Biology subjects

Harder, A. M.

Publications and source records attributed to Harder, A. M..

10 recordsLinked to original sources

bioRxiv2026

Pangenomics and machine learning reveal genetic variation to optimize carotenoids in sorghum grain

Enhancing grain carotenoid concentration to increase yellowness and provitamin A content in sorghum (Sorghum bicolor [L.] Moench) is a major breeding objective across sub-Saharan Africa. Carotenoid breeding is constrained by costly post-harvest phenotyping and can be accelerated through genetic markers that capture functional variation in key carotenoid biosynthesis genes. Zeaxanthin epoxidase (ZEP) is a major gene controlling sorghum grain carotenoid accumulation, and SNP-based KASP markers facilitate selection of high-carotenoid grain, although quantitative variation remains among lines carrying the favorable allele. We hypothesized that additional functional variation within ZEP and other carotenoid biosynthesis pathway genes contributes to this variation and can be revealed by a pangenome-informed analysis. Using a 33-member pangenome reference, we characterized sequence and structural variation at ZEP and other key carotenoid biosynthesis genes and applied pangenome-derived genotyping to study marker diversity associated with carotenoid accumulation. Evaluation of ZEP in the pangenome reference revealed previously uncharacterized structural variation that is absent from the BTx623 primary reference genome. A pangenome-based association analysis identified genetic markers associated with the accumulation of carotenoids which were specific to particular pangenome reference members, including in RTx430 and SRN39, both yellow endosperm lines. Machine learning identified markers in ZEP, {beta}-OH, ZDS, and Z-ISO as the most predictive for all carotenoid traits, suggesting a multi-locus genetic architecture underlies the accumulation of carotenoids in sorghum grain. By integrating sorghum pangenomic resources with machine learning, this study establishes a framework for pangenome-accelerated trait discovery and identifies new genetic targets for carotenoid biofortification in sorghum.

genomics↗

bioRxiv2025

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

O_LIEukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. C_LIO_LIHere, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the speciess current genetic diversity to catalogue variation in genome structure and content. C_LIO_LIAcross this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. C_LIO_LIOur findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop. C_LI

genomics↗

bioRxiv2025

Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes

While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating protein-coding gene annotations across pangenomes in a single pangene set remains challenging, both because of methodological inconsistency and biological presence-absence variation (PAV). Here, we review and experimentally evaluate the root of genome annotation and pangene set inconsistency using two polyploid plant pangenomes: cotton and soybean, which were chosen because of their existing diverse high-quality genomic resources and the known importance of gene presence-absence variation in their respective breeding programs. We first demonstrate that building pangene sets across different genome resources is highly error prone: PAV calculated directly from the genome annotations hosted on public repositories recapitulates structure in annotation methods and not biological sequence differences. Re-annotation of all genomes with a single identical pipeline largely resolves the broadest stroke issues; however, substantial challenges remain, including a surprisingly common case where exactly identical sequences have different gene model structural annotations. Combined, these results clearly show that pangenome gene model annotations must be carefully integrated before any biological inference can be made regarding sequence evolution, gene copy-number, or presence-absence variation.

bioinformatics↗

bioRxiv2025

Delivering trait-enhanced varieties to African smallholders through a pangenomic breeding network

Pangenomics has been promoted to accelerate breeding of orphan crops, but smallholder farmers in developing nations have seen little benefit so far. To address this gap, we built a global pangenomic breeding network, integrating African breeding programs, U.S. land grant universities, and international nonprofit research organizations. Here we demonstrate that pangenomics, when integrated with local crop improvement knowledge and global scientific partnerships, can facilitate breeding of drought and pest resilient varieties for smallholders. To breed trait-enhanced sorghum varieties with lgs1-1 resistance to witchweed (Striga hermonthica) for smallholders in Niger, one of the worlds least developed nations, we used population genomics across local and global scales to develop lgs1-1 Striga resistance markers, and deployed them for rapid introgression of resistance into locally-preferred varieties. Genomic characterization, along with controlled experiments in laboratory, pot, field stations, and smallholder farms, confirmed lgs1-1 resistance was introgressed without loss of essential local-preference traits. New pangenomic resources, including global resequencing and graph pangenomes, further accelerated design of broadly-applicable markers. Unlocking the potential of pangenomics for stress-resilience breeding depended on stakeholder input, strong inference, South-led decision support software, and a dense collaborative network. The experience of the network provides a scalable roadmap for collaborative pangenomic breeding of trait-enhanced varieties for the worlds lowest-resourced farmers.

genomics↗

bioRxiv2025

Developing future resilience from signatures of adaptation across the sorghum pangenome

While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum 1-4, and many other crops that were not homogenized during the green revolution 5, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes 6. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

genomics↗

bioRxiv2024

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa

Ancient whole-genome duplications (WGDs) are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent WGDs may contribute to evolvability within recent polyploids. Hybridization accompanying some WGDs may combine divergent gene content among diploid species. Some theory and evidence suggest that polyploids have a greater accumulation and tolerance of gene presence-absence and genomic structural variation, but it is unclear to what extent either is true. To test how recent polyploidy may influence pangenomic variation, we sequenced, assembled, and annotated twelve complete, chromosome-scale genomes of Camelina sativa, an allohexaploid biofuel crop with three distinct subgenomes. Using pangenomic comparative analyses, we characterized gene presence-absence and genomic structural variation both within and between the subgenomes. We found over 75% of ortholog gene clusters are core in Camelina sativa and <10% of sequence space was affected by genomic structural rearrangements. In contrast, 19% of gene clusters were unique to one subgenome, and the majority of these were Camelina-specific (no ortholog in Arabidopsis). We identified an inversion that may contribute to vernalization requirements in winter-type Camelina, and an enrichment of Camelina-specific genes with enzymatic processes related to seed oil quality and Camelinas unique glucosinolate profile. Genes related to these traits exhibited little presence-absence variation. Our results reveal minimal pangenomic variation in this species, and instead show how hybridization accompanied by WGD may benefit polyploids by merging diverged gene content of different species.

genomics↗

bioRxiv2022

Detectability of runs of homozygosity is influenced by analysis parameters as well as population-specific demographic history

Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical data sets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference. We also apply a sensitivity analysis to evaluate the effects of various parameter values on ROH-calling results and demonstrate its utility for parameter value selection. We show that ROH inferences can be biased when sequencing depth and the distribution of ROH length is not interpreted in light of demographic history as well as program-specific tendencies. This is particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermining conservation initiatives. Based on our observations, we suggest using a combination of ROH detection tools and ROH length-specific inferences to generate robust population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort typical of conservation genomics studies.

evolutionary biology↗

bioRxiv2021

High-quality reference genome for an arid-adapted mammal, the banner-tailed kangaroo rat (Dipodomys spectabilis)

Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semi-arid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (D. spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (D. ordii and D. stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes. Significance statementKangaroo rats in the genus Dipodomys occur in a wide variety of habitat types, ranging from scrublands to arid deserts, and are increasingly impacted by habitat fragmentation with populations of many species in strong decline. To facilitate population and conservation genomic studies of Dipodomys species, we generated the first reference genome assembly for the extensively studied banner-tailed kangaroo rat (D. spectabilis) from long read PacBio sequencing data. The genome assembly presented here will serve as a valuable resource for studies of Dipodomys species--which have long served as ecological and physiological models for the study of osmoregulation--comparative genomic surveys of mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.

genomics↗

bioRxiv2019

Incipient resistance to an effective pesticide results from genetic adaptation and the canalization of gene expression

The resistance of bacteria, disease vectors, and pest species to chemical controls has vast ecological, economic, and societal costs. In most cases, resistance is only detected after spreading throughout an entire population. Detecting resistance in its incipient stages, by comparison, provides time to implement preventative strategies. Incipient resistance can be detected by coupling standard toxicology assays with large-scale gene expression experiments. We apply this approach to a system where an invasive parasite, sea lamprey (Petromyzon marinus), has been treated with the highly-effective pesticide 3-trifluoromethyl-4-nitrophenol (TFM) for 60 years. Toxicological experiments revealed that lamprey from treated populations did not have higher survival to TFM exposure than lamprey from their native range, demonstrating that full-fledged resistance has not yet evolved. In contrast, we find hundreds of genes differentially expressed in response to TFM in the population with the longest history of exposure, many of which relate to TFMs primary mode of action, the uncoupling of oxidative phosphorylation and subsequent depletion of ATP. Three genes critical to oxidative phosphorylation, ATP5PB, PLCB1, and NDUFA9, were nearly fixed for alternative alleles in comparisons of SNPs between native and treated populations (FST > 5 SD from the mean). ATP5PB encodes subunit b of ATP synthase and an additional subunit, ATP5F1B, was canalized for high expression in treated populations, but remained plastic in response to TFM treatment in individuals from the native range. These combined genomic and transcriptomic results demonstrate that an adaptive, genetic response to TFM is driving incipient resistance in a damaging pest species.

genetics↗

bioRxiv2019

Among family variation in survival and gene expression uncovers adaptive genetic variation in a threatened fish

Variation in among-family transcriptional responses to different environmental conditions can help to identify adaptive genetic variation, even prior to a selective event. Coupling differential gene expression with formal survival analyses allows for the disentanglement of treatment effects, required for understanding how individuals plastically respond to environmental stressors, from the adaptive genetic variation responsible for among-family variation in survival and gene expression. We applied this experimental design to investigate responses to an emerging conservation issue, thiamine (vitamin B1) deficiency, in a threatened population of Atlantic salmon (Salmo salar). Thiamine is an essential vitamin that is increasingly limited in many ecosystems. In Lake Champlain, Atlantic salmon cannot acquire thiamine in sufficient quantities to support natural reproduction; fertilized eggs must be reared in hatcheries and treated with supplemental thiamine. We evaluated transcriptional responses (RNA-seq) to thiamine treatment across families and found 3,616 genes differentially expressed between control (no supplemental thiamine) and treatment individuals. Fewer genes changed expression additively (i.e., equally among families) than non-additively (i.e., family-by-treatment effects) in response to thiamine. Differentially expressed genes were related to known physiological effects of thiamine deficiency, including oxidative stress, cardiovascular irregularities, and neurological abnormalities. We also identified 1,446 putatively adaptive genes that were strongly associated with among-family survival in the absence of thiamine treatment, many of which related to neurogenesis and visual perception. Our results highlight the utility of coupling RNA-seq with formal survival analyses to identify candidate genes that underlie the among-family variation in survival required for an adaptive response to natural selection.

evolutionary biology↗