Biology subjects

Shannon, L. M.

Publications and source records attributed to Shannon, L. M..

8 recordsLinked to original sources

bioRxiv2026

Haplotype-resolved genome of autotetraploid alfalfa (Medicago sativa) Regen-SY27x uncovers large scale structural variation and resistance gene dynamics

Polyploid genome assembly presents unique challenges due to extensive heterozygosity and complex haplotype structure. We report a haplotype-resolved, chromosome-scale assembly of Regen-SY27x, a genotype of autotetraploid alfalfa (Medicago sativa), which is widely used for genetic modification because of its excellent regenerative capacity in tissue culture. Using PacBio HiFi long reads, Omni-C scaffolding, and linkage map guided phasing, we generated a 3.2 GB assembly comprising four haplotypes with high contiguity and completeness. Kmer-based validation confirmed accurate haplotype separation, while linkage map integration and dotplot analysis identified and corrected chimeric scaffolds. Gene annotation yielded 221,688 protein-coding genes, with more than 99% assigned to pseudochromosomes. Repetitive elements accounted for 62.7% of the genome, dominated by long terminal repeat retrotransposons and a high fraction of Helitrons. The spatial enrichment of Helitrons within gene-dense distal chromosome arms underscores their pivotal role as key drivers of genomic innovation and gene family expansion. We identified 3,696 nucleotide-binding leucine-rich repeat R genes, with Toll/interleukin-1 receptor-like and Rx-type subclasses forming large tandem clusters across haplotypes. Comparative analyses revealed strong macrosyntenic conservation among Regen-SY27x and the publicly available Chinese alfalfa genomes but extensive structural variation both within Regen-SY27x haplotypes and between Regen-SY27x and the Chinese genotypes with tens of thousands of duplications, inversions, and translocations detected. These results demonstrate that a single autotetraploid individual captures extensive structural diversity, but individuals from different populations vary greatly. The Regen-SY27x assembly provides a foundational genomic resource for investigating polyploid genome evolution and identifying genetic variation relevant to biological and agronomic improvement in alfalfa. Article SummaryThis study presents the first chromosome-scale, haplotype-resolved genome assembly of the US alfalfa germplasm, Regen-SY27x, a key alfalfa genotype used widely for genetic engineering. We integrated HiFi long reads, Omni-CTM scaffolding, and linkage map-guided phasing to reconstruct all four haplotypes of this complex autotetraploid. Our results identified 221,688 protein-coding genes and reveal immense intra-individual structural variations dominated by small duplications. This high-quality reference serves as a foundational tool for the alfalfa community, enabling researchers to link complex structural diversity with agronomic traits and further enhance the biotechnological potential of this essential forage crop.

genomics↗

bioRxiv2026

Single-Plant Genome-Wide Association Study Identifies Loci Controlling Multiple Vegetative Architecture Traits in Cultivated Northern Wild Rice (Zizania palustris L.)

Cultivated Northern Wild Rice (Zizania palustris L.) is an obligately outcrossing, self-incompatible cereal grown in aquatic paddies in the United States. Genetic improvement has relied primarily on phenotypic recurrent selection, and genomic approaches remain largely unexplored in this emerging crop. We applied a single-plant genome-wide association study (sp-GWAS) framework to dissect vegetative architecture traits in five open-pollinated cultivated populations evaluated across three years (n = 2,173 plants). Plant height (PH), basal stem width (BSW), primary stem width (PSW), flag leaf length (FLL), and flag leaf width (FLW) were analyzed using a mixed linear model accounting for population structure and kinship. Broad-sense heritability ranged from 0.03 to 0.34, and year effects explained up to 54% of phenotypic variance, indicating strong environmental influence. After filtering 73,363 SNPs, genome-wide linkage disequilibrium decayed rapidly (r{superscript 2} = 0.1 at [~]2.3 kb). A total of 124 significant SNPs (FDR < 0.01) were consolidated into 98 loci, of which 46 were associated with multiple traits and 11 were shared across four traits. Candidate genes near multi-trait loci included conserved regulatory classes implicated in grass architecture, including HLH/bHLH transcription factors. Diplotype analyses at candidate loci revealed both simple biallelic and complex multi-allelic haplotype structures, indicating that locus-level haplotype effects underlie several GWAS signals. Results demonstrate that sp-GWAS can detect statistically robust associations in a highly heterozygous, non-replicable crop system and suggest a polygenic, coordinated genetic architecture governing vegetative growth. These findings support genomic prediction and multi-trait selection strategies to accelerate improvement of cultivated Northern Wild Rice. PLAIN LANGUAGE SUMMARYCultivated Northern Wild Rice is an important specialty crop grown in flooded paddies in the United States. Unlike many major crops, it is naturally outcrossing and highly variable, which makes traditional breeding challenging and slow. Most improvement efforts have relied on selecting plants based only on how they look in the field, and genomic tools have rarely been used. In this study, we used DNA markers to better understand the genetics behind plant structure traits such as plant height, stem thickness, and leaf width. We evaluated more than 2,000 plants from five cultivated populations over three growing seasons. Because weather and growing conditions strongly influence these traits, we used statistical models to separate environmental effects from genetic effects. We identified 98 regions of the genome associated with variation in plant structure. Many of these regions influenced more than one trait, showing that plant height, stem strength, and leaf size are genetically connected. Several regions contained genes similar to those known to control plant growth and development in other grasses. We also found that, in some cases, combinations of nearby DNA variants (haplotypes) explained trait differences better than single genetic markers. Overall, this work shows that modern genomic tools can successfully identify useful genetic variation in cultivated Northern Wild Rice, even though it is highly outcrossing and genetically diverse. These results provide a foundation for using genomic selection to improve plant structure, lodging resistance, and overall performance in breeding programs. CORE IDEASO_LISingle-plant GWAS successfully detects genetic associations in obligately outcrossing cultivated Northern Wild Rice where conventional replicated mapping populations are impractical. C_LIO_LIVegetative architecture traits exhibit low heritability but retain recoverable polygenic signal, where nearly half of detected loci influence multiple architecture traits, indicating integrated developmental control. C_LIO_LIGenome-wide linkage disequilibrium decays rapidly ([~]2.3 kb), consistent with expectations for an obligately outcrossing species and supporting relatively localized association signals. C_LIO_LICandidate genes include conserved regulatory classes (TE1-like, HLH/bHLH, SPL). C_LIO_LIGiven extensive overlap between QTL and environmental effect, multi-trait, multi-environment genomic prediction provides a pragmatic breeding strategy to improve canopy efficiency, lodging resistance, and harvestability in aquatic production systems. C_LI

genomics↗

bioRxiv2026

Transcriptional architecture underlying development, adaptation, and domestication in Northern Wild Rice (Zizania palustris L.)

AO_SCPLOWBSTRACTC_SCPLOWZizania palustris (Northern Wild Rice) is an aquatic grass native to North America and a crop wild relative of Oryza sativa with ecological, cultural, and agricultural significance. Here, we present a transcriptomic atlas spanning 20 tissues across six major developmental stages. Seed tissues showed shifts in abscisic acid, gibberellin, and ethylene pathways that define the hormonal basis of deep dormancy in this recalcitrant species and its release. Leaf development showed stage-specific reprogramming, from hypoxia-responsive programs in submerged tissues to cell wall remodeling and redox regulation during aquatic-aerial transitions, with photosynthesis and carbohydrate metabolism defining flag leaves and SRG1 divergence emerging as a defining feature of leaf development in Z. palustris. Reproductive tissues expressed duplicated homologs of well-recognized shattering genes with divergent regulation, consistent with subfunctionalization after whole-genome duplication. These findings provide new insight into traits underlying ecological adaptation and domestication in Z. palustris and related grasses. CORE IDEASO_LIA first transcriptomic atlas for Northern Wild Rice maps gene expression across 20 tissues and six developmental stages, providing a foundational functional genomics resource for Zizania palustris. C_LIO_LISeed dormancy and release are driven by coordinated hormone reprogramming, with shifts in ABA, GA, and ethylene pathways across whole seed, embryo, and endosperm. C_LIO_LILeaf development is defined by aquatic-to-aerial transcriptional transitions, moving from hypoxia-responsive programs in submerged tissues to cell wall remodeling, redox regulation, and photosynthesis/metabolism in aerial and flag leaves. C_LIO_LIWhole-genome duplication underlies regulatory divergence in domestication traits, as duplicated homologs of canonical seed shattering genes show paralog- and tissue-specific expression consistent with subfunctionalization. C_LIO_LIThe atlas identifies tissue-specific modules and stable housekeeping candidates, enabling improved experimental design (e.g., expression normalization) and accelerating candidate prioritization for breeding, GWAS/eQTL, and trait discovery. C_LI PLAIN LANGUAGE SUMMARYNorthern Wild Rice (Zizania palustris) is an aquatic grass native to North America that is important for ecosystems, agriculture, and Indigenous cultures. In this study, we created a detailed gene expression map across 20 different tissues and six stages of plant development. We found that seeds strongly regulate plant hormones that control dormancy, helping explain why Northern Wild Rice seeds remain dormant for long periods and how they eventually germinate. Leaves showed clear changes in gene activity as plants moved from underwater growth to above-water growth, shifting from low-oxygen stress responses to processes that support photosynthesis and structural strength. In flowers, we identified duplicated genes involved in seed shattering that are regulated differently, likely due to past genome duplication events. Together, these results improve our understanding of how Northern Wild Rice is adapted to aquatic environments and how key traits relevant to domestication have evolved.

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↗

bioRxiv2024

Targeted genotyping-by-sequencing of potato and software for imputation

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTM technology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTM SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics. Core IdeasO_LIA mid-density, targeted genotyping-by-sequencing (GBS) assay was developed for potato. C_LIO_LIThe GBS assay includes markers for resistance to potato virus Y, golden cyst nematode, and potato wart. C_LIO_LIThe GBS assay includes multi-allelic markers for potato maturity and tuber shape. C_LIO_LIThe polyBreedR software has functions for manipulating and imputing polyploid marker data in Variant Call Format. C_LIO_LILinkage Analysis was more accurate than the Random Forest method when imputing from 2K to 10K markers. C_LI

genomics↗

bioRxiv2023

A scalable, low-cost phenotyping strategy to assess tuber size, shape, and the colorimetric features of tuber skin and flesh in potato breeding populations

Tuber size, shape, colorimetric characteristics, and defect susceptibility are all factors that influence the acceptance of new potato cultivars. Despite the importance of these characteristics, our understanding of their inheritance is substantially limited by our inability to precisely measure these features quantitatively on the scale needed to evaluate breeding populations. To alleviate this bottleneck, we developed a low-cost, semi-automated workflow to capture data and measure each of these characteristics using machine vision. This workflow was applied to assess the phenotypic variation present within 189 F1 progeny of the A08241 breeding population. Our results provide an example of quantitative measurements acquired using machine vision methods that are reliable, heritable, and can be used to understand and select upon multiple traits simultaneously in structured potato breeding populations.

plant biology↗

bioRxiv2022

Genetic Analysis of Wild and Cultivated Populations of Northern Wild Rice (Zizania palustris L.) Reveal New Insights into Gene Flow and Domestication

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and a Zizania aquatica outgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

genetics↗

bioRxiv2019

Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying novel associations and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. Author SummaryComplex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants - from 173,000 to 24 million - that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.

genomics↗