Evolutionary And Functional Genetics Of Disease Resistance In Theobroma Cacao And Its Wild Relatives

Download or read book Evolutionary and Functional Genetics of Disease Resistance in Theobroma Cacao and Its Wild Relatives written by Noah Winters and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants have complex and dynamic immune systems that have evolved over millennia to help them resist pathogen invasion. Humans have worked to incorporate these evolved defenses into crops through breeding. However, many crop cultivars only harness a fraction of the overall genetic diversity available to a given species, or have such a long history of domestication that most diversity has been lost. Evaluating previously neglected germplasm for desirable traits, such as disease resistance, is therefore an essential step towards breeding crops that are adapted to both current and emerging threats. In this dissertation, we examine the evolution of defense response across populations of Theobroma cacao L. and wild species of Theobroma, with the goal of identifying genetic elements essential for protection against the cacao pathogen Phytophthora palmivora. In Chapter 2, we combine data from RNA-sequencing, un-targeted metabolomics, and whole genome sequencing to discover genes and pathways associated with resistance. We found significant differences in transcriptional response across populations, indicating lineage-specific defenses. Among the processes shared across populations, however, was phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One of the genes in this pathway, caffeoyl-shikimate esterase (CSE), was up-regulated in response to pathogen challenge across all four populations, indicating its broad importance for cacao's defense response. Further experimental evidence suggested this gene synthesizes the antimicrobial compound caffeic acid, a known inhibitor of Phytophthora species. Together, our results indicate most of the expression variation associated with resistance is unique to populations. Moreover, they suggest using a small subset of clones to determine the basis of resistance to P. palmivora, as has been done in breeding programs for over five decades, provides limited power for discovering potentially useful genetic variation. Natural variation in resistance to P. palmivora is well documented across cacao lineages, but little is known about resistance in its wild, non-cacao relatives. In Chapter 3, we use non-cacao Theobroma species to investigate the evolution of defense response across the genus. We discovered both lineage-specific and conserved aspects of defense response, including upregulation of the phenylpropanoid pathway. Of particular interest were TcBBE8 and TcWRKY29, a pair of genes that were upregulated in response to pathogen challenge across five species of Theobroma and displayed evidence of positive selection. These results suggest some aspects of defense against P. palmivora are orthologous and, therefore, of fundamental important to defense across Theobroma. Nucleotide-binding leucine rich repeats receptors (NLR) are essential components of plant immunity. NLR evolution is complex and dynamic, full of rapid expansions, contractions, and polymorphism. The hundreds of high-quality plant genomes generated over the last two decades have provided substantial insight into the evolutionary dynamics of NLR genes. Despite steadily decreasing sequencing costs, the difficulty of sequencing, assembling, and annotating high-quality genomes has resulted in comparatively little genome-wide information on intraspecies NLR diversity. In Chapter 4, we investigate the evolution of NLR genes across 11 high quality genomes of cacao. We found 3-fold variation in NLR copy number across genotypes, a pattern primarily driven by the expansion of NLR clusters by tandem and proximal duplication. Together, our results suggest local duplications can radically reshape gene families over short evolutionary time scales, creating a source of NLR diversity that could be utilized to enrich our understanding of both plant-pathogen interactions and resistance breeding. This dissertation helps advance genomic research and resistance breeding in cacao in two significant ways. First, it identifies both conserved and lineage-specific aspects of Theobroma's defense against P. palmivora, indicating the potential value of wild germplasm to breeding programs. In doing so, it also identifies several high priority candidate genes for further functional characterization. Second, it classifies and analyzes immune receptor complement across a diverse set of cacao accessions, generating new knowledge about intraspecific evolution of large gene families and creating a resource for future NLR experimentation.