Biology subjects

Duarte-Delgado, D.

Publications and source records attributed to Duarte-Delgado, D..

3 recordsLinked to original sources

bioRxiv2024

TILLCANN: A TILLING platform in Cannabis sativa for mutation discovery and crop improvement

Cultivation of Cannabis sativa is increasing because of its therapeutic value and recognition as a multi-purpose and sustainable crop. Targeting Induced Local Lesions in Genomes (TILLING) is a versatile reverse genetics approach that unlocks induced variation through mutagenesis to accelerate the development of new cultivars and contribute to the functional validation of genes. Increasingly efficient next-generation sequencing technologies and genomic resources have combined to make TILLING by sequencing (TbyS) an attractive technique that can be applied in cannabis. Here we describe the development of a mutagenesis protocol for C. sativa and the development of the TILLCANN platform composed of 1,633 M2 families. As a demonstration of the functionality of the platform, we used TbyS to perform a high throughput screening of novel mutations in amplicons for genes associated with important agronomic and biochemical traits in a set of 512 M2 families. We confirmed 14 of the identified mutations and calculated an average mutation frequency range of 1/263 to 1/320 kb. We found that heterozygous mutants in the cannabis homologue of Class II TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP4) are linked to alterations in leaf number and morphology. We expect that the novel genetic variability unlocked in the TILLCANN platform for performing forward or reverse genetic screens can significantly boost breeding programs geared toward both medicinal cannabis and industrial hemp. Gene & accession numbersRaw sequencing data generated in this study was deposited at the European Nucleotide Archive with accession numbers xxx and xxx. Genes and accession numbers discussed within this manuscript correspond to the Cannabis sativa cs10 genome assembly deposited in National Center for Biotechnology Information with accession number GCA_900626175.2.

plant biology↗

bioRxiv2024

Expression interplay of calcium-binding genes and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca2+ signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding genes was found to be specific for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of EF-hand genes, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding genes, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3-UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability. Key messageThe fine-tuned expression of calcium-binding genes and transcription factors during the osmotic phase underlies the susceptibility and tolerance to salt stress responses of contrasting bread wheat genotypes.

molecular biology↗

bioRxiv2019

A systemic approach provides insights into the salt stress adaptation mechanisms of contrasting bread wheat genotypes

Bread wheat is one of the most important crops for human diet but the increasing soil salinization is causing yield reductions worldwide. Physiological, genetic, transcriptomics and bioinformatics analyses were integrated to study the salt stress adaptation response in bread wheat. A comparative analysis to uncover the dynamic transcriptomic response of contrasting genotypes from two wheat populations was performed at both osmotic and ionic phases in time points defined by physiologic measurements. The differential stress effect on the expression of photosynthesis, calcium binding and oxidative stress response genes in the contrasting genotypes supported the greater photosynthesis inhibition observed in the susceptible genotype at the osmotic phase. At the ionic phase genes involved in metal ion binding and transporter activity were up-regulated and down-regulated in the tolerant and susceptible genotypes, respectively. The stress effect on mechanisms related with protein synthesis and breakdown was identified at both stress phases. Based on the linkage disequilibrium blocks it was possible to select salt-responsive genes as potential components operating in the salt stress response pathways leading to salt stress resilience specific traits. Therefore, the implementation of a systemic approach provided insights into the adaptation response mechanisms of contrasting bread wheat genotypes at both salt stress phases.\n\nHighlightThe implementation of a systemic approach provided insights into salt stress adaptation response mechanisms of contrasting bread wheat genotypes from two mapping populations at both osmotic and ionic phases.

systems biology↗