Biology subjects

Smart, C. D.

Publications and source records attributed to Smart, C. D..

9 recordsLinked to original sources

bioRxiv2026

Mobile genetic elements accompany the emergence of clonal crop lineages from weed-associated populations of Xanthomonas campestris

Xanthomonas campestris is a destructive pathogen of cruciferous vegetables and ornamentals and is frequently isolated from related weed species growing near agricultural land. However, the evolutionary relationships, genomic features, and biosecurity significance of weed-associated strains remain poorly understood. Here, we integrate phylogenomic and pangenomic analyses of X. campestris, including nine newly sequenced strains isolated from invasive garlic mustard (Alliaria petiolata), to compare strains from cultivated and non-cultivated hosts across multiple pathovars. Weed-isolated strains predominantly clustered within basal, genetically diverse lineages associated with broad host ranges, whereas crop-isolated strains were concentrated in host-associated clonal lineages. The emergence of specialized crop-associated lineages coincided with multiple inferred acquisitions of large mobile elements, including integrative conjugative and mobilizable elements and plasmids carrying genes previously associated with pathogenicity and host range. Although these elements were enriched in clonal crop-associated lineages, they also occurred in diverse weed-associated strains, indicating that genetic material associated with crop infection is distributed among divergent lineages and persists in wild and weedy systems. These findings identify invasive weeds as ancillary hosts that may harbor pathogen diversity and provide opportunities for genetic exchange, underscoring the importance of surveillance beyond agricultural fields to monitor pathogen diversification and emerging threats. Our pangenomic analysis also identified crop-associated pathogen factors and putative host resistance targets for future investigation, providing a foundation for developing critically needed black rot-resistant cultivars.

microbiology↗

bioRxiv2026

Spatial and temporal localization of Serratia ureilytica causing cucurbit yellow vine disease in cucurbits indicates phloem-associated colonization and systemic movement

Cucurbit yellow vine disease (CYVD), caused by the bacterium Serratia ureilytica, is a phloem-associated disease of cucurbits. This study characterized the spatial and temporal distribution of S. ureilytica in Cucurbita pepo cultivar Delicata plants under greenhouse conditions using a GFP-tagged isolate (P01). Seedlings were sampled weekly for four weeks. Transverse sections from the stem, petiole, leaf, shoot apex, and root were imaged by laser scanning confocal and fluorescent dissecting microscopy. In parallel, bacterial abundance in each plant tissue was assessed by quantifying colony-forming units (CFU) via droplet plating over a 4-week time course. Across plant tissues and time points, S. ureilytica fluorescent signal was primarily concentrated in the inner and outer periphery of the bicollateral vascular bundles, with higher magnification images revealing mainly symplastic localization within phloem-associated cells. Consistent with the imaging results, bacterial quantification data showed a high abundance of CFUs in the main stem across weeks, with an irregular pattern of presence in the distal tissues at later time points. These results suggest that S. ureilytica is predominantly localized within phloem-associated cells and spreads both acropetally and basipetally during infection.

plant biology↗

bioRxiv2021

Quantitative genetic analysis of interactions in the pepper-Phytophthora capsici pathosystem

The development of pepper cultivars with durable resistance to the oomycete Phytophthora capsici has been challenging due to differential interactions between the species that allow certain pathogen isolates to cause disease on otherwise resistant host genotypes. Currently, little is known about the pathogen genes that are involved in these interactions. To investigate the genetic basis of P. capsici virulence on individual pepper genotypes, we inoculated sixteen pepper accessions - representing commercial varieties, sources of resistance, and host differentials - with 117 isolates of P. capsici, for a total of 1,864 host-pathogen combinations. Analysis of disease outcomes revealed a significant effect of inter-species genotype-by-genotype interactions, although these interactions were quantitative rather than qualitative in scale. Isolates were classified into five pathogen subpopulations, as determined by their genotypes at over 60,000 single-nucleotide polymorphisms (SNPs). While absolute virulence levels on certain pepper accessions significantly differed between subpopulations, a multivariate phenotype reflecting relative virulence levels on certain pepper genotypes compared to others showed the strongest association with pathogen subpopulation. A genome-wide association study (GWAS) identified four pathogen loci significantly associated with virulence, two of which colocalized with putative RXLR effector genes and another with a polygalacturonase gene cluster. All four loci appeared to represent broad-spectrum virulence genes, as significant SNPs demonstrated consistent effects regardless of the host genotype tested. Host genotype-specific virulence variants in P. capsici may be difficult to map via GWAS, perhaps controlled by many genes of small effect or by multiple alleles that have arisen independently at the same loci.

plant biology↗

bioRxiv2021

Morphometric relationships and their contribution to biomass and cannabinoid yield in hybrids of hemp (Cannabis sativa)

The breeding of hybrid cultivars of hemp (Cannabis sativa L.) is not well described, especially the segregation and inheritance of traits that are important for yield. A total of 23 families were produced from genetically diverse parents to investigate the inheritance of morphological traits and their association with biomass accumulation and cannabinoid yield. In addition, a novel classification method for canopy architecture was developed. The strong linear relationship between wet and dry biomass provided an accurate estimate of final dry stripped floral biomass. Of all field and aerial measurements, basal stem diameter was determined to be the single best selection criterion for final dry stripped floral biomass yield. Along with stem diameter, canopy architecture and stem growth predictors described the majority of the explainable variation of biomass yield. Within-family variance for morphological and cannabinoid measurements reflected the heterozygosity of the parents. While selfed populations suffered from inbreeding depression, hybrid development in hemp will require at least one inbred parent to achieve uniform growth and biomass yield. Nevertheless, floral phenology remains a confounding factor in selection because of its underlying influence on biomass production highlighting the need to understand the genetic basis for flowering time in the breeding of uniform cultivars. HighlightStem and canopy architecture traits are superior predictors of floral biomass yield and offer a good indication of hybrid uniformity in field plantings of genetically diverse cannabinoid hemp populations.

plant biology↗

bioRxiv2020

A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash

Phytophthora root and crown rot, caused by the soilborne oomycete pathogen Phytophthora capsici, leads to severe yield losses in squash (Cucurbita pepo). To identify quantitative trait loci (QTL) involved in resistance to this disease, we crossed a partially resistant squash breeding line with a susceptible zucchini cultivar and evaluated over 13,000 F2 seedlings in a greenhouse screen. Bulked segregant analysis with whole genome resequencing (BSA-Seq) resulted in the identification of five genomic regions - on chromosomes 4, 5, 8, 12, and 16 - featuring significant allele frequency differentiation between susceptible and resistant bulks in each of two independent replicates. In addition, we conducted linkage mapping using a population of 176 F3 families derived from individually genotyped F2 individuals. Variation in disease severity among these families was best explained by a four-QTL model, comprising the same loci identified via BSA-Seq on chromosomes 4, 5, and 8 as well as an additional locus on chromosome 19, for a combined total of six QTL identified between both methods. Loci, whether those identified by BSA-Seq or linkage mapping, were of small to moderate effect, collectively accounting for 28-35% and individually for 2-10% of the phenotypic variance explained. However, a multiple linear regression model using one marker in each BSA-Seq QTL could predict F2:3 disease severity with only a slight drop in cross-validation accuracy compared to genomic prediction models using genome-wide markers. These results suggest that marker-assisted selection could be a suitable approach for improving Phytophthora crown and root rot resistance in squash.

plant biology↗

bioRxiv2020

Sexual dimorphism and sex ratio bias in the dioecious willow Salix purpurea L.

PremiseSexual dimorphism in dioecious plant species is often not obvious or is absent. Dioecious species populations also often exhibit deviations from expected sex ratios. Previous studies on members of the Salicaceae family have shown strong, partial, and no sexual dimorphism. Some studies have shown sex-biased ratios in several Salix spp., however, S. purpurea has never been examined for evidence of sexual dimorphism or for the presence of sex-ratio bias, and therefore a comprehensive phenotypic study is needed to fill this knowledge gap. MethodsThis study examined a suite of morphological, phenological, physiological and wood composition traits from multi-environment and multi-year replicated field trials in a diversity panel of unrelated S. purpurea accessions and in full-sib F1 and F2 families produced through controlled cross pollinations to test for sexual dimorphism and sex ratio bias. Key ResultsSignificant evidence of sexual dimorphism was found in vegetative traits with greater means for many traits in male genotypes compared to females across three populations of S. purpurea, measured across multiple years that were highly predictive of biomass yield. Male plants exhibited greater nitrogen accumulation under fertilizer amendment as measured by SPAD in the diversity panel, and males showed greater susceptibility to fungal infection by Melampsora spp in the F2 family. There were also consistent female-biased sex ratios in both the F1 and F2 families. ConclusionsThese results provide the first evidence of sexual dimorphism in S. purpurea and also confirm the prevalence of female-biased sex ratios previously found in other Salix species.

plant biology↗

bioRxiv2020

Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity

Phytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) State and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single-nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam insensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam insensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA Polymerase I, the enzyme that has been hypothesized to be the target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.

plant biology↗

bioRxiv2019

The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2/RipBN

Race 1 strains of Pseudomonas syringae pv. tomato, which causes bacterial speck disease of tomato, are becoming increasingly common and no simply-inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 Pst strains by recognizing the type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein thereby activating RPS2-mediated immunity. Ptr1 also recognized homologs of AvrRpt2 from diverse bacteria including one in Ralstonia pseudosolanacearum and this correlated with the ability of AvrRpt2 to degrade RIN4. Using site-directed mutagenesis of AvrRpt2 we found that Ptr1 and RPS2 recognize identical features of AvrRpt2. However, the genome sequence of S. lycopersicoides revealed no RPS2 homolog in the Ptr1 region. Ptr1 could play an important role in controlling bacterial speck disease and its future cloning may shed light on an example of convergent evolution for recognition of a widespread type III effector.

plant biology↗

bioRxiv2016

Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici

Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a pathogenic organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a growers field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed pathogenic isolates collected in 2009-13 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-10; mixed generational in 2011; and ultimately all inbred in 2012-13. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.

evolutionary biology↗