Biology subjects

Holusova, K.

Publications and source records attributed to Holusova, K..

4 recordsLinked to original sources

bioRxiv2025

Single-nucleus transcriptome analysis provides new insights into B chromosome elimination in sorghum

B chromosomes (Bs) are supernumerary entities found in many plant species, with some exhibiting tissue-specific elimination. In Sorghum purpureosericeum, extensive level of the B chromosome elimination occurs during embryogenesis. It progresses quickly and affects most of the embryonic organs, leaving the B chromosome maintained mainly in limited regions of meristems. Dynamic of the process and rarity of the transcripts associated with elimination make its capturing challenging. To address this, we performed single-nucleus RNA sequencing (snRNA-seq) on embryos actively undergoing B chromosome elimination. The snRNA-seq approach enabled the detection of a greater number of B-linked transcripts compared to previous method. Among all, we identified the nuclei with B-specific transcripts, which prevalently clustered together forming cluster 10 and contributing to cluster G2/M. The detailed analysis of cluster 10 revealed two distinct subpopulations of B-containing nuclei with divergent transcriptional profiles. The genes expressed in one subpopulation (sCL10-1) indicated that elimination of the B chromosome might be a factor for the split of the two subpopulations; namely that nuclei in sCL10-1 prepare for / undergo elimination, while the other subpopulation is expected to exhibit regular segregation of the B chromosome. Our analysis shows a direction so far missing in current studies and highlights a clear benefit of the single-cell approaches for studying specific behaviour of the B chromosomes.

plant biology↗

bioRxiv2025

Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes

BackgroundSelective DNA elimination occurs across diverse species and plays a crucial role in evolution and development. This process encompasses small deletions, complete removal of chromosomes, or even the elimination of entire parental genomes. Despite its importance, the molecular mechanisms governing selective DNA elimination remain poorly understood. Our study focused on the tissue-specific elimination of Sorghum purpureosericeum B chromosome(s) during embryo development. ResultsIn situ B chromosome visualisation, complemented by transcriptomic profiling and gene-enrichment analysis, allowed us to identify 28 candidate genes poten-tially linked to chromosome elimination. We show that elimination is a developmentally programmed process, peaking during mid-embryogenesis and nearly completed at later stages, leaving B chromosomes only in restricted meristematic regions. Genome sequencing revealed that the sorghum B chromosome is of multi-A chromosomal origin, has reduced gene density, is enriched in repetitive sequences, and carries a novel centromeric repeat (SpuCL166). Transcriptome analyses identified B-specific variants of kinetochore, cohesion, and checkpoint genes that are expressed during active elimination, while structural modeling of CENH3 and CENP-C indicated functional divergence at the kinetochore interface. ConclusionHere, we provide the first comprehensive genomic and transcriptomic characterization of B chromosome and its elimination in Sorghum purpureosericeum. Our findings suggest that B chromosomes express modified mitotic machinery to control their own fate. By establishing a framework of candidate genes, this study opens new avenues for dissecting the molecular mechanisms of chromosome elimination and provides a critical foundation for understanding how genomes evolve to regulate and tolerate supernumerary chromosomal elements.

plant biology↗

bioRxiv2022

A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley (Hordeum spp.). The barley leaf rust resistance locus Rph7, located on the short arm of chromosome 3H, confers defence at all growth stages and was previously shown to have unusually high sequence and haplotype divergence. Earlier, four candidate genes for Rph7 were reported and, despite an in-depth comparative sequence analysis and haplotypic characterisation, the causal gene could not be resolved. Here, we successfully cloned Rph7 utilising a fine mapping approach in combination with an RNA-Seq based expression analysis. We identified three up-regulated and pathogen-induced genes with presence/absence variation (PAV) at this locus. Sequence analysis of chemically induced Rph7 knockout mutant lines identified multiple independent non-synonymous variants, including a premature stop codon in a single non-canonical resistance gene that encodes a 302-amino acid protein. Progeny from four independent transgenic lines segregated for the expected avirulent Rph7 infection type in response to several avirulent P. hordei pathotypes, however, all plants were susceptible to a single virulent pathotype confirming the specificity. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor, as it shares structural similarity to ANAC019 from Arabidopsis, with a C-terminal BED domain. A global gene expression analysis suggests Rph7 is involved in the activation of basal defence.

genetics↗

bioRxiv2017

Association mapping and haplotype analysis of the pre-harvest sprouting resistance locus Phs-A1 reveals a causal role of TaMKK3-A in global germplasm

Pre-harvest sprouting (PHS) is an important cause of quality loss in many cereal crops and is particularly prevalent and damaging in wheat. Resistance to PHS is therefore a valuable target trait in many breeding programmes. The Phs-A1 locus on wheat chromosome arm 4AL has been consistently shown to account for a significant proportion of natural variation to PHS in diverse mapping populations. However the deployment of sprouting resistance is confounded by the fact that different candidate genes, including the tandem duplicated Plasma Membrane 19 (PM19) genes and the mitogen-activated protein kinase kinase 3 (TaMKK3-A) gene, have been proposed to underlie Phs-A1. To further define the Phs-A1 locus, we constructed a physical map across this interval in hexaploid and tetraploid wheat. We established close proximity of the proposed candidate genes which are located within a 1.2 Mb interval. An association analysis of diverse germplasm used in previous genetic mapping studies suggests that TaMKK3-A, and not PM19, is the major gene underlying the Phs-A1 effect in European, North American, Australian and Asian germplasm. We identified the non-dormant TaMKK3-A allele at low frequencies within the A-genome diploid progenitor Triticum urartu genepool, and show an increase in the allele frequency in modern varieties. In UK varieties, the frequency of the dormant TaMKK3-A allele was significantly higher in bread-making quality varieties compared to feed and biscuit-making cultivars. Analysis of exome capture data from 58 diverse hexaploid wheat accessions identified fourteen haplotypes across the extended Phs-A1 locus and four haplotypes for TaMKK3-A. Analysis of these haplotypes in a collection of UK and Australian cultivars revealed distinct major dormant and non-dormant Phs-A1 haplotypes in each country, which were either rare or absent in the opposing germplasm set. The diagnostic markers and haplotype information reported in the study will help inform the choice of germplasm and breeding strategies for the deployment of Phs-A1 resistance into breeding germplasm.

plant biology↗