Biology subjects

Prohens, J.

Publications and source records attributed to Prohens, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Genetic dissection of a Solanum elaeagnifolium tertiary genepool introgression associated with 4-O-caffeoylquinic acid accumulation in eggplant

Caffeoylquinic acids (CQAs) are the major phenolic compounds in eggplant (Solanum melongena) fruit, with 5-O-caffeoylquinic acid (5-CQA; chlorogenic acid) as the predominant isomer, while crop wild relatives may offer novel variation for diversifying these profiles. Previous work detected a distinct phenolic acid profile in S. elaeagnifolium, a tertiary genepool wild relative of eggplant, and in advanced backcross materials carrying introgressions from this species. This profile was characterized by a secondary chromatographic peak eluting after 5-CQA, but the identity of this compound and the associated chromosome 1 region remained unresolved. Here, we combined HPLC-MS-based metabolite identification, fine mapping, and comparative microsynteny analysis to characterize this phenotype. The secondary peak was identified as 4-O-caffeoylquinic acid (4-CQA). Fine mapping across three consecutive selfing generations, involving 612 screened individuals and 21 informative recombinants, reduced the associated interval from 2.753 Mb to 0.211 Mb, delimiting a region containing 30 annotated genes. The 4-CQA peak was detected in both homozygous and heterozygous introgression-derived materials, consistent with dominant control of the trait. Structural comparison of the fine-mapped interval revealed broad conservation between S. melongena and S. elaeagnifolium, but also identified a localized structurally divergent block potentially underlying the secondary 4-CQA peak. Within this block, the S. elaeagnifolium interval harbors acetylajmalan esterase-like/GDSL-type genes and a transcript-supported putative novel donor-specific gene. Overall, this study highlights S. elaeagnifolium introgressions as a promising source of phenolic diversification and providing markers to facilitate the development of eggplant lines with a more diverse CQA profile and potentially enhanced functional quality.

plant biology↗

bioRxiv2026

Impact of Water Deficit on Growth, Biochemical, and Physiological Traits in Eggplant MAGIC Lines

Climate change exacerbates agricultural water scarcity, necessitating the development of drought-tolerant crop varieties. This study evaluates 12 eggplant lines from a MAGIC (Multi-parent Advanced Generation Intercross) population, previously selected for contrasting responses to water deficit during the vegetative stage. To validate tolerance under adult production conditions, plants underwent five irrigation-withholding cycles over a 170-day greenhouse growing period. Yield components, the Stress Tolerance Index (STI), and physiological parameters (water status and stomatal conductance) were evaluated. Additionally, photosynthetic pigments, oxidative stress markers, antioxidant compounds, and osmolytes were quantified to characterize the biochemical basis of tolerance alongside final biomass production. The results showed that four of the five lines that were previously classified as tolerant in the vegetative stage remained among the most tolerant at the reproductive stage. Specifically, lines L13, L78 and L179 were the most productive under water-limited conditions. While L13 and L179 exhibited stable tolerance throughout all developmental stages, L78 displayed stage-specific tolerance, manifested only during the reproductive growth phase. These findings emphasise the importance of integrating early-stage screening with adult-stage validation in order to capture the full spectrum of genetic drought tolerance. The most productive lines were characterised by moderate aboveground biomass, high leaf hydration and maintained stomatal conductance. However, the strategies employed differed: while L179 exhibited high photosynthetic pigment content, L13 was characterised by high total sugar accumulation. Overall, these results provide a multi-trait roadmap and identify elite MAGIC parental lines for breeding climate-resilient eggplant cultivars.

plant biology↗

bioRxiv2026

CRISPR/Cas12a-mediated allele engineering of SmAPRR2 and SmGLK2 reveals complementary control of fruit peel and flesh chlorophyll pigmentation in eggplant

Eggplant (Solanum melongena L.) displays extensive fruit color diversity, in which chlorophyll-related pigmentation contributes to both external appearance and market value. Previous genetic studies identified SmAPRR2 and SmGLK2 as major candidate genes controlling uniform green pigmentation and green netting in fruit, respectively, but their individual and combined functional contributions had not been validated through targeted mutagenesis in a common genetic background. Here, we established a multiplex CRISPR/Cas12a system in eggplant accession MEL3, representing, to our knowledge, the first application of this nuclease for genome editing in eggplant. Transformation efficiency was 2.0%, but all 15 genotyped regenerants were edited, yielding four SmAPRR2 and six SmGLK2 alleles. Segregation and crossing enabled the recovery of six transgene-free lines carrying single or combined edited alleles. Disruption of SmGLK2 abolished the reticulated green netting pattern while preserving a uniformly green peel and the internal green ring. Conversely, disruption of SmAPRR2 reduced the background uniform peel pigmentation and eliminated the green ring while retaining green netting. Double mutants carrying disruptive alleles at both loci produced white fruits lacking internal green pigmentation, whereas putatively hypomorphic SmAPRR2 and SmGLK2 alleles generated intermediate phenotypes. Whole-genome resequencing identified only two predicted off-target sites under a canonical TTTV PAM search allowing up to four mismatches. Both were fully covered, and no edited-line-specific candidate variants were detected. These findings establish complementary and partially separable roles for SmAPRR2 and SmGLK2 in fruit peel and flesh chlorophyll pigmentation and demonstrate the potential of Cas12a for functional genomics, allele engineering, and precision breeding in eggplant.

plant biology↗

bioRxiv2026

Multi-trait evaluation of a tomato MAGIC population identifies promising lines with improved nitrogen use efficiency (NUE)

Nitrogen-use efficiency (NUE) is a pivotal breeding target in tomato (Solanum lycopersicum L.) to sustain production under reduced N inputs. Here, we leveraged a recently developed tomato multi-parent advanced generation inter-cross (ToMAGIC) population to identify lines with superior performance under reduced N availability. The eight founders and a core subset of 118 ToMAGIC lines were characterized with 10,684 SNP markers and evaluated under optimal (opN, 15 mM) and suboptimal (subN, 8 mM) N supply in an experiment totalling 1,576 plants, generating 48,068 data points across 61 phenotypic variables. Under both N treatments, ToMAGIC lines exhibited transgressive segregation for most traits, confirming the value of this population as a reservoir of untapped variation. Notably, under subN conditions, harvest index (Hi) increased by 29-44%, suggesting adaptive resource redistribution toward reproductive sinks. Variance partitioning revealed that agronomic and NUE-related traits were largely under genetic control, with heritability estimates frequently above 0.80 and broadly conserved across N treatments. Multivariate trait analysis identified fruit yield N concentration (NUE component, CN,y), shoot biomass N content (NAb), and shoot growth-related traits as the main drivers of treatment differentiation. Finally, proxy traits were prioritized by integrating response magnitude, heritability, trait correlations, and treatment-discriminatory power into multi-trait selection indices. This strategy generated favorable predicted genetic gains, reaching 158% for high-performance lines and 170% for subN-adapted lines, and consistently identified lines 402, 428, 518, 800, and 816 as promising pre-breeding materials. Overall, this study supports ToMAGIC as a powerful resource for developing N-efficient cultivars suited for sustainable agriculture.

plant biology↗

bioRxiv2026

A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation

Neofunctionalization is a rare fate of gene duplication, classically defined as the acquisition of novel functions that potentiate the emergence of new traits. Rather than evolving to function autonomously, neofunctionalized genes may also remain embedded within their ancestral regulatory networks, potentially reshaping the genetic trajectories through which phenotypic change occurs. Testing this hypothesis, we leveraged a pan-genetic platform comprising ten Solanaceae species and show that a paralog of the flowering hormone florigen neofunctionalized into a flowering antagonist and was repeatedly selected during crop domestication and adaptation of wild plants across 50 million years of evolution. Independent selection of cis-regulatory and coding mutations in SELF-PRUNING 5G (SP5G) enabled rapid flowering in the wild ancestor of domesticated tomato from Central America as well as major and indigenous eggplant crop lineages domesticated in Asia and Africa. We further found that cis-regulatory sequence changes reduced SP5G expression and flowering time in wild species native to distinct environments in the Americas and Australia, relationships that we validated by genome editing. Together with similar patterns observed across diverse species and developmental networks, we propose that antagonistic neofunctionalized paralogs create evolutionary contingencies that channel adaptive trajectories across plant lineages.

plant biology↗

bioRxiv2026

Multidimensional analysis of drought response in an inter-specific tomato population (ToMAGIC)

Drought stress poses a significant threat to agricultural productivity, particularly in regions with limited water availability. This study delves into the drought response in a multiparental interspecific tomato MAGIC population (ToMAGIC), developed by intercrossing Solanum pimpinellifolium (SP) and S. lycopersicum var. cerasiforme (SLC). A core collection of 139 recombinant lines, selected for their genetic diversity, was evaluated under both control and water stress conditions over two consecutive years. Phenotypic data were collected for 25 traits, including vegetative growth, flowering, fruit production, and physiological traits, providing a comprehensive assessment of drought response. Genome-wide association studies (GWAS) identified 15 significant genomic regions associated with drought response across eight chromosomes, highlighting key loci related to growth, earliness, fruit set, and physiological traits such as stomatal conductance and proline accumulation. Transgressive lines, such as S5_T_600 and S5_T_601, which exhibit enhanced drought resilience compared to the parental lines, were identified through genomic assisted selection, highlighting their potential as valuable breeding materials. The study emphasizes the importance of the ToMAGIC population in uncovering the polygenic nature of drought response. These findings offer valuable insights for developing drought-resilient tomato cultivars supporting agricultural sustainability in water-limited environments.

genomics↗

bioRxiv2025

Characterization of a dominant SmNac-like gene as a candidate for photosensitivity in the fruit peel of eggplant

Anthocyanins in the fruit peel of photosensitive eggplants exhibit a different distribution pattern compared to the photo-insensitive ones. The latter exhibits a uniform anthocyanin content, whereas photosensitive eggplants lack anthocyanin accumulation in areas not exposed to light, such as under the calyx, or have lower concentrations in less-exposed areas. In the current research work, genetic analysis of F1 and F2 populations revealed that the photo-insensitive phenotype in eggplants follows an autosomal dominant inheritance with a 3:1 ratio, indicating that the photosensitive trait is regulated by a single dominant gene. To locate and narrow down the genomic region underlying photosensitivity, a segregating F2 population was used for bulked segregant analysis sequencing (BSA-seq) and compared with previous QTLs identified in previous developed eggplants populations (ILs and MAGIC population). The accumulation of QTLs at the end of chromosome 10 postulate that chromose region as a hot spot for anthocyanin related traits. In our population all the QTLs considered overlap between the genomic region 84,1-87,9 Mb. Moreover, no DNA mutations in the progenitors of the eggplant accessions used were found. A RNA-seq analysis of bagged photosensitive and photo- insensitive eggplants was performed, as a result we identified the SmNAC1-like protein gene as a promising gene to be involved in fruit photosensitivity trait. In the photo-insensitive accession (IVIA- 371) SmNAC1-like protein was depply repressed compare to the photosensitive accession (ASI-S-1). No consistent mutations in the coding sequences (CDS) of SmNac-like protein locus among all the different eggplants accessions used were found, suggesting that other layer of regulation maybe acting in our eggplant accessions. These findings provide new insight into the regulation of the molecular mechanisms of anthocyanin biosynthesis in eggplant as point out for the first time the possible role of NAC transcription factors in the anthocyanin biosynthesis in eggplant.

plant biology↗

bioRxiv2025

Water Stress Tolerance, Genomic Selection and Identification of Genomic Regions in a MAGIC Population of Eggplant

Horticultural crops are increasingly affected by water stress due to climate change, making the development of stress-tolerant varieties an urgent need. In this study, we evaluated a set of 184 Multi-parent Advanced Generation Inter-Cross (MAGIC) eggplant lines under water stress conditions, consisting of irrigation at 30% of field capacity. After 21 days of stress, we assessed traits related to growth, water content, plant pigments, and proline content. The MAGIC population displayed a high variability for water stress tolerance, as transgressive lines over parental values were found for most of the traits. Key traits associated with water stress tolerance were identified, including increased root growth and elevated proline, and flavonoid content. Genome-Wide Association Study (GWAS) analysis allowed identification of three genomic regions associated with total dry weight, water content and flavonoids, traits that contribute significantly to stress tolerance. Additionally, a linear genomic selection index was constructed based on total dry weight, dry weight increase during the stress period, root dry weight, water content, and proline content to identify water stress-tolerant and susceptible lines. The models predictive ability was calculated, and the value of the selection index was predicted for 141 unevaluated MAGIC lines, with prediction accuracy for the index traits ranging from 0.11 to 0.53. This study presents a comprehensive analysis, identifying critical traits, genomic regions and lines with genetic potential, providing valuable information for future breeding programmes to improve water stress tolerance in eggplant.

genetics↗

bioRxiv2025

Comparative genomics-driven design of virus-delivered short RNA inserts triggering robust gene silencing

Engineered RNA viruses can downregulate target genes through virus-induced gene silencing (VIGS). Largely optimized using the model plant Nicotiana benthamiana, current VIGS protocols rely on viral vectors engineered to deliver 200-400 nt inserts with homology to a target gene, often located in less conserved regions to ensure specificity. Given the N. benthamiana allopolyploidy and functional redundancy, we leveraged enhanced genomics and transcriptomics resources to obtain curated locus annotations, which guided the design of virus-delivered short RNA inserts (vsRNAi) for simultaneous targeting of homeologous gene pairs. Our results showed that quantitative silencing phenotypes could be obtained using 24-, 28-, and 32-nt vsRNAi that targeted conserved regions of functionally redundant gene pairs. vsRNAi triggered informative transcriptome-wide changes, and target transcript downregulation was linked to gene-pair-specific production of 21- and 22-nt sRNAs. The portability of vsRNAi to crops was confirmed in tomato (Solanum lycopersicum) and scarlet eggplant (Solanum aethiopicum). Overall, our results support the usefulness of vsRNAi-based approaches in functional genomics and trait reprogramming of the model species N. benthamiana, as well as of crops that contribute to global and local food provisions. HIGHLIGHTS O_LIComparative genomics enables design of virus-delivered short RNA inserts (vsRNAi) C_LIO_LI32-, 28-, and 24-nt vsRNAi resulted in quantitative gene silencing phenotypes C_LIO_LIvsRNAi trigger transcriptome-wide changes for gene functional characterization C_LIO_LIvsRNAi elicit production of 21- and 22-nt small RNAs and gene downregulation C_LIO_LIvsRNAi approaches assist functional genomics and phenotypic alteration in crops C_LI

plant biology↗

bioRxiv2025

Resequencing and phenotyping of the first highly inbred eggplant multiparent population reveal SmLBD13 as a key gene associated with root morphology

The MEGGIC (Magic EGGplant InCanum) population here presented is the first highly inbred eggplant (Solanum melongena) multiparent advanced generation intercross (MAGIC) population developed so far, derived from seven cultivated accessions and one wild S. incanum from arid regions. The final 325 S5 lines were high-throughput genotyped using low-coverage whole-genome sequencing (lcWGS) at 3X, yielding 293,783 high-quality SNPs after stringent filtering. Principal component analysis (PCA) and neighbour-joining clustering revealed extensive genetic diversity, lack of genetic structure, and the distinct genetic profile of the wild founder. The eight founders and a core subset of 212 lines were phenotyped for above- and below-ground traits, revealing wide phenotypic diversity. Root morphology traits displayed moderate heritability values, and strong correlation were found between root and aerial traits, suggesting that a well-developed root system supports greater above-ground growth. Genome-wide association studies (GWAS) identified a genomic region on chromosome 6 associated with root biomass (RB), total root length (RL), and root surface area (SA). Within this region, SmLBD13, a LOB-domain protein involved in lateral root development, was identified as a candidate gene. The S. incanum haplotype in this region was linked to reduced lateral root branching density, a trait that may enhance deeper soil exploration and resource uptake. These findings provide key insights into root genetics in eggplant, demonstrating MEGGIC potential for high-resolution trait mapping. Furthermore, they highlight the role of exotic wild germplasm in breeding more resilient cultivars and rootstocks with improved root architecture and enhanced nutrient uptake efficiency.

genomics↗

bioRxiv2025

Micro-Mel and Mini-Mel short life cycle dwarf lines with Solanum anguivi introgressions as the first model varieties for eggplant research and breeding

Eggplant (Solanum melongena) research has been hindered by the lack of suitable model plants. The development of Micro-Mel and Mini-Mel, two short-cycle dwarf model lines with introgressions from the wild relative S. anguivi, represents a breakthrough in eggplant research. Both lines were characterized with 30 phenotypic descriptors and compared to their parental lines and the Micro-Tom tomato. Micro-Mel has determinate growth, early flowering (41.0 days post-transplantation), and physiological fruit maturity at 103.7 days. Mini-Mel exhibits indeterminate growth, later flowering (57.2 days) and fruit maturity (114.7 days), with a more conventional architecture. Micro-Mel and Mini-Mel complete 3.5 and 3.0 full seed-to-seed cycles per year, respectively. Their compact size makes them ideal for space-limited environments, controlled growth chambers, speed breeding, ornamental horticulture, and urban horticulture. To validate their potential for gene editing, in vitro regeneration experiments were performed on a medium containing zeatin riboside. Regeneration was similar to parental S. melongena (1.2 shoots/explant), with Micro-Mel developing 1.0 and Mini-Mel 0.8. Whole-genome sequencing (23X coverage) identified 179,653 SNPs between the parental lines, revealing heterozygosity rates of 0.00098% for Micro-Mel and 0.00123% in Mini-Mel. Approximately 8.50% and 10.79% of their genomes were introgressed from S. anguivi, respectively. Analysis identified 18 shared introgressions from S. anguivi among Micro-Mel, Mini-Mel, and four backcross dwarf materials derived from the same original plant. Notably, three orthologues of genes associated with dwarfism in tomato (SlDREB1, SlER, and SlSERK1) were identified within these introgressions. Micro-Mel and Mini-Mel represent transformative tools for eggplant research, accelerating genetic, physiological, and breeding studies.

plant biology↗

bioRxiv2024

Association analyses reveal both anthropic and environmental selective events during eggplant domestication

Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the Genome-wide association (GWA) of historical genebank phenotypic data on a genotyped worldwide collection of 3,449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a Genotype-Environment Association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association (OA) identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.

genomics↗

bioRxiv2024

Benchmarking of Low Coverage Sequencing Workflows for Precision Genotyping in Eggplant

Low-coverage whole-genome sequencing (lcWGS) presents a cost-effective solution for genotyping, particularly in applications requiring high marker density and reduced costs. In this study, we evaluated lcWGS for eggplant genotyping using eight founder accessions from the first eggplant MAGIC population (MEGGIC), testing various sequencing coverages and minimum depth of coverage (DP) thresholds with two SNP callers, Freebayes and GATK. Reference SNP panels were used to estimate the percentage of common biallelic SNPs (i.e, true positives, TP) relative to the low coverage datasets (accuracy) and the SNP panels themselves (sensitivity), along with the percentage of TP with the same genotype across the two datasets (genotypic concordance). Sequencing coverages as low as 1X and 2X achieved high accuracy but lacked sufficient sensitivity and genotypic concordance. However, 3X sequencing reached approximately 10% less sensitivity than 5X while maintaining genotypic concordance above 90% at any DP threshold. Freebayes outperformed GATK in terms of sensitivity and genotypic concordance. Therefore, we used this software to conduct a pilot test with some MEGGIC lines from the fifth generation of selfing (S5), comparing their datasets with a gold standard (GS). Sequencing coverages as low as 1X identified a substantial number of TP, with 3X significantly increasing the yield, particularly at moderate DP thresholds. Additionally, at least 30% of the TP were consistently genotyped in all lines when using coverages greater than 2X, regardless of the DP threshold applied. This study highlights the importance of using a GS to reduce false positives and demonstrates that lcWGS, with proper filtering, is a valuable alternative to high-coverage sequencing for eggplant genotyping, with potential applications to other crops.

genomics↗

bioRxiv2024

New QTLs involved in the control of stigma position in tomato

The tomato mating system was strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP control in domesticated forms retaining a non-inserted or a heat-inducible SP needs elucidation. To widen the possibility of identifying SP genetic determinants, we analysed the trait in four populations (two germplasm collections, a multiparental recombinant inbred and a biparental progeny) under different environmental conditions (normal and heat stressed). Overall, 36 markers significantly associated with the trait were discovered. Several co-localizations were found, both among regions firstly reported in this work and among them and previously reported positions. This supported the reliability of the analysis. Three of such regions, in the long arms of chromosome 1, 8 and 11, were validated in an independent segregating population and candidate genes in confidence intervals were identified among transcription factors and hormone, stress and cell-wall-related genes. In conclusion, the work supported the hypothesis that the SP phenotype is controlled by different key-genes in tomato, paving the way to identifying novel players and novel mechanisms involved in the regulation of herkogamy. HighlightThe study of three germplasm collections in tomato allowed the identification new significant markers for the stigma position trait while confirmed several previously reported QTLs.

plant biology↗

bioRxiv2024

Validation and identification of new QTLs for plant and fruit developmental and composition traits in eggplant under low N conditions

Enhancing plant adaptation to low input conditions is a fundamental goal for implementing sustainable agriculture. In the present study, two eggplant (Solanum melongena) accessions (MEL1 and MEL5), two introgression lines (ILs) derived from eggplant wild relatives S. dasyphyllum (IL-M1-D1) and S. insanum (IL-M5-I9), and a heterozygous version of this last IL (ILHet-M5-I9), along with hybrids among them were evaluated under low N (LN) conditions. IL-M1-D1 carries an introgressed fragment of 4.9 Mb in homozygosis from S. dasyphyllum on chromosome 2, while IL-M5-I9 and ILHet-M5-I9 carry an introgression of 21.5 Mb on chromosome 9 in homozygosis and heterozygosis, respectively, from S. insanum. Multiple quantitative trait loci (QTLs) for several traits of interest were associated with both introgressions under LN conditions in a previous study with segregating advanced backcrosses. Here we evaluated the performance of these materials for 22 agronomic and developmental traits under low N fertilization (LN) conditions. Hybrids with the ILs enabled the study of genetic background effects on QTLs expression. The materials evaluated showed a significant phenotypic variation, particularly within hybrids segregating for the introgression from S. insanum in chromosome 9. Statistical analysis revealed no significant differences among hybrids carrying or not the introgression on chromosome 2 of S. dasyphyllum, and only slight differences were observed between the IL-M1-D1 and its recurrent parent S. melongena MEL1, suggesting a limited impact of this introgression on chromosome 2 on the phenotype variation. However, the differences observed between IL-M5-I9 and its recurrent parent S. melongena MEL5, together with the association between genotypic and phenotypic variation in hybrids segregating for this introgression, allowed the identification of 13 QTLs on chromosome 9. These results successfully validated the previously identified QTLs for flavonol content in leaves, nitrogen balanced index, fruit mean weight, and nitrogen content in leaves and, also revealed nine new QTLs associated with the introgressed genomic region in chromosome 9. This study emphasizes the influence of environmental conditions, genotypes, and genetic backgrounds on the phenotypic expression of eggplant QTLs introgressed from wild relatives and highlights the importance of QTL validation. These findings contribute valuable insights for developing new eggplant cultivars for a more sustainable agriculture, particularly with adaptation to LN conditions.

plant biology↗

bioRxiv2024

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

We developed a novel eight-way tomato multi-parental advanced generation inter-cross (MAGIC) population to improve the accessibility of the genetic resources of tomato relatives to geneticists and breeders. The inter-specific MAGIC population (ToMAGIC) was obtained by inter-crossing four accessions each of Solanum lycopersicum var. cerasiforme (SLC) and S. pimpinellifolium (SP), which respectively are the weedy relative and the ancestor of cultivated tomato. 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 (SPET) panel and yielded 6,488 high-quality SNPs. The genotyping data revealed a high degree of homozygosity (average 93.69%), an absence of genetic structure, and a balanced representation (11.62% to 14.16%) of the founder genomes. To evaluate the potential of the ToMAGIC population for tomato genetics and breeding, a proof-of-concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness traits. Genome-wide association studies (GWAS) 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 breeding. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

plant biology↗

bioRxiv2024

Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. Here we genetically dissected repeated origins and losses of prickles, sharp epidermal projections, that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Strikingly, homologs promote prickle formation across angiosperms that collectively diverged over 150 million years ago. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone-activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.

evolutionary biology↗

bioRxiv2023

The irregular fruit green netting: An eggplant domestication trait controlled by the SmGLK2 gene with implications in fruit colour diversification

The distribution of chlorophylls in the eggplant (Solanum melongena) fruit peel can be uniform or display an irregular green netting pattern. The fruit green netting phenotype, manifested as a gradient of dark green netting, more intense in the proximal part of the fruit on a pale green background, is commonly present in eggplant wild relatives as well as in some eggplant landraces. During domestication and modern breeding of eggplant, uniform fruit colour has been selected. However, the fruit green netting contributes to a greater diversity of fruit colours. Here, we have used over 2,300 individuals from several germplasm and experimental populations, including a multi-parental MAGIC population for candidate genomic region identification, an F2 population for BSA-Seq, and advanced backcrosses for edges-to-core fine mapping, to determine that SmGLK2 is the gene underlying the irregular netting in eggplant fruits. We have also analysed the gene sequence of 178 S. melongena accessions and 22 wild relative species for tracing the evolutionary changes that the gene has undergone over the course of domestication. Three different mutations were identified leading to the absence of netting. The main causative indel results in the appearance of a premature stop codon disrupting the protein conformation and function, which was confirmed by Western blotting analysis and confocal microscopy observations. SmGLK2 has a major role in the regulation of chlorophyll biosynthesis in eggplant fruit peel, and therefore in eggplant fruit photosynthesis.

genetics↗