Comparative transcriptomics and eQTL mapping of response to Melampsora americana in selected Salix purpurea F2 progeny

Polygenic pathogen networks influence transcriptional plasticity in the Arabidopsis-Botrytis pathosystem

Bidirectional flow of information shapes the outcome of the host-pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to genetic variation in both the host and pathogen. To study co-transcriptome plasticity, we conducted transcriptomics using natural genetic variation in the pathogen, Botrytis cinerea, and large-effect genetic variation abolishing defense signaling pathways within the host, Arabidopsis thaliana. We show that genetic variation in the pathogen has a greater influence on the co-transcriptome than mutations that abolish defense signaling pathways in the host. Genome-wide association mapping using the pathogens' genetic variation and both organisms' transcriptomes allowed an assessment of how the pathogen modulates plasticity in response to the host. This showed that the differences in both organism's responses were linked to trans-expression quantitative trait loci (eQTL) hotspots within the pathogen's genome. These hotspots control gene sets in either the host or pathogen and show differential allele sensitivity to the host's genetic variation rather than qualitative host specificity. Interestingly, nearly all the trans-eQTL hotspots were unique to the host or pathogen transcriptomes. In this system of differential plasticity, the pathogen mediates the shift in the co-transcriptome more than the host.

De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions

Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance.

Evidence of Asexual Overwintering of Melampsora paradoxa and Mapping of Stem Rust Host Resistance in Salix

Melampsora rust is a devastating disease of shrub willow in North America. Previous work has identified Melampsora paradoxa as one of two identified rust species in New York State that infect Salix purpurea and other important Salix host species, however little is known about the population of this rust species in this region. Genotyping-by-sequencing was used to identify single nucleotide polymorphisms (SNPs) and assess population diversity of M. paradoxa isolates collected from three Salix breeding populations in Geneva, NY between 2015 and 2020. Statistical analyses of SNP revealed that all isolates collected were clonally derived even though they were collected across years. In 2020, isolates were collected from stem infections where uredospore pustules were observed, and these isolates were also identical to M. paradoxa collected in previous seasons. These data suggest that M. paradoxa sampled across multiple years overwintered and reproduced asexually and that stem infection is a possible mechanism for overwintering, both of which are novel findings for this rust species. Additionally, field disease ratings were conducted on a S. purpurea × S. suchowensis F₁ breeding population with high disease severity, enabling the discovery of QTL for resistance on chromosomes 1 and 19. Lastly, Colletotrichum salicis was frequently associated with stem rust and may play a role in M. paradoxa stem infection. Together, this work is the first substantial exploration into M. paradoxa population biology, stem infection, and host resistance in Salix.

The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.