Biology subjects

Adamski, N. M.

Publications and source records attributed to Adamski, N. M..

6 recordsLinked to original sources

bioRxiv2024

Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution

The diversity of plant inflorescence architectures is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base which initiate first but subsequently lag in development compared with central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, the spatio-temporal dynamics and gradients along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, using spatial transcriptomics, we profiled 200 genes across four stages of wheat inflorescence development to cellular resolution. Cell segmentation and unsupervised clustering identified 18 expression domains and their enriched genes, revealing dynamic spatio-temporal organisation along the apical-basal axis of the inflorescence. Along this axis, we uncovered distinct and spatially coordinated gene expression gradients patterning meristems prior to the visible delay in basal spikelet development. This study demonstrates the potential for spatial transcriptomics time-series to advance plant developmental biology.

plant biology↗

bioRxiv2024

TILLCANN: A TILLING platform in Cannabis sativa for mutation discovery and crop improvement

Cultivation of Cannabis sativa is increasing because of its therapeutic value and recognition as a multi-purpose and sustainable crop. Targeting Induced Local Lesions in Genomes (TILLING) is a versatile reverse genetics approach that unlocks induced variation through mutagenesis to accelerate the development of new cultivars and contribute to the functional validation of genes. Increasingly efficient next-generation sequencing technologies and genomic resources have combined to make TILLING by sequencing (TbyS) an attractive technique that can be applied in cannabis. Here we describe the development of a mutagenesis protocol for C. sativa and the development of the TILLCANN platform composed of 1,633 M2 families. As a demonstration of the functionality of the platform, we used TbyS to perform a high throughput screening of novel mutations in amplicons for genes associated with important agronomic and biochemical traits in a set of 512 M2 families. We confirmed 14 of the identified mutations and calculated an average mutation frequency range of 1/263 to 1/320 kb. We found that heterozygous mutants in the cannabis homologue of Class II TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP4) are linked to alterations in leaf number and morphology. We expect that the novel genetic variability unlocked in the TILLCANN platform for performing forward or reverse genetic screens can significantly boost breeding programs geared toward both medicinal cannabis and industrial hemp. Gene & accession numbersRaw sequencing data generated in this study was deposited at the European Nucleotide Archive with accession numbers xxx and xxx. Genes and accession numbers discussed within this manuscript correspond to the Cannabis sativa cs10 genome assembly deposited in National Center for Biotechnology Information with accession number GCA_900626175.2.

plant biology↗

bioRxiv2022

The T. ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1

In rice and wheat, glume and floral organ length are positively correlated with grain size, making them an important target to increase grain size and potentially yield. The wheat subspecies Triticum ispahanicum is known to develop elongated glumes and floral organs as well as long grains. These multiple phenotypic effects are controlled by the P2 locus, which was previously mapped to wheat chromosome 7B. Using three mapping populations, we show that the long glume locus P2 does not map to chromosome 7B, but instead maps to a 1.68 Mbp interval on chromosome 6A. Within this interval, we identified SVP-A1, a MADS box transcription factor which is the direct ortholog of the maize gene underlying the pod corn Tunicate locus and is a paralog to the T. polonicum elongated glume P1 gene. In T. ispahanicum, we identified a private allele which has a 482-bp deletion in the SVP-A1 promoter and is associated with ectopic and higher expression of SVP-A1 in the elongated glumes and floral organs. We used near-isogenic lines (NILs) to show that P2 has a consistent positive effect on the length of glume, lemma, palea, spike and grain. Based on the mapping data, natural variation, biological function of SVP genes in cereals and expression analyses, we propose the MADS-box transcription factor SVP-A1 as a promising candidate for P2. Key messageWe propose the MADS-box transcription factor SVP-A1 as a promising candidate gene for the elongated glume locus P2, which maps to chromosome 6A instead of the previously proposed chromosome 7B.

plant biology↗

bioRxiv2021

High expression of VRT2 during wheat spikelet initiation increases the number of rudimentary basal spikelets

Spikelets are the fundamental building blocks of Poaceae inflorescences and their development and branching patterns determine the various inflorescence architectures and grain yield of grasses. In wheat, the central spikelets produce the most and largest grains, while spikelet size gradually decreases acro- and basipetally, giving rise to the characteristic lanceolate shape of wheat spikes. The acropetal gradient correlates with the developmental age of spikelets, however the basal spikelets are developed first and the cause of their small size and rudimentary development is unclear. Here, we adapted G&T-seq, a low-input transcriptomics approach, to characterise gene expression profiles within spatial sections of individual spikes before and after the establishment of the lanceolate shape. We observed larger differences in gene expression profiles between the apical, central and basal sections of a single spike than between any section belonging to consecutive developmental timepoints. We found that SVP MADS-box transcription factors, including VRT-A2, are expressed highest in the basal section of the wheat spike and display the opposite expression gradient to flowering E-class SEP1 genes. Based on multi-year field trials and transgenic lines, we show that higher expression of VRT-A2 in the basal sections of the spike is associated with increased numbers of rudimentary basal spikelets. Our results, supported by computational modelling, suggest that the delayed transition of basal spikelets from vegetative to floral developmental programmes results in the lanceolate shape of wheat spikes. This study highlights the value of spatially resolved transcriptomics to gain new insights into developmental genetics pathways of grass inflorescences. One sentence summaryLarge transcriptional gradients exist within a wheat spike and are associated with rudimentary basal spikelet development, resulting in the characteristic lanceolate shape of wheat spikes.

plant biology↗

bioRxiv2020

Increased and ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner

Flower development is a major determinant of yield in crops. In wheat, natural variation for the size of spikelet and floral organs is particularly evident in Triticum polonicum, a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VRT2, a MADS-box transcription factor belonging to the SVP family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence re-arrangement in intron-1 that results in both increased and ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum species defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can impact on agronomic traits in a dosage-dependent manner in polyploid crops. One-sentence summaryAn intron-1 rearrangement in the MADS-box transcription factor VRT-A2 leads to its misexpression and defines the long-glume phenotype of Polish wheat (T. polonicum).

plant biology↗

bioRxiv2018

BED-domain containing immune receptors confer diverse resistance spectra to yellow rust

Introductory paragraph Introductory paragraph Main Methods Author contributions Data availability Competing interests References Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security1. Genetic resistance can reduce crop losses in the field and can be selected for through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst)2. This highlights the need to (i) identify genes that alone or in combination provide broad-spectrum resistance and (ii) increase our understanding of the underlying molecular mod ...

plant biology↗