Biology subjects

Holliday, J. A.

Publications and source records attributed to Holliday, J. A..

4 recordsLinked to original sources

bioRxiv2025

Variation in responses to temperature across admixed genotypes of Populus trichocarpa x P. balsamifera predict geographic shifts in regions where hybrids are favored

O_LIPlastic responses of plants to their environment vary as a result of genetic differentiation within and among species. To accurately predict rangewide responses to climate change, it is necessary to characterize genotype-specific reaction norms across the continuum of historic and future climate conditions comprising a species range. C_LIO_LIThe North American hybrid zone of Populus trichocarpa and P. balsamifera represents a natural system that has been shaped by climate, geography, and introgression. We leverage a dataset containing 45 clonal genotypes from this natural hybrid zone, planted across 17 replicated common garden experiments spanning a broad climatic range. Growth and mortality were measured over two years, enabling us to model reaction norms for each genotype across these tested environments. C_LIO_LISpecies ancestry and intraspecific genomic variation significantly influenced growth across environments, with genotypic variation in reaction norms reflecting a trade-off between cold tolerance and growth. Using modeled reaction norms for each genotype, we predicted that genotypes with more P. trichocarpa ancestry may gain an advantage under warmer climates. C_LIO_LISpatial shifts of the hybrid zone could facilitate the spread of beneficial alleles into novel climates. These results highlight that genotypic variation in responses to temperature will have landscape-level effects. C_LI

evolutionary biology↗

bioRxiv2023

The road to restoration: Identifying and conserving the adaptive legacy of American chestnut

The American chestnut (Castanea dentata) is a functionally extinct tree species that was decimated by an invasive fungal pathogen in the early 20th century. Disease resistant chestnuts have been developed through hybridization and genetic modification, but these populations may lack the adaptive genomic diversity necessary to restore the species across its climatically diverse historical range. An understanding of the genomic architecture of local adaptation in wild American chestnut and identification of seed zones for germplasm conservation are necessary in order to deploy locally adapted, disease-resistant American chestnut populations. Here, we characterize the genomic basis of climate adaptation in remnant wild American chestnut, define seed zones based on climate envelopes and adaptive diversity, and make sampling recommendations for germplasm conservation. Whole genome re-sequencing of 384 trees coupled with genotype-environment association methods suggest the species range can be most parsimoniously subdivided into three seed zones characterized by relatively homogeneous allele frequencies relative to rangewide adaptive diversity. Using these data, we developed a method to estimate the number of samples required from each seed zone to recapitulate standing adaptive diversity in each seed zone, and found that on average, 21-29 trees will need to be conserved to capture 95% of the wild adaptive diversity. Taken together, these results will inform the development of an ex situ germplasm conservation and breeding plan to develop locally adapted blight-resistant American chestnut populations, and provide a blueprint for developing restoration plans for other imperiled tree species.

genomics↗

bioRxiv2022

Whole-genome resequencing reveals the population structure, genomic diversity, and demographic history of American chestnut (Castanea dentata)

American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the United States. In the first half of the 20th century, an exotic fungal pathogen - Cryphonectria parasitica - decimated the species, killing approximately four billion trees. Two approaches to developing blight resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted reforestation populations. Here we characterize population structure, demographic history, and genomic diversity in a range-wide sample of 384 wild American chestnuts to inform conservation and breeding with blight resistant varieties. Population structure analyses with DAPC and ADMIXTURE suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within-population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defense against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant populations. These populations will serve as management units for breeding adaptive genetic variation into the blight-resistant tree populations for targeted reintroduction efforts.

genomics↗

bioRxiv2019

Genomic selection analyses reveal tradeoff between chestnut blight tolerance and genome inheritance from American chestnut (Castanea dentata) in (C. dentata x C. mollissima) x C. dentata backcross populations

American chestnut was once a foundation species of eastern North American forests, but was rendered functionally extinct in the early 20th century by an exotic fungal blight (Cryphonectria parasitica). Over the past 30 years, The American Chestnut Foundation (TACF) has pursued backcross breeding to generate hybrids that combine the timber-type form of American chestnut with the blight tolerance of Chinese chestnut. The backcross strategy has been implemented based on the hypothesis that blight tolerance is conferred by few major effect alleles. We tested this hypothesis by developing genomic prediction models for five presence/absence blight phenotypes of 1,230 BC3F2 selection candidates and average canker severity of their BC3F3 progeny. We also genotyped pure Chinese and American chestnut reference panels to estimate the proportion of BC3F2 genomes inherited from parent species. We found that genomic prediction from a method that assumes an infinitesimal model of inheritance (HBLUP) has a similar predictive ability to a method that tends to perform well for traits controlled by major genes (Bayes C). Furthermore, the proportion of BC3F2 trees genomes inherited from American chestnut was negatively correlated with the blight tolerance of BC3F2 trees and their progeny. On average, selected BC3F2 trees inherited 83% of their genome from American chestnut and have blight-tolerance that is intermediate between F1 hybrids and American chestnut. Results suggest polygenic rather than major gene inheritance for blight tolerance. The blight-tolerance of restoration populations will be enhanced by advancing additional sources of blight-tolerance through fewer backcross generations and by potentially by breeding with transgenic blight-tolerant trees.

genomics↗