Browsing by Author "Westbrook, Jared W."

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    A genome-guided strategy for climate resilience in American chestnut restoration populations
    Sandercock, Alexander M.; Westbrook, Jared W.; Zhang, Qian; Holliday, Jason A. (National Academy of Sciences, 2024-07-16)
    American chestnut (Castanea dentata) is a deciduous tree species of eastern North America that was decimated by the introduction of the chestnut blight fungus (Cryphonectria parasitica) in the early 20th century. Although millions of American chestnuts survive as root collar sprouts, these trees rarely reproduce. Thus, the species is considered functionally extinct. American chestnuts with improved blight resistance have been developed through interspecific hybridization followed by conspecific backcrossing, and by genetic engineering. Incorporating adaptive genomic diversity into these backcross families and transgenic lines is important for restoring the species across broad climatic gradients. To develop sampling recommendations for ex situ conservation of wild adaptive genetic variation, we coupled whole-genome resequencing of 384 stump sprouts with genotype–environment association analyses and found that the species range can be subdivided into three seed zones characterized by relatively homogeneous adaptive allele frequencies. We estimated that 21 to 29 trees per seed zone will need to be conserved to capture most extant adaptive diversity. We also resequenced the genomes of 269 backcross trees to understand the extent to which the breeding program has already captured wild adaptive diversity, and to estimate optimal reintroduction sites for specific families on the basis of their adaptive portfolio and future climate projections. Taken together, these results inform the development of an ex situ germplasm conservation and breeding plan to target blight-resistant breeding populations to specific environments and provides a blueprint for developing restoration plans for other imperiled tree species.
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    Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade‐off with American chestnut ancestry implies resistance is polygenic
    Westbrook, Jared W.; Zhang, Qian; Mandal, Mihir Kumar; Jenkins, Eric V.; Barth, Laura E.; Jenkins, Jerry W.; Grimwood, Jane; Schmutz, Jeremy; Holliday, Jason A. (Wiley, 2019-10-02)
    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 resistance of Chinese chestnut based on a hypothesis of major gene resistance. To accelerate selection within two backcross populations that descended from two Chinese chestnuts, we developed 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 similar accuracy 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 resistance of these trees and their progeny. On average, selected BC₃F₂ trees inherited 83% of their genome from American chestnut and have blight resistance that is intermediate between F₁ hybrids and American chestnut. Results suggest polygenic inheritance of blight resistance. The blight resistance of restoration populations will be enhanced through recurrent selection, by advancing additional sources of resistance through fewer backcross generations, and by potentially by breeding with transgenic blight‐tolerant trees.
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    A reference genome assembly and adaptive trait analysis of Castanea mollissima 'Vanuxem,' a source of resistance to chestnut blight in restoration breeding
    Staton, Margaret; Addo-Quaye, Charles; Cannon, Nathaniel; Yu, Jiali; Zhebentyayeva, Tetyana; Huff, Matthew; Islam-Faridi, Nurul; Fan, Shenghua; Georgi, Laura L.; Nelson, C. Dana; Bellis, Emily; Fitzsimmons, Sara; Henry, Nathan; Drautz-Moses, Daniela; Noorai, Rooksana E.; Ficklin, Stephen; Saski, Christopher; Mandal, Mihir Kumar; Wagner, Tyler K.; Zembower, Nicole; Bodenes, Catherine; Holliday, Jason A.; Westbrook, Jared W.; Lasky, Jesse; Hebard, Frederick, V; Schuster, Stephan C.; Abbott, Albert G.; Carlson, John E. (2020-07-23)
    Forest tree species are increasingly subject to severe mortalities from exotic pests, pathogens, and invasive organisms, accelerated by climate change. Such forest health issues are threatening multiple species and ecosystem sustainability globally. One of the most extreme examples of forest ecosystem disruption is the extirpation of the American chestnut (Castanea dentata) caused by the introduction of chestnut blight and root rot pathogens from Asia. Asian species of chestnut are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of a reference genome for Chinese chestnut (C. mollissima) "Vanuxem," one of the donors of disease resistance for American chestnut restoration. From the de novo assembly of the complete genome (725.2 Mb in 14,110 contigs), over half of the sequences have been anchored to the 12 genetic linkage groups. The anchoring is validated by genetic maps and in situ hybridization to chromosomes. We demonstrate the value of the genome as a platform for research and species restoration, including signatures of selection differentiating American chestnut from Chinese chestnut to identify important candidate genes for disease resistance, comparisons of genome organization with other woody species, and a genome-wide examination of progress in backcross breeding for blight resistance. This reference assembly should prove of great value in the understanding, improvement, and restoration of chestnut species.