Biology subjects

Sharpe, A. G.

Publications and source records attributed to Sharpe, A. G..

11 recordsLinked to original sources

bioRxiv2026

Comparative Transcriptome Analysis Unveils Mechanisms of Salt Tolerance in Bluebunch Wheatgrass

Bluebunch wheatgrass (Pseudoroegneria spicata) exhibits substantial variation in its response to salt stress, making it a valuable model for studying salinity-tolerance mechanisms for use in crop improvement. In this study, we identified two P. spicata genotypes with contrasting responses to salt stress: the tolerant W6 56551, which maintained growth with green foliage under saline conditions, and the susceptible PI693916, which exhibited severe leaf chlorosis and stunted growth. To better understand the molecular basis of salt tolerance in blue-bunch wheatgrass, we conducted RNA-sequencing at 0, 1, and 4 days (D0, D1, and D4) after salt treatment at 160 mM level to examine changes in gene expression of salt-tolerant and salt-susceptible genotypes. Comparative analysis across time points identified 6,154 and 1,086 differentially expressed genes (DEGs) at D4 and D1 in PI693916, and 4,638 and 3,302 DEGs at D4 and D1 in W6 56551, respectively, relative to control (D0). Functional analysis of these DEGs showed that the salt-tolerant geno-type displayed an early and broad transcriptional reprogramming, including induction of photosynthesis, carbon metabolism, and flavonoid biosynthesis pathways, whereas the salt-susceptible genotype exhibited delayed and less coordinated responses, with enrichment of cyanoamino acid metabolism and repression of antioxidant-associated pathways. Notably, calcium signaling, ion transporter regulation, and osmolyte biosynthesis genes showed contrasting expression between genotypes, highlighting distinct strategies for ionic and osmotic homeostasis. Collectively, these results demonstrate that salt tolerance in P. spicata is associated with rapid metabolic adjustment, enhanced photosynthetic stability, and differential regulation of ion transport and osmoprotectant pathways.

genomics↗

bioRxiv2026

Haplotype-resolved Genome Assemblies of Hybrid Wheatgrass and Bluebunch Wheatgrass Reveal the Stepwise Polyploid Origin and Biased Subgenome Dominance

Concerns over climate change have intensified the demand for stress resistant crops like hybrid wheatgrass (HWG; Elymus hoffmannii, StStStStHH), a perennial forage species known for its exceptional salt and drought tolerance. However, hexaploidy and high heterozygosity have complicated efforts to resolve its genomic structure and evolutionary history. Here, we present high-quality, haplotype-resolved, chromosome-level genome assemblies for HWG (CDC Saltking) and its putative progenitor, bluebunch wheatgrass (Pseudoroegneria spicata, StSt). By integrating PacBio HiFi and ultra-long Oxford Nanopore sequencing with Hi-C scaffolding, we assembled the 10.7 Gb HWG genome into 21 pseudochromosomes per haplotype. Our phylogenomic analysis redefines the origin of the H subgenome, positioning it as an intermediate between Old-World Hordeum marinum (sea barley) and Hordeum brevisubulatum. Notably, we identified significant chromosomal rearrangements, including a unique duplication on St chromosome 4. Transcriptome analysis across multiple tissues revealed a pronounced expression dominance of the H subgenome. This dominance was not associated with reduced LTR density, suggesting that selective pressures for rapid adaptation of the latest subgenome entrant may drive its dominance. Finally, using the f-branch statistic, population genomic analysis of 189 accessions representing eight Elymus and Pseudoroegneria species revealed extensive reticulate evolutionary relationships and identified P. spicata as a major, asymmetric genetic donor within the wheatgrass complex. These resources provide a foundational framework for future genomic research and genetic improvement in grasses and for the introgression of stress-tolerance traits into cereal crops such as wheat. Key MessagesO_LIDevelopment of world-first high-quality chromosomal-level haplotype-resolved genome assemblies of hexaploid HWG and diploid progenitor, Pseudoroegneria spicata, enabled the identification of the subgenome origins. C_LIO_LIThis study resolved the evolutionary placement of the St genome and clarified the history of polyploidization and hybridization in HWG. C_LIO_LIHomeolog expression bias in the H subgenome likely reflects selective pressure favoring greater gene retention and upregulation of functionally important genes, thereby enhancing hybrid fitness. C_LIO_LIPopulation structure analysis distinctly differentiates P. spicata, E. repens, E. hoffmannii from other European Pseudoroegneria species. C_LIO_LIThe findings reveal the complex patterns of interspecific gene flow and population dynamics within the Elymus and Pseudoroegneria species. C_LI

genomics↗

bioRxiv2026

High-quality genome assemblies of diploid Bromus species enhance understanding of genome complexity and uncover large DNA satellite structures.

Genus Bromus includes important cool-season forage grasses, but large genome sizes and complex ploidy hinder genomic studies. Here we carried out long read sequencing of two diploid genomes, Bromus riparius and Bromus squarrosus, generating highly contiguous assemblies with contig N50 values of 294.76 Mb and 98.78 Mb, respectively. These assemblies uncovered high-order centromeric repeats and two unique large sub-telomeric repeats on chromosome 5 and 7. Repeat expansion in Bromus appears relatively recent compared to speciation events ([~]9.75 million years ago); yet strong synteny persists across species. Transposable elements such as Angela, SIRE, Athila, CRM, and Retand were identified as major contributors to genome expansion in related Bromus species. Population structure analysis resolved six major subpopulations, with wild relatives exhibiting a higher genetic divergence than cultivated types. Hybrid bromegrass lines showed a higher proportion of genomic contribution from B. inermis than B. riparius. Together, these genomic resources provide a foundation for investigating traits of interest and advancing bromegrass breeding.

genomics↗

bioRxiv2025

A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximity

Camelina sativa is an oilseed of the Brassicaceae, whose close relatives vary in ploidy number, providing a novel platform for studying plant genome evolution. The availability of diploid, tetraploid and hexaploid species of Camelina allow the evolutionary trajectory and fate of duplicated genes in the neopolyploid Camelina species to be elucidated. Here we report an improved assembly of the widely used C. sativa reference DH55 and three new genome assemblies of Camelina microcarpa; one tetraploid CN119243 (2n = 26), and two hexaploids with divergent chromosome numbers, Type 1 - CN119205 (2n=40) and Type 2 - CN120025 (2n=38). The tetraploid represents the first step in the evolutionary path to form C. sativa, while the hexaploids suggest three divergent lineages in the formation of higher ploidy Camelina species. The previously uncharacterized fourth subgenome found in C. microcarpa Type 2, although showing some homology to the C. sativa diploid progenitor genome, C. neglecta, showed numerous unique chromosomal rearrangements differentiating it from other subgenomes present in known Camelina species. Although this species was recently formed, the second subgenome showed gene expression dominance, which was in contrast to both 2n=40 Camelina species where the third subgenome was dominant. The expression dominance in Type 2 C. microcarpa contradicted the accepted two-step evolutionary process which led to the generation of related Brassicaceae species. However, the observed genome dominance in all Camelina species was negatively correlated with inter-subgenome chromatin interaction frequencies, suggesting that chromosome confirmation and proximity in the nucleus contributes to this mechanism of genome evolution. Despite the differences in genome structure, successful inter-specific hybridization provided evidence of chromosomal exchange between the divergent third sub-genomes of C. sativa and C. microcarpa Type 2, opening up a novel avenue to new diversity in the established oilseed. Key pointsO_LIAn improved genomic understanding of Camelina species and identification of distinct subgenome structures and relationships, which will facilitate strategies to increase the genetic diversity in C. sativa. C_LIO_LISubgenome evolution and subgenome dominance in polyploids is associated with chromosomal architecture and proximity in the nucleus. C_LIO_LIGenome assemblies representing all ploidy levels in the Camelina genus provide a unique and valuable platform for polyploid research. C_LI

genomics↗

bioRxiv2025

Genomic Analysis Reveals Genetic Diversity, Population Structure and Evolutionary Dynamics in Bluebunch wheatgrass (Pseudoroegneria species)

Bluebunch wheatgrass (BBWG: Pseudoroegneria species) is an outcrossing perennial grass of considerable ecological and agricultural importance due to its resilience in adverse environmental conditions. To gain a deeper understanding of the diversity, population structure, and genetic relationship within the Pseudoroegneria genus, we analyzed genomic variations of 145 genotypes representing seven species (P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata) from major global lineages, using genotyping-by-sequencing. Our results identify six distinct genetic clusters, with P. spicata (a North America species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutional history of Eurasian BBWG species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, which revealed potential gene flow events. Our findings suggest that the Eurasian BBWG species have undergone reticulate evolution, characterized by substantial gene flow.

genomics↗

bioRxiv2024

Harnessing genome prediction in Brassica napus through a nested association mapping population

Genome prediction (GP) significantly enhances genetic gain by improving selection efficiency and shortening crop breeding cycles. Using a nested association mapping (NAM) population a set of diverse scenarios were assessed to evaluate GP for vital agronomic traits in B. napus. GP accuracy was examined by employing different models, marker sets, population sizes, marker densities, and incorporating genome-wide association (GWAS) markers. Eight models, including linear and semi-parametric approaches, were tested. The choice of model minimally impacted GP accuracy across traits. Notably, two models, rrBLUP and RKHS, consistently yielded the highest prediction accuracies. Employing a training population of 1500 lines or more resulted in increased prediction accuracies. Inclusion of single nucleotide absence polymorphism (SNaP) markers significantly improved prediction accuracy, with gains of up to 15%. Utilizing the Brassica 60K Illumina SNP array, our study effectively revealed the genetic potential of the B. napus NAM panel. It provided estimates of genomic predictions for crucial agronomic traits through varied prediction scenarios, shedding light on achievable genetic gains. These insights, coupled with marker application, can advance the breeding cycle acceleration in B. napus. Core ideasO_LIGenome prediction (GP) enhances genetic gains by improving selection efficiency and shortening breeding cycles. C_LIO_LIFactors influencing GP accuracy include model choice, marker types, and population size. C_LIO_LIInclusion of SNaP markers and highly significant GWAS markers improves prediction accuracy, shedding light on achievable genetic gains. C_LI Plain SummaryGenome prediction (GP) is a powerful tool that helps us improve crops more efficiently. In this study, we assessed how well GP works for predicting important traits in Brassica napus plants. We tested different models and marker sets to see which ones were most accurate. We found that two models, rrBLUP and RKHS, were consistently the best. Also, including certain types of genetic markers, like SNaP markers and highly significant GWAS markers, improved the predictions. Overall, our study shows that GP can help us understand the genetic potential of B. napus plants and improve breeding strategies, which can be exploited to develop better varieties more quickly, which is good news for farmers and the food supply.

genomics↗

bioRxiv2023

Enhancing Rice Growth and Yield with Weed Endophytic Bacteria Alcaligenes faecalis and Metabacillus indicus Under Reduced Chemical Fertilization

Endophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified as Alcaligenes faecalis (BTCP01) from Eleusine indica (Goose grass) and Metabacillus indicus (BTDR03) from Cynodon dactylon (Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection of nifH and ipdC genes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.

microbiology↗

bioRxiv2023

GPFN: Prior-Data Fitted Networks for Genomic Prediction

Genomic Prediction (GP) methods predict the breeding value of unphenotyped individuals in order to select parental candidates in breeding populations. Among models for GP, classical linear models have remained consistently popular, while more complex nonlinear methods such as deep neural networks have shown comparable accuracy at best. In this work, we propose the Genomic Prior-Data Fitted Network (GPFN) as a new paradigm for GP. GPFNs perform amortized Bayesian inference by simulating hundreds of thousands or millions of plant or animal populations. This allows GPFNs to be deployed without requiring any training or tuning, providing predictions in a single inference pass. On three populations of plants across two different crop species, GPFNs perform significantly better than the linear baseline on 13 out of 16 traits. On a challenging betweenfamilies structured prediction task on a third crop species, the GPFN matches the performance of the linear baseline while outperforming it in one location. GPFNs represent a completely new direction for the field of genomic prediction, and have the potential to unlock levels of selection accuracy not possible with existing methods, especially in diverse populations.

bioinformatics↗

bioRxiv2022

Quantitative Evaluation of Nonlinear Methods for Population Structure Visualization & Inference

Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between sub-populations in a population as a result of non-random mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics it is an important confounding variable in genome wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this paper, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is either known a-priori through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to PCA, while neural network based methods fall behind.

bioinformatics↗

bioRxiv2020

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

The ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity and aggressiveness were determined in a population of 127 isolates from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was an unique haplotype. Analysis of molecular variation showed 97% was due to isolate and 3% to geographical location. Testing of mycelium compatibility identified clones of mutually compatible isolates, and stings of pairwise compatible isolates not seen before. Importantly, mutually compatible isolates had similar SSR haplotype, in contrast to high diversity among incompatible isolates. Isolates from the Province of Manitoba had higher allelic richness and higher mycelium compatibility (61%) than Alberta (35%) and Saskatchewan (39%). All compatible Manitoba isolates were interconnected in clones and strings, which can be explained by wetter growing seasons and more susceptible crops species both favouring more mycelium interaction and life cycles. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus and restricted outcrossing due to mycelium incompatibility, and only one meiosis per lifecycle. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides, not withstanding the high mutation rate of SSRs compared to genes. It seems accumulation of these polymorphisms lead to increasing mycelium incompatibility in a population over time. A phylogenetic tree grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Results were significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs. Since the S. sclerotiorum life cycle is universal, conclusions on sources of genomic diversity extrapolates to populations in other geographical areas and host crops. Author summarySclerotinia sclerotiorum populations from various plant species and geographical areas have been studied extensively using mycelium compatibility tests and genotyping with a shared set of 6-13 SSR markers published in 2001. Most conclude the pathogen is clonally propagated with some degree of outcrossing. In the present study, a population of S. sclerotiorum isolates from 1.5 million km2 area in western Canada were tested for mycelium compatibility, and genotyped with 9 published and 30 newly developed SSR markers targeting all chromosomes in the dikaryot genome (8+8). A new way of visualizing mycelium compatibility results revealed clones of mutual compatible isolates, as well as long and short strings of pairwise compatible isolates. Importantly, clonal isolates had similar SSR haplotype, while incompatible isolates were highly dissimilar; a relationship difficult to discern previously. Analysis of population structure found a lack of linkage disequilibrium ruling out random recombination. Outcrossing, a result of alignment of non-sister chromosomes during meiosis, is unlikely in S. sclerotiorum, since mycelium incompatibility prevents karyogamy, and compatibility only occur between isolates with similar genomic composition. Instead, genomic diversity comprise transfer of nuclei through hyphal anastomosis, allelic modifications during cell division and point mutation. Genomic polymorphisms accumulate over time likely result in gradual divergence of individuals, which seems to resemble the ring-species concept. We are currently studying whether nuclei in microconidia might also contribute to diversity. A phylogenetic analysis grouped isolates into 17 sub-populations. One isolate from each sub-population showed different level of aggressiveness when inoculated onto B. napus lines previously determined to have quantitative resistance to a single isolate. Seed of these lines and S. sclerotiorum isolates have been transferred to plant breeders, and can be requested from the corresponding author for breeding purposes. Quantitative resistance is likely to hold up over time, since the rate of genomic change is relatively slow in S. sclerotiorum.

microbiology↗

bioRxiv2020

High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome.

High-quality nanopore genome assemblies were generated for two Brassica nigra genotypes (Ni100 and CN115125); a member of the agronomically important Brassica species. The N50 contig length for the two assemblies were 17.1 Mb (58 contigs) and 0.29 Mb (963 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short read assembly for Ni100 corroborated genome integrity and quantified sequence related error rates (0.002%). The contiguity and coverage allowed unprecedented access to low complexity regions of the genome. Pericentromeric regions and coincidence of hypo-methylation enabled localization of active centromeres and identified a novel centromere-associated ALE class I element which appears to have proliferated through relatively recent nested transposition events (<1 million years ago). Computational abstraction was used to define a post-triplication Brassica specific ancestral genome and to calculate the extensive rearrangements that define the genomic distance separating B. nigra from its diploid relatives.

genomics↗