Biology subjects

Craddock, J. H.

Publications and source records attributed to Craddock, J. H..

3 recordsLinked to original sources

bioRxiv2025

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree.

genomics↗

bioRxiv2021

Environmental niche and demographic modeling of American chestnut near its southwestern range limit

AO_SCPLOWBSTRACTC_SCPLOWThe inadvertent introduction and rapid spread of chestnut blight (caused by Cryphonectria parasitica (Murr.) Barr) in the early 20th century resulted in the demise of American chestnut (Castanea dentata (Marsh.) Borkh.; Fagaceae) as a major component of forest canopies and had negative impacts on eastern forest communities. Research efforts over the last century have documented the persistence of occasional trees and root crown/stump sprouts throughout much of the species historic range providing the basis for ongoing breeding of blight-resistant stock and restoration efforts. Unfortunately, it remains unclear how much of the historic range remains climatically suitable for remnant trees that may harbor unique genetic variation for successful reintroduction efforts. Here we investigate whether the southwestern portion of the historical range remains environmentally suitable for undiscovered remnant populations of C. dentata using environmental niche modeling. We also use stage-structured matrix projection models to investigate the potential demographic future of C. dentata in W Tennessee, N Mississippi, SW Kentucky, and NW Alabama based upon observations of American chestnut in these areas over the last several decades. We found that suitable habitat associated with higher elevations and areas of high forest canopy cover occurs throughout much of the southwestern portion of the historical range and that populations of American chestnut in these areas are predicted to drastically decline over the next ~100-200 years without conservation interventions to mitigate the negative consequences of chestnut blight.

ecology↗

bioRxiv2019

Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis

The genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

plant biology↗