Cultivated Tomato (Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes

Adaptation to bioinvasions: When does it occur?

The presence of alien species represents a major cause of habitat degradation and biodiversity loss worldwide, constituting a critical environmental challenge of our time. Despite sometimes experiencing reduced propagule pressure, leading to a reduced genetic diversity and an increased chance of inbreeding depression, alien invaders are often able to thrive in the habitats of introduction, giving rise to the so-called "genetic paradox" of biological invasions. The adaptation of alien species to the new habitats is therefore a complex aspect of biological invasions, encompassing genetic, epigenetic, and ecological processes. Albeit numerous studies and reviews investigated the mechanistic foundation of the invaders' success, and aimed to solve the genetic paradox, still remains a crucial oversight regarding the temporal context in which adaptation takes place. Given the profound knowledge and management implications, this neglected aspect of invasion biology should receive more attention when examining invaders' ability to thrive in the habitats of introduction. Here, we discuss the adaptation mechanisms exhibited by alien species with the purpose of highlighting the timing of their occurrence during the invasion process. We analyze each stage of the invasion separately, providing evidence that adaptation mechanisms play a role in all of them. However, these mechanisms vary across the different stages of invasion, and are also influenced by other factors, such as the transport speed, the reproduction type of the invader, and the presence of human interventions. Finally, we provide insights into the implications for management, and identify knowledge gaps, suggesting avenues for future research that can shed light on species adaptability. This, in turn, will contribute to a more comprehensive understanding of biological invasions.

Natural genetic variation in dynamic photosynthesis is correlated with stomatal anatomical traits in diverse tomato species across geographical habitats

Plants grown under field conditions experience fluctuating light. Understanding the natural genetic variations for a similarly dynamic photosynthetic response among untapped germplasm resources, as well as the underlying mechanisms, may offer breeding strategies to improve production using molecular approaches. Here, we measured gas exchange under fluctuating light, along with stomatal density and size, in eight wild tomato species and two tomato cultivars. The photosynthetic induction response showed significant diversity, with some wild species having faster induction rates than the two cultivars. Species with faster photosynthetic induction rates had higher daily integrated photosynthesis, but lower average water use efficiency because of high stomatal conductance under natural fluctuating light. The variation in photosynthetic induction was closely associated with the speed of stomatal responses, highlighting its critical role in maximizing photosynthesis under fluctuating light conditions. Moreover, stomatal size was negatively correlated with stomatal density within a species, and plants with smaller stomata at a higher density had a quicker photosynthetic response than those with larger stomata at lower density. Our findings show that the response of stomatal conductance plays a pivotal role in photosynthetic induction, with smaller stomata at higher density proving advantageous for photosynthesis under fluctuating light in tomato species. The interspecific variation in the rate of stomatal responses could offer an untapped resource for optimizing dynamic photosynthetic responses under field conditions.

Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution

In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K _A/K _S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.

Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico

Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.

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.

Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species

Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.

Morphological Diversity, Genetic Characterization, and Phytochemical Assessment of the Cypriot Tomato Germplasm

Tomato (Solanum lycopersicum L.) is considered one of the most valuable and versatile vegetable crops globally and also serves as a significant model species for fruit developmental biology. Despite its significance, a severe genetic bottleneck and intense selection of genotypes with specific qualitative traits have resulted in the prevalence of a restricted number of (geno)types, also causing a lack of diversity across widespread cultivated types. As a result, the re-emergence of landraces as well as traditional and heirloom varieties is largely acknowledged as a countermeasure to restore phenotypic, phytochemical and genetic diversity while enriching the aroma/taste tomato palette. On those grounds, the Cypriot tomato germplasm was assessed and characterized. Ten landrace accessions were evaluated under greenhouse conditions and data were collected for 24 IPGRI discrete phenotypic traits. Grouping of accessions largely reflected the fruit shape and size; four different fruit types were recorded across accessions (flattened, heart-shaped, rounded and highly rounded). Moreover, a single run panel consisting of ten SSRs was developed and applied in order to genetically characterize 190 Cypriot genotypes and foreign heirloom varieties. Based on genetic indexes it was established that tomato landraces have a rather low level of heterogeneity and genetic variation. Finally, mineral and phytochemical analyses were conducted in order to estimate biochemical attributes (total phenolics, ascorbic acid, lycopene, β-carotene, total soluble content, titratable acidity) across genotypes; thus, ascertaining that the Cypriot panel has a high nutritional value. Due to the thermo-drought adaptation and tolerance of these genotypes, the current study serves as a roadmap for future breeding efforts in order to incorporate desirable traits or develop novel tomato lines combining resilience and alimentary value.

The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.