Biology subjects

Bunting, V.

Publications and source records attributed to Bunting, V..

4 recordsLinked to original sources

bioRxiv2026

Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover (Trifolium incarnatum L.) for breeding purposes

AO_SCPLOWBSTRACTC_SCPLOWCrimson clover (Trifolium incarnatum L.) is an obligately outcrossing, cool-season annual legume valued for forage and cover cropping, yet genomic resources to support systematic improvement are limited. We performed the first and most comprehensive whole-genome resequencing (WGR) of global crimson clover germplasm to (i) characterize diversity and population structure and (ii) develop a public mid-density enrichment capture panel for breeding applications. A core set of 45 accessions sequenced at [~]50X generated 5.84 million variants, while 149 additional accessions sequenced at [~]2.54X yielded 17.05 million variants. After stringent filtering, we retained 542,790 high-confidence SNPs from the high-coverage dataset and [~]2.4 million from the low-pass cohort. Population analyses (PCA, ADMIXTURE) revealed compact clustering of cultivars, broader dispersion of wild and uncertain-status accessions, and low overall differentiation (FST = 0.0105) with excess heterozygosity (FIS = -0.0592), consistent with obligate outcrossing. Guided by these resources, we designed a 28,913-SNP TWIST hybrid-capture panel enriched for genic regions and evenly distributed across seven chromosomes. This panel is being deployed within Auburn Universitys crimson clover breeding program to support population improvement and cultivar development. The resulting genomic resources provide a reproducible, mid-density genotyping platform for trait discovery, predictive breeding, and diversity monitoring. Together, these advances bring crimson clover genomic resources on par with other legumes such as soybean (Glycine max (L.) Merr.) and alfalfa (Medicago sativa), establishing a robust foundation for genomics-assisted improvement of this key cover and forage crop in U.S. sustainable agriculture. CORE IDEASO_LIWhole-genome re-sequencing of 194 crimson clover accessions revealed >21 M variants. C_LIO_LIHigh-confidence SNP catalogs from 50X and 2X data enable cost-effective genotyping. C_LIO_LIGenetic diversity is weakly structured, with cultivars clustering narrowly by origin. C_LIO_LIA 28,913 SNP enrichment panel delivers uniform genome coverage and >75% genic content. C_LIO_LIThese genomic tools accelerate GWAS, genomic selection, and breeding innovation. C_LI

genomics↗

bioRxiv2025

Engineering anaerobic fungal-bacterial consortia for medium-chain fatty acid production from lignocellulosic biomass

Lignocellulosic biomass is a renewable feedstock for sustainable fuels and chemicals, yet industrial conversion remains constrained by carbohydrate solubilization. Inspired by herbivore rumen microbiomes, we engineered an anaerobic fungal-bacterial consortium converting native lignocellulose into medium-chain fatty acids (MCFAs) without pretreatment. Systematic screening identified a newly isolated anaerobic fungus, Neocallimastix sp. FC1, in co-culture with Megasphaera hexanoica as a top-performing pair, achieving a lignocellulose-to-MCFA yield of 21.0 % (carbon-to-carbon basis) through tight lactate cross-feeding without competition for soluble sugars. Because fungal lactate production rate constrained the growth of M. hexanoica, the bacterium reallocated protein from growth toward chain elongation, resulting in increased MCFAs production over butyrate. These results demonstrate that high lignocellulose-to-MCFA conversion by the consortium requires high lactate-producing capability and operating regimes sustaining low lactate concentrations at high flux. Technoeconomic analysis further identifies the cost and yield thresholds required for economically viable deployment, establishing quantitative design targets for pretreatment-free fungal-bacterial lignocellulose upgrading.

bioengineering↗

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

Hydrophobins from Aspergillus mediate fungal interactions with microplastics

Microplastics present myriad ecological and human health risks including serving as a vector for pathogens in human and animal food chains. However, the specific mechanisms by which pathogenic fungi colonize these microplastics have yet to be explored. In this work, we examine the opportunistic fungal pathogen, Aspergillus fumigatus, and other common soil and marine Aspergilli, which we found bind microplastics tightly. Up to 3.85+/-1.48 g microplastic plastic/g fungi were bound and flocculated for polypropylene (PP), polyethylene (PE), and polyethylene terephthalate (PET) powders and particles ranging in size from 0.05 - 5 mm. Gene knockouts revealed hydrophobins as a key biomolecule driving microplastic-fungi binding. Moreover, purified hydrophobins were still able to flocculate microplastics independent of the fungus. Our work elucidates a role for hydrophobins in fungal colonization of microplastics and highlights a potential target for mitigating the harm of microplastics through engineered fungal-microplastic interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/622132v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@13eb679org.highwire.dtl.DTLVardef@3dc9c0org.highwire.dtl.DTLVardef@888c96org.highwire.dtl.DTLVardef@c5e1aa_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementMicroplastics pose serious ecological and human health effects by introducing pathogens and toxins into animal and human food chains. Many pathogenic microorganisms preferentially form biofilms on microplastic particles that are then ingested. Here, we demonstrate that hydrophobins, highly hydrophobic, cell surface proteins, enable microplastic binding and colonization by the opportunistic pathogen Aspergillus fumigatus and other fungi within the Aspergillus genus. Our work recognizes a novel role for hydrophobin proteins, identifying potential strategies for pathogen control and protein-based microplastics recovery.

molecular biology↗