Exploring the Genomic Basis of Traits Relevant to Evolution and Ecology of Chestnut (Castanea) Using High-throughput DNA Sequencing and Bioinformatics
Abstract
Introduced pests and pathogens have devastated forest ecosystems in the temperate zone; in eastern North America, introduced pests and pathogens have led to the elimination of most mature elms (Ulmus), ashes (Fraxinus), hemlocks (Tsuga) and chestnuts (Castanea) over large areas where these genera were formerly abundant and important for local ecosystems. The restoration of species affected by introduced pests and pathogens requires the development and propagation of trees that possess heritable resistance. High-throughput DNA sequencing and genomics provide opportunities for researchers to identify resistance gene candidates, screen germplasm, and develop markers for marker-assisted selection in breeding programs, with the goal of restoring ecologically important wild trees to the landscape. American chestnut (Castanea dentata) is currently the focus of a major research effort that intends to restore the species by incorporating blight resistance from Chinese chestnut (Castanea mollissima), a species that is generally resistant to chestnut blight. I investigated several aspects of chestnut genomics and blight resistance with the goal of aiding the blight resistance breeding program for American chestnut. I tested a detached-leaf assay for chestnut blight resistance and learned that it may not be useful for screening advanced backcross (BC3) progeny in chestnut blight resistance breeding programs (Chapter 2). Utilizing a recent draft assembly of the Chinese chestnut reference genome, I analyzed patterns of genetic variation across regions associated with chestnut blight resistance, and found that several loci associated with blight resistance show markedly elevated nucleotide diversity in the most resistant Chinese chestnuts relative to more susceptible trees. At other blight-associated loci, genetic diversity was low in all C. mollissima (Chapter 3). This indicates that while maintaining high allelic diversity at blight resistance loci is desirable for a resistance breeding program, it may not be essential. Assessing potential unintended effects of hybrid breeding on the ecological behavior of restored chestnuts, I found that several genetic loci in third backcross (BC3) chestnut appear to affect caching decisions by squirrels due to inheritance of C. mollissima alleles that influence seed traits (Chapter 4). The reason for backcrossing in the American chestnut breeding program is to avoid the short, branchy mature form of C. mollissima. By sequencing the genomes of wild and orchard-derived Chinese chestnuts, I showed that some genomic loci under selection in orchard chestnuts (i.e., artificially selected by humans) may influence crown form (Chapter 5). This work should provide the basis for further investigations that validate the phenotypic effects of the proposed candidate genes, and utilize information on genetic polymorphisms identified here to accelerate chestnut improvement programs.
Degree
Ph.D.
Advisors
Woeste, Purdue University.
Subject Area
Genetics|Forestry|Plant sciences|Physiology
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