Biology subjects

Solana, A.

Publications and source records attributed to Solana, A..

4 recordsLinked to original sources

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↗

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↗

bioRxiv2024

Automatic parameter estimation and detection of Saimaa ringed seal knocking vocalizations

Passive acoustic monitoring (PAM) offers a non-invasive method for monitoring elusive pinnipeds, but manual analysis of large recording datasets limits its scalability. For the endangered Saimaa ringed seal ( Pusa saimensis ), PAM provides a rare opportunity to study breeding-season behavior beneath seasonal ice cover. We evaluated automated methods for detecting and characterizing the species' distinctive knocking vocalizations using recordings from Lake Saimaa. Annotated data ( n = 12 565 calls) were used to develop pulse repetition rate (PRR) estimation and call-detection systems. The best-performing PRR estimator matched manual measurements with a mean absolute error of 1.50 Hz, while a spectrogram-based convolutional neural network detected knocking calls with a mean F1-score of up to 99.28%. These results show close agreement with manual approaches, indicating that automated detection and characterization are achievable at a standard that could substantially reduce PAM analysis effort. This represents an important step toward scalable, long-term acoustic monitoring of this endangered seal.

ecology↗

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↗