These findings suggest the usefulness of exploiting SV information when fine mapping and cloning the causal genes underlying quantitative traits as well as the high potential of using SV clusters for the prediction of phenotypes in diverse germplasm sets.

genomics↗

bioRxiv2021

Cis-regulatory divergence underpins the evolution of C3-C4 intermediate photosynthesis in Moricandia

Altered transcript abundances and cell specific gene expression patterns that are caused by regulatory divergence play an important role in the evolution of C4 photosynthesis. How these altered gene expression patterns are achieved and whether they are driven by cis- or trans-regulatory changes is mostly unknown. To address this question, we investigated the regulatory divergence between C3 and C3-C4 intermediates, using allele specific gene expression (ASE) analyses of Moricandia arvensis (C3-C4), M. moricandioides (C3) and their interspecific F1 hybrids. ASE analysis on SNP-level showed similar relative proportions of regulatory effects among hybrids: 36% and 6% of SNPs were controlled by cis-only and trans-only changes, respectively. GO terms associated with metabolic processes and the positioning of chloroplast in cells were abundant in transcripts with cis-SNPs shared by all studied hybrids. Transcripts with cis-specificity expressed bias toward the allele from the C3-C4 intermediate genotype. Additionally, ASE evaluated on transcript-level indicated that [~]27% of transcripts show signals of ASE in Moricandia hybrids. Promoter-GUS assays on selected genes revealed altered spatial gene expression patterns, which likely result from regulatory divergence in their promoter regions. Assessing ASE in Moricandia interspecific hybrids contributes to the understanding of early evolutionary steps towards C4 photosynthesis and highlights the impact and importance of altered transcriptional regulations in this process.

plant biology↗