Biology subjects

Ziarsolo, P.

Publications and source records attributed to Ziarsolo, P..

5 recordsLinked to original sources

bioRxiv2021

European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types. HighlightThe high phenotypic diversity observed among European vintage varieties was created by traditional farmers by combining very few polymorphic loci subjected to balancing selection.

plant biology↗

bioRxiv2021

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

A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to be involved in its domestication: the fully wild Solanum pimpinellifolium (SP), the wild and semi-domesticated S. lycopersicum var. cerasiforme (SLC) and the cultivated S. l. var. lycopersicum (SLL). The Procrustes approach showed that SP evolved into SLC during a gradual migration from the Peruvian deserts to the Mexican rainforests and that Peruvian and Ecuadorian SLC populations were the result of more recent hybridizations. Our model was supported by independent evidence, including ecological data from the accession collection site and morphological data. Furthermore, we showed that photosynthesis-, and flowering time-related genes were selected during the latitudinal migrations.

evolutionary biology↗

bioRxiv2020

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

genetics↗

bioRxiv2019

A stable pollination environment limits current but not potential evolution of floral traits

The vast variation in floral traits at a macroevolutionary level is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of long periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection on floral traits, or by low trait ability to respond even if selection is present. We studied Ulex parviflorus, a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of floral traits, using genome-wide molecular relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability observed in the wild is not heritable. A separate trait, floral weight, in turn presents high heritability, but is not currently under selection. We show how a stable environment can lead to a lack of evolutionary change, yet maintain heritable variation to respond to future selection pressures.

evolutionary biology↗

bioRxiv2017

De-novo assembly of zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus

The Cucurbita genus (squashes, pumpkins, gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb, 34,240 gene models, includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules, that represent 81.4% of the assembly, and it is integrated with a genetic map of 7,718 SNPs. Despite its small genome size three independent evidences support that the C. pepo genome is the result of a Whole Genome Duplication: the topology of the gene family phylogenies, the karyotype organization, and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analyzed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analyzed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have happened 30 {+/-} 4 Mya in the ancestral species that gave rise to the genus.

genomics↗