Biology subjects

Buell, C. R.

Publications and source records attributed to Buell, C. R..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatially resolved transcriptomics of poplar reveals tissue organization across shoot-associated organs

Poplar (Populus spp.) is a model for tree biology and a platform for engineering woody biomass, biofuels, biomaterials, and bioproducts. Many relevant traits depend on tissue position, developmental stage, and cell type, yet these spatial relationships are difficult to recover from bulk or single-cell transcriptomes. Here, we generated a spatial transcriptome atlas of Populus tremula x P. alba INRA 717-1B4 across the shoot apex, axillary bud, stem, and petiole. After quality control, the atlas retained 29,687 spatial spots from 45 tissue sections and detected 58,748 genes. Histology-guided clustering and marker analysis resolved meristematic, epidermal, cortical, vascular, and organ-specific domains. Cross-organ comparisons assessed whether published markers retained tissue-associated expression across different anatomical contexts and developmental stages, while de novo analysis identified additional domain-enriched candidates. As case studies of the utility of the atlas, we examined the emergence of trichome-associated programs in the shoot apex and adaxial - abaxial expression differences in petioles. A trichome identity score based on poplar markers from the single-cell shoot atlas peaked along the inferred meristem-to-primordium trajectory, revealing spatially localized expression of trichome-associated programs during early leaf development. Petiole expression differences were concentrated in the epidermis and cortex and involved polarity-associated, auxin-responsive, and cell-wall-remodeling genes, with distinct expression profiles across leaf positions. Together, these data provide a spatial reference for investigating tissue differentiation and developmental patterning in a transformable poplar genotype.

plant biology↗

bioRxiv2026

Time-dependent transcriptomic changes following protoplast isolation in plants

Protoplast isolation is widely used for plant functional genomics and single-cell analyses, but its impact on transcriptional and cell state dynamics remains incompletely understood. Here, we generated time-course RNA-seq data from leaf protoplasts of Arabidopsis, maize, and poplar, sampling at multiple time points following isolation, to systematically characterize global transcriptional dynamics across species. We identified two major drivers of transcriptional variation: a persistent protoplast isolation effect and a progressive time-dependent transcriptional program, which can be divided into early, middle, and late stages corresponding to an immediate stress response, metabolic and chromatin regulation dynamics, and sustained metabolic and proteostasis regulation, together with species-specific differences across stages. We observed a rapid loss of cell-type-specific transcriptional signatures within 6 hours in Arabidopsis and maize, whereas poplar showed a slower decline. Single-nucleus RNA-seq at 6 hours in maize confirmed attenuation of cell-type-specific transcriptional structure. Furthermore, leveraging this time-course dataset enables the identification of aberrant cell states in single-cell RNA-seq data, exemplified by clusters showing elevated activity of protoplast isolation-associated, middle-, and late-stage transcriptional programs characteristic of stress-like states. Together, our results provide a cross-species framework for dissecting protoplast-induced transcriptional and cell state dynamics and facilitate the systematic identification of stress-associated cell states in single-cell transcriptomic data.

plant biology↗

bioRxiv2026

A Comprehensive Epidermal Map from a Poplar Single-Cell Shoot Atlas Reveals New Trichome-Specific Genes

Poplar (Populus spp.) is a model system for tree biology. Specifically, P. tremula x P. alba INRA 717-1B4 (hereafter "poplar 717") has become an important platform for functional genomics and synthetic biology due to its rapid growth and ease of transgenesis. Here, we present a single-cell RNA-seq atlas of the poplar 717 shoot, including apical meristem, primary and secondary stems, and three stages of leaf development. Analysis of ca. 159,000 cells resolved 40 transcriptionally distinct clusters representing 7 major cell types, providing a high-resolution view of shoot development and tissue organization. We focused on the epidermis which constituted >15% of cells in the shoot atlas for in-depth characterization of epidermal heterogeneity. By integrating known marker genes with transcriptomic signatures consistent with established poplar leaf phytochemistry, we annotated epidermal cell subclusters corresponding to developmental stages, spatial location, and specialized cell types, including a distinct population of non-glandular trichomes. Coupling the single-cell RNA-seq atlas with bulk transcriptome data from glabrous mutants enabled the identification of novel trichome markers. Experimental validation of a representative trichome-specific promoter established a tool with potential to support cell type-targeted-metabolic engineering. We provide the poplar 717 atlas to the community through the BioPoplar Atlas Viewer (http://bio-poplar-atlas.com), providing a platform to explore the poplar transcriptome at single-cell resolution and a foundation for data-driven cell type-aware genetic engineering strategies in poplar.

plant biology↗

bioRxiv2026

Satellite DNA Editing Enables Meiosis-Independent Chromosome Engineering

Chromosome{square}scale genome engineering in plants typically relies on locus-specific recombination during meiosis to select desirable outcomes, limiting its application in species with long generation times. Here, we show that CRISPR targeting of abundant satellite DNA enables multiplexed chromosome restructuring in aspen, generating diverse large-scale structural variants in the first generation. These megabase rearrangements remain mitotically stable through clonal propagation and regeneration with no obvious growth defects.

plant biology↗

bioRxiv2026

Engineering carotenoid and steroidal glycoalkaloid depleted tomato fruit for heterologous production of high value terpenes

Plants produce specialized metabolites that function in plant defense and as attractants to pollinators and symbionts. One class of specialized metabolites are terpenoids that are synthesized from universal C5 building blocks via activities including terpene synthases, cytochromes P450, and glycosyl transferases. Some terpenes are highly valued for their use as insect repellants, fragrances, antimicrobial compounds, low calorie sweeteners, flavors, and medicines. Low abundance in target tissues, present in complex mixtures, as well as challenging extraction logistics are barriers to economic sustainable production of these compounds from their native species. While heterologous expression of terpenoid biosynthetic genes is feasible, the potential derivation of the products into conjugates via endogenous cytochromes P450 and glycosyl transferases limits this approach. In this project, we used multiplex gene editing technologies to overcome these challenges by creating novel tomato chassis with altered terpenoid biosynthetic capacity in fruit. Excluding central metabolic genes to minimalize impacts on growth and development, we selected 23 known and potential terpene-related genes expressed specifically in the fruit for gene editing. Fruit production and metabolic profiles of three chassis lines with alterations in the major classes of fruit specialized metabolites indicate loss of these genes is tolerated for fruit production. These combinatorial knockouts also showed modulation of native carbon reallocation toward endogenous sinks beneficial for a biosynthetic chassis. Establishing metabolite-modified fruit chassis demonstrates efficient combinatorial editing of entire branches of plant specialized metabolism, facilitating engineering of heterologous terpenes of industrial interest in tomato fruit.

plant biology↗

bioRxiv2025

Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding

Commercial potato in North America is a clonal autotetraploid crop, which complicates breeding. Efforts are underway to convert potato to a diploid inbred-hybrid crop that is amenable to additional breeding strategies and allows breeders to more quickly respond to demands for crop improvement. With the goal of preserving haplotypes developed over the last 200 years of selection, diploid potato breeding in the US started with the creation of diploids from tetraploid commercial varieties and advanced breeding lines through prickle pollination. This is an effective but slow method which presents a barrier to entry for individual breeding programs. Therefore, we developed 97 publicly available dihaploids (diploids from prickle pollination of tetraploids) as a resource for diploid breeding in the U.S. These clones contain the majority of alleles in the US breeding population for three market classes: chips, russets, and fresh market reds. To facilitate genomic informed breeding, all clones have been resequenced using short read sequencing technology, and we have developed de novo assemblies based on PacBio HiFi long reads for 20 individuals. As an illustration of how these data will be used in breeding, we explored the maturity locus (StCDF1) and identified 15 different alleles. The majority of dihaploids were heterozygous for early and late alleles, resulting in intermediate maturity. Beyond informing breeding, this data facilitates investigations into potato genomics. The dihaploid population is both highly heterozygous and incredibly diverse on a population level. In particular, there is extensive structural diversity, including copy number variation, segregating within the population. This contrasts with a relatively low genome-wide historical recombination rate ({rho}). Taken together, these findings indicate that potato is highly diverse, with much of that diversity found within long linkage blocks.

plant biology↗

bioRxiv2025

Single cell mass spectrometry reveals intercellular compartmentalization of camptothecin biosynthesis in the tree Camptotheca acuminata

The medicinal tree Camptotheca acuminata produces camptothecin, a monoterpenoid indole al- kaloid (MIA) precursor for several leading chemotherapeutic agents (Lorence and Nessler 2004). Alt- hough the biosynthesis of camptothecin remains poorly understood, a putative route has been hypothe- sized based on in planta metabolite profiling and feeding studies (Fig. 1a) (Sheriha and Rapoport 1976; Sadre et al. 2016). However, pathways proposed on whole-tissue or organ-level metabolomic and tran- scriptomic data lack resolution on the intricate, cell-specific compartmentalization of natural products biosynthesis. Such gaps could be addressed by single cell technologies, which have recently shown tremendous potential to transform gene discovery in herbaceous plants (Li et al. 2023; Zhan et al. 2023; Vu et al. 2024; Wu et al. 2024; McClune et al. 2025). Nevertheless, single cell mass spectrometry (scMS) has not been adapted for woody species, largely due to the challenges associated with their highly lignified tissue and complex cellular architecture. In this study, we developed an scMS pipeline for the woody tree C. acuminata to investigate the intercellular organization of camptothecin biosynthesis. O_FIG O_LINKSMALLFIG WIDTH=144 HEIGHT=200 SRC="FIGDIR/small/661346v1_fig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@17f7710org.highwire.dtl.DTLVardef@161c469org.highwire.dtl.DTLVardef@1a5ee1borg.highwire.dtl.DTLVardef@b361b9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Single cell metabolomics of Camptotheca acuminata. (a) Proposed camptothecin biosynthetic pathway. (b) Schematic experimental pipeline. (c) Dot plots showing concentrations of key metabolites in single cells across organs. Each data point rep- resents a protoplast. For each metabolite, dots were offset from the center based on the distribution of concentrations among sin- gle cells. (N.D.: not detected). (d) Stacked bars showing concentrations in individual cells of loganic acid, secologanic acid, strictosidinic acid, strictosamide, pumiloside, and camptothecin). Cells are organized into groups with loganic acid only (A), secologanic acid only (B), loganic and secologanic (C), strictosidinic acid only (D), and other alkaloids (strictosamide, pumiloside, and camptothecin) (E). In each group, cells are ordered by total metabolite concentration with highest concentration in the center and lower producers closer to the edges. Panel widths scale with the number of cells in each group, and colours cor- respond to individual metabolites. C_FIG

biochemistry↗

bioRxiv2025

Chromosome-scale genome assembly for Yellow Wood sorrel, Oxalis stricta

Yellow wood sorrel (Oxalis stricta L.), also known as sourgrass, juicy fruit, or sheep weed, is a member of the Oxalidaceae family. Yellow wood sorrel is commonly considered a weed and while native to North America, it is distributed across Europe, Asia, and Africa. To date, only two other genomes from the Oxalidaceae family have been published, star fruit (Averrhoa carambola L.) and Oxalis articulata Savingy. Here, we present a chromosome-scale assembly for O. stricta, revealing its allotetraploid nature and synteny within its two subgenomes as well as synteny with A. carambola and O. articulata. Using Oxford Nanopore Technologies long-read sequences coupled with chromatin capture sequencing, we generated a 436 Mb chromosome-scale assembly of O. stricta with a scaffold N50 length of 36.2 Mb that is anchored to 12 chromosomes across the two subgenomes. Assessment of the final genome assembly using the Long Terminal Repeat Assembly Index yielded a score of 13.12 and assessment of Benchmarking Universal Single Copy Orthologs revealed 99.3% complete orthologs; both metrics are suggestive of a high-quality reference genome. Total repetitive sequence content in the O. stricta genome was 39.7% with retroelements being the largest class of transposable elements. Annotation of protein-coding genes yielded 61,550 high confidence genes encoding 115,089 gene models. Synteny between the two O. stricta subgenomes was present in 91 syntenic blocks containing 40,705 genes, of which, 76.6% were present in 1:1 syntenic relationships between the two subgenomes. The availability of an annotated chromosome-scale high quality genome assembly for O. stricta will provide a launching point to understand the high fecundity of this weed and provide further foundation for comparative genomics within the Oxalidaceae.

genomics↗

bioRxiv2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

plant biology↗

bioRxiv2025

Discovery of iridoid cyclase completes the iridoid pathway in asterids

Iridoids are specialized monoterpenes ancestral to asterid flowering plants (Albach et al, 2001; Stull et al, 2018). Iridoids play key roles in plant defense and are also essential precursors for pharmacologically important alkaloids (Dobler et al, 2011; Eisner, 1964). The biosynthesis of all iridoids involves the cyclization of a reactive enol intermediate. While this cyclization occurs spontaneously at low yields, it has long been hypothesized that a dedicated enzyme is involved in this process (Geu-Flores et al, 2012; Lichman et al, 2019b). Here, we report the discovery of asterid iridoid cyclases (ICYC). We show that these enzymes catalyze cyclization of the reactive intermediate to form the two major iridoid stereoisomers found in plants. Our work uncovers the last missing key step in the otherwise well-characterized iridoid biosynthesis pathway in asterids. This discovery unlocks the possibility to generate previously inaccessible iridoid stereoisomers, which will enable metabolic engineering for the sustainable production of valuable iridoid and iridoid-derived compounds.

plant biology↗

bioRxiv2025

Single cell omics extends metabolic regulon via orthologous transcription factors from a pair of medicinal plant species

Camptotheca acuminata Decne is a woody medicinal tree that produces over a hundred bioactive compounds, including camptothecin, which has been used as the starting material to semi-synthesize many leading anticancer drugs (Lorence and Nessler 2004). Camptothecin and its derivatives are potent inhibitors of DNA topoisomerase I and are widely used for the treatment of lung, cervical, ovarian, and colon cancers. Camptothecin biosynthesis in C. acuminata involves complex catalytic steps, most of which remain undeciphered. In this pathway, tryptamine and secologanic acid are coupled, leading to strictosidinic acid. The formation of strictosidinic acid is catalyzed by strictosidine/strictosidine acid syn-thase enzymes (STR) (Fig. 1A). While a biosynthetic route for the conversion of the indole ring to the quinoline ring has been proposed, most of the underlying biosynthetic genes have yet to be identified (Fig. 1A) (Sadre et al. 2016). In addition, the cell type specificity of this pathway also remains undescribed. Here, we generated a single cell multiome (RNA-seq and Assay for Transposase Accessible Chromatin by sequencing [ATAC-seq] from the same nuclei) to probe the cell type specificity of camptothecin biosyn-thetic genes. O_FIG O_LINKSMALLFIG WIDTH=149 HEIGHT=200 SRC="FIGDIR/small/650021v2_fig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@81dcf0org.highwire.dtl.DTLVardef@1d03ae1org.highwire.dtl.DTLVardef@1c9b0a9org.highwire.dtl.DTLVardef@6d5238_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Single cell multi-ome of Camptotheca acuminata leaf. (A) The proposed biosynthetic pathway for camptotheci . Solid arrows indicate previously characterized enzymatic steps. Dashed arrows indicate proposed enzymatic steps (see Table S7 for gene name abbreviations). (B) Uniform Manifold Approximation and Projection (UMAP) of nuclei of the single nuclei RNA-seq dataset (n = 4,012), color coded by cell clusters. (C) Gene expression heatmap of MIA biosynthetic genes across cell clusters. Rows are expressed biosynthetic genes, which are ordered from upstream to downstream. Color scale shows the average scaled expression of each gene at each cell cluster. Cell clusters are sorted by cell types. Dot size indicates the percentage of cells where a given gene is detected. The predicted cell type for each cell cluster is annotated by the color strip below the x-axis. Box highlights expression of STR genes. (D) Heat map showing accessibility of cell type marker peaks across cell clusters. Each row is an ATAC-seq peak. Each column is a cell cluster. Color scale is maxed out at 90th percentile of normalized ATAC-seq signal. The predicted cell type for each cell cluster is annotated by the color strip below the x-axis, with the same color palette as (B). (E) Heatmap showing gene expression across cell clusters. Each row is a gene within 2-kb of a STR+ marker peak. Each column is a cell cluster. The predicted cell type for each cell cluster is annotated by the color strip below the x-axis, with the same color palette as (B). (F) DNA motif enriched in STR+ marker peaks, as well as a reference MYB motif. C_FIG

plant biology↗

bioRxiv2025

High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes

Photoperiodic changes in diel cycles of gene expression are pervasive in plants. Timing of circadian regulators together with light signals regulate multiple photoperiod dependent responses such as growth, flowering or tuber formation. However, for most genes the importance of cyclic mRNA levels is less clear. We analyzed the diel transcriptome of modern cultivated potato, a highly heterozygous autotetraploid. Clonal propagation and limited meiosis have led to the accumulation of deleterious alleles and therefore tetraploid potato is an ideal model system to investigate the conservation of cyclic expression and cyclic genes during the artificial selection process. We observed that cyclic alleles were more highly expressed than non-cyclic ones and were highly co-expressed not only under diel cycles but also across tissues, developmental stages and stress conditions. Moreover, the smaller ratio of non-synonymous to synonymous differences within cyclic as compared to non-cyclic allelic groups indicates that cyclic genes, in general, have more conserved core functions than those of non-cyclic ones. In accordance with this observation, fully rhythmic allelic groups were highly enriched in photosynthesis and ribosome biogenesis genes, which play core functions in plants. Furthermore, we investigated differences in cyclic expression patterns between photoperiods. We identified transcription factors potentially regulating the strong differences in phase between photoperiods observed in ribosome biogenesis and pathogen response genes. Finally, analyses of genes involved in tuber formation suggests that the regulation of CO gene transcription is not the only factor enabling tuberization under long days in modern cultivated potato. This study not only provides high quality diel transcriptomic datasets of cultivated potato but also important insight on the role of allelic diversity in rhythmic expression in plants.

plant biology↗

bioRxiv2025

A reference-quality NLRome for the hexaploid sweetpotato and diploid wild relatives

Breeding for sweetpotato (Ipomea batatas) resistance requires accelerating our understanding genomic of sources of resistance. Nucleotide-binding domain leucine-rich repeat receptors (NLRs) proteins represent a key component of the plant immune system that mediate plant immune responses. We cataloged the NLR diversity in 32 hexaploid sweetpotato genotypes and three diploid wild relatives using resistance gene enrichment sequencing (RenSeq) to capture and sequence full NLRs. A custom designed NLR bait-library enriched NLR genes with an average 97% target capture rate. We employed a curated database of cloned and functionally characterized NLRs to assign sequenced sweetpotato NLRs to canonical phylogenetic clades. We identified between 800 to 1,200 complete NLRs, highlighting the expanded diversity of coiled-coil NLRs (CNLs) across all genotypes. NLRs among sweetpotato genotypes exhibited large conservation across genotypes. Phylogenetic distance between 6X (hexaploid) and 2X (diploid) genotypes revealed that a small repertoire of I. batatas CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid (Ipomoea trifida) genomes and recorded clustering of NLRs on chromosomes arms. Our study provides a catalog of NLR genes that can be used to accelerate breeding and increase our understanding of evolutionary dynamics of sweetpotato NLRs.

plant biology↗

bioRxiv2024

Enzymatic epimerization of monoterpene indole alkaloids in Kratom

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-{beta}-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contain a non-canonical 3R stereocenter. Herein, we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (Kratom). We discover the presence of the iminium species, 20S-3-dehydrocorynantheidine, which led us to hypothesize that isomerization of 3S to 3R occurs by oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments implicated young leaves and stems as the sites for pathway biosynthesis, facilitating the identification of an oxidase/reductase pair that catalyzes this epimerization. This enzyme pair has broad substrate specificity, suggesting that the oxidase and reductase may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in Kratom. These enzymes allow biocatalytic access to a range of previously inaccessible pharmacologically active compounds.

biochemistry↗

bioRxiv2024

Jan and mini-Jan, a model system for potato functional genomics

Potato (Solanum tuberosum) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, Jan, which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two "mini-Jan" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato.

plant biology↗

bioRxiv2024

Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato

The hexaploid sweetpotato (Ipomoea batatas [L.] Lam.) is a globally important stable crop and plays a significant role in biofortification. The high resilience and adaptability of sweetpotato provide it with advantages in addressing food security and climate change issues. Here we report a haplotype-resolved chromosome-level genome assembly of an African cultivar, Tanzania, which enables ancestry inference along the haplotype-phased chromosomes. Our analyses reveal that the wild tetraploid I. aequatoriensis, currently found in coastal Ecuador, is the closest known relative of sweetpotato and likely a direct descendant of one of the sweetpotato progenitors. The other unknown progenitor(s) of sweetpotato have a closer genetic relationship to the wild tetraploid I. batatas 4x, distributed in Central America, than to I. aequatoriensis. The different ancestral sequences are not distributed in typical subgenomes but are intertwined on the same chromosomes, possibly due to the known non-preferential recombination among haplotypes. Although I. batatas 4x was not involved in the hexaploidization event, introgression from I. batatas 4x to the hexaploid sweetpotato is evident. Our study improves our understanding of sweetpotato origin and provides valuable genomic resources to accelerate sweetpotato breeding.

plant biology↗

bioRxiv2024

K-mer Genome-wide Association Study for Anthracnose and BCMV Resistance in the Andean Diversity Panel

Limited genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) have limited breeders from fully utilizing molecular genetics technologies to maximize genetic gain. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and Bean Common Mosaic Virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results--albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to k-mer mapping criteria and the absence of target loci in the reference genome due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers were mapped to the reference genome. To determine the genetic context of cis-associated k-mers, we generated whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible. CORE IDEASO_LIK-mer-based GWAS offers new advantages for mapping pan-genomic variation C_LIO_LIComparison of reference-based SNP to reference-free k-mer GWAS C_LIO_LINovel discovery of cis-associated k-mers for dry bean disease resistance C_LI PLAIN LANGUAGE SUMMARYImproving disease resistance in crop species such as bean is critical. We surveyed the genomes of a diverse set of bean lines and identified sequences associated with resistance to a fungal and viral pathogen. Access to the genomes of this diversity panel of beans will permit additional discoveries on the role of structural variation in phenotypes, including disease resistance.

plant biology↗

bioRxiv2024

Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression

Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome-scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. There is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large-scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of inter-species hybridizations in Salvia. PLAIN LANGUAGE SUMMARYChia pinta is an economically important crop due to the high fatty acid present in the seeds. There are multiple types of Chia based on the seeds color including mixed which and black (Chia pinta), black (Chia negra), and white (Chia blanca). We generated a genome assembly of Chia pinta and compared it to existing genome assemblies. While the assemblies are highly similar there are key differences in terpene synthase composition between Chia pinta and Chia negra. We also sequenced 20 other Chia accessions with different seed color and geographic origin to determine a population structure within Chia. We generated genomic resources to further our understanding of this food crop. ABBREVIATIONSBGC Biosynthetic gene cluster BUSCO Benchmarking Universal Single Copy Orthologs GO Gene ontology SNP Single nucleotide polymorphism TIR Terminal inverted repeat TPS Terpene synthase WGS Whole genome shotgun

genomics↗