Biology subjects

Vielle-Calzada, J. P.

Publications and source records attributed to Vielle-Calzada, J. P..

4 recordsLinked to original sources

bioRxiv2025

Scaling up orphan crop research: A global genetic perspective of cowpea (Vigna unguiculata) diversity from 10,617 accessions

Cowpea (Vigna unguiculata L. Walp) is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia, and Latin America. However, as a typical "orphan crop", cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10,617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterized the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

plant biology↗

bioRxiv2022

Differential RNA-silencing and plasmodesmata callose deposition in leaves and stems of transgenic tobacco plants during Tobacco etch virus infection recovery

Viruses are amongst the most prevalent pathogens that threaten plants. Plants have evolved a sequence-specific defense mechanism against viruses to ensure survival, known as RNA silencing, which includes transcriptional and post-transcriptional gene silencing. After a viral infection, some plants undergo recovery and become further resistant to viral infection. To identify additional mechanisms underlying disease recovery besides the known RNA silencing, we analyzed transgenic tobacco plants expressing a transcript derived from the Nuclear Inclusion "a" protein (NIa) cistron of the tobacco etch virus (TEV), which had recovered from infection three weeks following viral inoculation. Using in situ hybridizations and qRT-PCR, we detected the viral RNA and the transgene-derived transcript in stem sections adjacent to the recovered leaves. To further characterize the silenced and non-silenced conditions, we undertook tissue-specific RNA-Seq and small RNA-Seq analyses in leaf and stem. We found more differentially expressed genes (DEGs) in the recovered leaf, primarily related to defense, silencing, and hormone signaling responses. Finally, we observed differences in plasmodesmata callose deposition and callose-related genes. Overall, our findings suggest that cell-to-cell viral restriction movement also participates in the recovery of TEV infection in transgenic tobacco plants, besides the key function of RNA silencing.

plant biology↗

bioRxiv2020

The Arabidopsis TTL3 protein interconnects brassinosteroid signalling and cytoskeleton during lateral root development

Lateral roots are essential components of the plant edaphic interface, contributing to water and nutrient uptake, biotic and abiotic interactions, stress survival, and plant anchorage. We have identified the TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE 3 (TTL3) being related to lateral root emergence and later development. TTL3 interacts with microtubules and potentially interconnects cytoskeletal function with the brassinosteroid signalling pathway. Loss of function of TTL3 leads to a reduced number of emerged lateral roots due to delayed development of lateral root primordia. Lateral root growth of the ttl3 mutant is less sensitive to BR treatment. Timing and spatial distribution of TTL3 expression is consistent with its role in development of lateral root primordia before their emergence and subsequent development into lateral roots. TTL3 is a novel component of the root system morphogenesis regulatory network.

developmental biology↗

bioRxiv2020

Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

O_LIThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), which is a conserved mechanism that involves noncoding-RNAs to control the expansion of intergenic regions. However, little is known about relationship between plant genome size reductions and DNA methylation. C_LIO_LIBecause the compact genome size of the carnivorous plant Utricularia gibba, we investigate in this plant the noncoding-RNA landscape and DNA methylation through a combination of cytological, evolutionary, and genome-wide transcriptomic and methylation approaches. C_LIO_LIWe report an unusual distribution of noncoding RNAs in U. gibba in comparison with other characterized angiosperms, which correlated with a lower level of global genome methylation, as determined by a novel strategy based on long-read DNA sequencing and corroborated by whole-genome bisulfite analysis. Moreover, found that genes involved in the RdDM pathway may not be functionally active in U. gibba, including a truncated DICER-LIKE 3 (DCL3), involved in the production of 24-nt small-RNAs. C_LIO_LIOur findings suggest that selective pressure to conserve a fully functional RdDM pathway might be reduced in compact genomes and a defective DCL3 correlate with a decreased proportion of 24-nt small-RNAs and developmental alterations in U. gibba, which could represent an initial step in the evolution of apomixis. C_LI

plant biology↗