Biology subjects

Baraja-Fonseca, V.

Publications and source records attributed to Baraja-Fonseca, V..

5 recordsLinked to original sources

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

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

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↗

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↗