Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations

Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution

In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.

A novel tomato interspecific (Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm

We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

Beneath the blooms: Unearthing the effect of rhizospheric bacteria on floral signals and pollinator preferences

The relationship between plants and pollinators is known to be influenced by ecological interactions with other community members. While most research has focused on aboveground communities affecting plant-pollinator interactions, it is increasingly recognized that soil-dwelling organisms can directly or indirectly impact these interactions. Although studies have examined the effects of arbuscular mycorrhizal fungi on floral traits, there is a gap in research regarding similar effects associated with plant growth-promoting rhizobacteria (PGPR), particularly concerning floral scent. Our study aimed to investigate the influence of the PGPR Bacillus amyloliquefaciens on the floral traits of wild (Solanum habrochaites, Solanum pimpinellifolium and Solanum peruvianum) and cultivated tomato (Solanum lycopersicum), as well as the impact of microbially-driven changes in floral scent on the foraging behaviour of the stingless bee Melipona quadrifasciata. Our findings revealed that inoculating tomatoes with PGPR led to an increased number of flowers and enhanced overall floral volatile emission. Additionally, we observed higher flower biomass and pollen levels in all species, except S. peruvianum. Importantly, these changes in volatile emissions influenced the foraging behaviour of M. quadrifasciata significantly. Our results highlight the impact of beneficial soil microbes on plant-pollinator interactions, shedding light on the multiple effects that plant-microbial interactions can have on aboveground organisms.

Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops

MAIN CONCLUSION

Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.

Fruit quality and shelf-life of Sardinian tomato (Solanum lycopersicum L.) landraces

The conservation and characterization of landraces have key roles in the safeguarding and valorization of agrobiodiversity. Indeed, these plant genetic resources represent an important crop heritage with quality and sensory characteristics that can be of great use to consumers and industry. In addition, the preservation of genetic resources from the risk of progressive genetic erosion, and the enhancement of their potential can contribute to food security and improve the nutritional value of food. Accordingly, this study aimed to investigate a collection of Sardinian tomato landraces for parameters that have determinant roles in evaluating their responses to conservation, and therefore to consumer acceptance. Six Sardinian landraces and two commercial varieties were cultivated in a two-years off-season trial, harvested at two different maturity stages (turning, red-ripe) and characterized using 14 fruit-related quality parameters that define the marketability, nutritional value, and flavor of the fruit. Data were collected at intervals of 10 days, starting from the harvest date and over 30 days of storage under refrigeration. The simultaneous analysis of all the qualitative characteristics for the different genotypes allowed to clearly differentiate the local varieties from the commercial varieties and a few landraces emerged for their satisfactory performances, e.g. "Tamatta kaki" ad "Tamatta groga de appiccai". In particular, the "Tamatta groga de appiccai" showed satisfactory lycopene content at marketable stages (average 5.65 mg 100g-1 FF), a peculiar orange-pink color with the highest hue angle values (range: H°T0 = 72.55-H°T30 = 48.26), and the highest firmness among the landraces of the red-ripe group (range: EpT0 = 1.64-EpT30 = 0.54 N mm-1). These results highlight the potential of some of the Sardinian tomato landraces for developing new varieties or promoting their direct valorization in local markets and could considerably increase the effectiveness and efficiency of agrobiodiversity conservation strategies.

Two teosintes made modern maize

The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.

Structural variation underlies functional diversity at methyl salicylate loci in tomato

Methyl salicylate is an important inter- and intra-plant signaling molecule, but is deemed undesirable by humans when it accumulates to high levels in ripe fruits. Balancing the tradeoff between consumer satisfaction and overall plant health is challenging as the mechanisms regulating volatile levels have not yet been fully elucidated. In this study, we investigated the accumulation of methyl salicylate in ripe fruits of tomatoes that belong to the red-fruited clade. We determine the genetic diversity and the interaction of four known loci controlling methyl salicylate levels in ripe fruits. In addition to Non-Smoky Glucosyl Transferase 1 (NSGT1), we uncovered extensive genome structural variation (SV) at the Methylesterase (MES) locus. This locus contains four tandemly duplicated Methylesterase genes and genome sequence investigations at the locus identified nine distinct haplotypes. Based on gene expression and results from biparental crosses, functional and non-functional haplotypes for MES were identified. The combination of the non-functional MES haplotype 2 and the non-functional NSGT1 haplotype IV or V in a GWAS panel showed high methyl salicylate levels in ripe fruits, particularly in accessions from Ecuador, demonstrating a strong interaction between these two loci and suggesting an ecological advantage. The genetic variation at the other two known loci, Salicylic Acid Methyl Transferase 1 (SAMT1) and tomato UDP Glycosyl Transferase 5 (SlUGT5), did not explain volatile variation in the red-fruited tomato germplasm, suggesting a minor role in methyl salicylate production in red-fruited tomato. Lastly, we found that most heirloom and modern tomato accessions carried a functional MES and a non-functional NSGT1 haplotype, ensuring acceptable levels of methyl salicylate in fruits. Yet, future selection of the functional NSGT1 allele could potentially improve flavor in the modern germplasm.

Differential defensive and nutritional traits among cultivated tomato and its wild relatives shape their interactions with a specialist herbivore

Cultivated tomato presented lower constitutive volatiles, reduced morphological and chemical defenses, and increased leaf nutritional quality that affect its resistance against the specialist herbivore Tuta absoluta compared to its wild relatives. Plant domestication process has selected desirable agronomic attributes that can both intentionally and unintentionally compromise other important traits, such as plant defense and nutritional value. However, the effect of domestication on defensive and nutritional traits of plant organs not exposed to selection and the consequent interactions with specialist herbivores are only partly known. Here, we hypothesized that the modern cultivated tomato has reduced levels of constitutive defense and increased levels of nutritional value compared with its wild relatives, and such differences affect the preference and performance of the South American tomato pinworm, Tuta absoluta-an insect pest that co-evolved with tomato. To test this hypothesis, we compared plant volatile emissions, leaf defensive (glandular and non-glandular trichome density, and total phenolic content), and nutritional traits (nitrogen content) among the cultivated tomato Solanum lycopersicum and its wild relatives S. pennellii and S. habrochaites. We also determined the attraction and ovipositional preference of female moths and larval performance on cultivated and wild tomatoes. Volatile emissions were qualitatively and quantitatively different among the cultivated and wild species. Glandular trichomes density and total phenolics were lower in S. lycopersicum. In contrast, this species had a greater non-glandular trichome density and leaf nitrogen content. Female moths were more attracted and consistently laid more eggs on the cultivated S. lycopersicum. Larvae fed on S. lycopersicum leaves had a better performance reaching shorter larval developmental times and increasing the pupal weight compared to those fed on wild tomatoes. Overall, our study documents that agronomic selection for increased yields has altered the defensive and nutritional traits in tomato plants, affecting their resistance to T. absoluta.

Characterizing rhizosphere microbial communities associated with tolerance to aboveground herbivory in wild and domesticated tomatoes

Root-associated microbial communities are well known for their ability to prime and augment plant defenses that reduce herbivore survival or alter behavior (i.e., resistance). In contrast, the role root microbes play in plant tolerance to herbivory, an evolutionarily sustainable alternative to resistance, is overlooked. In this study, we aimed to expand our limited understanding of what role rhizosphere microbial communities play in supporting tolerance to insect damage. Using domesticated tomatoes and their wild ancestors (Solanum spp.), we first documented how tobacco hornworm (Manduca sexta) herbivory impacted tomato fruit production in order to quantify plant tolerance. We then characterized the bacterial and fungal rhizosphere communities harbored by high and low tolerance plants. Wild tomatoes excelled at tolerating hornworm herbivory, experiencing no significant yield loss despite 50% leaf area removal. Their domesticated counterparts, on the other hand, suffered 26% yield losses under hornworm herbivory, indicating low tolerance. Ontogeny (i.e., mid- vs. late-season sampling) explained the most variation in rhizosphere community structure, with tomato line, tolerance, and domestication status also shaping rhizosphere communities. Fungal and bacterial community traits that associated with the high tolerance line include (1) high species richness, (2) relatively stable community composition under herbivory, and (3) the relative abundance of taxa belonging to Stenotrophomonas, Sphingobacterium, and Sphingomonas. Characterizing tolerance-associating microbiomes may open new avenues through which plant defenses are amended in pest management, such as plant breeding efforts that enhance crop recruitment of beneficial microbiomes.

Phenotypic and Genotypic Diversity of the Tomato Germplasm From the Lazio Region in Central Italy, With a Focus on Landrace Distinctiveness

Italy is a recognized secondary center of diversification for cultivated tomato (Solanum lycopersicum L.). The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation and valorization. Here, we set up to study the tomato germplasm collected in the region of Lazio in Central Italy, with a focus on the distinctiveness among landraces and the attribution of membership to unnamed accessions. Our regional collection included 32 accessions belonging to eight different locally recognized landraces and 19 unnamed accessions. All accessions were gathered from local farmers and are preserved in the collection held at the Regional Agency for the Development and the Innovation of Lazio Agriculture (ARSIAL) and at the University of Tuscia. We included 13 control genotypes comprising nine landraces from neighbor regions and four reference cultivars. The collection showed wide phenotypic variability for several qualitative and quantitative traits, such as leaf border and shape, inflorescence type, fruit shape, green shoulder, fruit weight (range 14-277 g), locule number (2-12), shape index (0.54-2.65), yield (0.24-3.08 kg/plant), and soluble solids (3.4-7.5°B). A few landraces showed uncommon phenotypes, such as potato leaf, colorless fruit epidermis, or delayed ripening. Multivariate analysis of 25 cardinal phenotypic variables separated the accessions into two distinct groups; accessions showing a flattened-ribbed fruit were distinguished from those with round to elongate fruits with smooth structure. Genotyping analysis of 7,720 SNPs was performed using the tomato array platform SolCAP, to point out the genetic relationship among the studied accessions. A neighbor-joining tree analysis allowed to confirm or deny phenotypic data and to assign some of the unnamed accessions to recognized groups. Allelic status at marker loci linked to resistance genes commonly used in breeding identified accessions putatively derived from modern material or commercial hybrids, thus not classifiable as landraces. Overall, this study provided the information useful to preserve, valorize, and juridically protect tomato local landraces from the Lazio region and will in addition be helpful to their improvement by breeding.

Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication

Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.