Biology subjects

Snowdon, R. J.

Publications and source records attributed to Snowdon, R. J..

8 recordsLinked to original sources

bioRxiv2026

High-throughput sequencing of unmethylated DNA (UMR-seq) reveals extensive epigenetic variation in the hypomethylome of diverse plant species

The unmethylated regions (UMRs) in a genome can reveal the location of genes and gene regulatory loci. However, discovering UMR variation across and between entire genomes and disentangling the contribution of genetics and epigenetics to traits are challenging because they require separate and costly whole-DNA methylome and whole-genome genetic analyses. In many species this is prohibitively expensive for even a small number of samples, curtailing analysis on a population or breeding scale. Here we introduce UMR-seq, a method for the specific capture of UMRs from a genome and simultaneous sequencing of genetic variants in a single economical and scalable assay. UMR-seq charts the hypomethylome, revealing that it is highly enriched with functionally important regulatory loci. While UMRs are highly stable between vegetative tissues in plants, we find they are dynamic in the endosperm and vary substantially between accessions. Adaptable to diverse species, using this method we uncover a positive correlation between gene number in a species and UMR content, reflecting gene regulatory space in a genome. At 1/50th of the conventional cost of methylome sequencing in wheat, UMR-seq enables simultaneous population scale analysis of genetic and epigenetic variation in the functional genomic space. We reveal that in a panel of 187 elite wheat cultivars, profiling UMR variation improved genomic prediction across population groups, and UMR-based association mapping identified trait associations that were largely distinct from those detected with SNPs, providing new opportunities to understand trait biology and to enhance predictive breeding.

genomics↗

bioRxiv2025

Machine learning and multi-omic analysis reveal contrasting recombination landscape of A and C subgenomes of winter oilseed rape

Meiotic recombination is essential for generating genetic diversity, driving plant evolution, and enabling crop improvement, yet its uneven distribution across genomes constrains breeding efforts. Here, we investigated the multi-omic landmarks that shape the recombination landscape in Brassica napus by integrating epigenomic, genomic and transcriptomic data with recombination maps derived from large multi-parental rapeseed populations. Predictive machine-learning accurately predicted recombination rates and hotspot location using only feature information. Recombination was generally suppressed in centromeres and other repeat-rich, methylated regions and enriched in gene-dense, transcriptionally active domains. Proxies for chromatin configuration--such as DNA methylation, transposable elements or genes-- consistently achieved the highest predictive power with the random forest algorithm. We discovered distinct recombination landscape patterns between subgenomes, with crossovers clustering near subtelomeres in the A subgenome and more evenly spread across the C subgenome. Models trained on A-subgenome data outperformed those based on the C subgenome, although combining both subgenomes improved overall accuracy.

bioinformatics↗

bioRxiv2024

Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus

BackgroundUnderstanding genetic diversity is crucial for enhancing crop productivity. This study explores species-wide genome structural variation and its role in intraspecific and ecogeographical diversification of Brassica napus, a recently evolved, globally important allopolyploid crop. ResultsWe performed whole-genome long-read DNA-sequencing and constructed reference-guided genome assemblies for 94 diverse, homozygous accessions, including winter-type, spring-type, and East Asian oilseed, along with kale forms and swedes/rutabagas. We investigated pangenomic patterns of genomic structural variants (SV) and determined pangenome-wide distributions and frequencies of inversions, gene presence-absence variants, and collective SV including insertions and deletions. Results revealed pangenome-wide patterns for insertions, deletions, inversions, and large chromosomal deletions/duplications, reflecting evolutionary diversification across morphotypes and ecotypes. Collective SV were unevenly distributed and biased toward subgenome A, with asymmetrical selection pattern favoring subgenome C. Selection signatures for inversions exhibited no subgenome asymmetry; however, selection signal strength and frequency increased in paracentric chromosome regions, highlighting their evolutionary significance. Selective sweep analysis identified regions for collective SV and inversions, harboring genes for organ formation, cell division and expansion in swede, and stress responses in East Asian oilseed rape. Large chromosomal duplications and deletions distinguished swede from oilseed rape, particularly in subgenome C, including copy-number variation in flowering-time genes BnFLC.C09 and BnATX2.C08, and cell wall development gene BnCEL2.C08. ConclusionsThese findings underscore functional and evolutionary significance of pangenomic SV formation during B. napus diversification. Information on SV patterns with putative functional relevance, provides breeding insights, particularly for developing molecular markers to optimize performance of B. napus and other Brassica crops.

genomics↗

bioRxiv2024

Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus

Structural variants (SVs, eg. insertions and deletions) are genomic variations > 50 bp that are known to be associated with a range of crop traits, from yield to flowering behaviour and stress responses. Recently, pangenome graphs have emerged as a powerful framework for analysing genomic data by encoding population- or species-level diversity in one data structure. Pangenome graphs have the potential to serve as unbiased references for downstream applications, including SV genotyping and pan-transcriptomic analyses. In this work, we hypothesized that extensive variation affects transcript quantification and expression quantitative trait locus (eQTL) analysis when relying on a single reference, and that using pangenome graphs can mitigate reference sequence bias. We combined long and short read whole genome sequencing data with expression profiling of Brassica napus (oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. We demonstrate that pangenome graphs provides a superior framework for eQTL analysis by eliminating single reference bias in gene expression quantification. Combined with the graph-based genotyping of SVs, we identified 240 eQTL-SVs found in close proximity of target loci. These SVs affect expression of genes related to important traits, are often not in linkage with SNPs and represent diversity unaccounted for in classical SNP-based analyses. This study highlights the multiple advantages of graph-based approaches in population-scale studies and provides novel insight into gene expression regulation in an important crop.

plant biology↗

bioRxiv2022

Benchmarking Oxford Nanopore Read Alignment-Based Structural Variant Detection Tools in Crop Plant Genomes

Structural variations (SVs) are larger polymorphisms (>50 bp in length), which consist of insertions, deletions, inversions, duplications, and translocations. They can have a strong impact on agronomical traits and play an important role in environmental adaptation. The development of long-read sequencing technologies, including Oxford Nanopore, allows for comprehensive SV discovery and characterization even in complex polyploid crop genomes. However, many of the SV discovery pipeline benchmarks do not include complex plant genome datasets. In this study, we benchmarked popular long-read alignment-based SV detection tools for crop plant genomes. We used real and simulated Oxford Nanopore reads for two crops, allotetraploid Brassica napus (oilseed rape) and diploid Solanum lycopersicum (tomato), and evaluated several read aligners and SV callers across 5x, 10x, and 20x coverages typically used in re-sequencing studies. Our benchmarks provide a useful guide for designing Oxford Nanopore re-sequencing projects and SV discovery pipelines for crop plants.

bioinformatics↗

bioRxiv2022

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

The enhanced performance of hybrids though heterosis remains a key aspect in plant breeding, however the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigour, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing technologies. A total of 71217, 773, 79518 and 31825 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differential expression and methylation patterns observed could be explained due to parental dominance levels. Via gene ontology enrichment and microRNA-target association analyses during seed development we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation. This contrasts to the general maternal gamete demethylation reported during gametogenesis in most plant species. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were found in regions flanking genes that had no differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insight into genes and mechanisms with a potential role in early heterosis. Key messageTranscriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape.

plant biology↗

bioRxiv2022

Frequent spontaneous structural rearrangements promote transgenerational genome diversification in Brassica napus

In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.

genomics↗

bioRxiv2020

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP). In recent years there have been a number of studies associating large, chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloging small (30 to 10,000 bp) to mid-scale (10,000 bp to 30,000 bp) SV and their impact on evolution and adaptation related traits in plants. This might be attributed to complex and highly-duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using short read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage, long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

genomics↗