Molecular markers play an important role in identifying the species variation, characterizing the genic diversity, and also linking the identified markers to trait of interest. Genome- and transcriptome-derived molecular markers have been widely used to understand the geographical diversity and have also played a major role in the development of high-density linkage maps. In the present protocol, we present a detailed protocol on bioinformatics approaches towards the whole-genome and transcriptome-assisted simple sequence repeats (SSRs) marker mining in Brachypodium distachyon and identification of orthologus SSRs and their validation in Brachypodium ecotypes. We also present a protocol for the validation of the identified markers.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-4939-7278-4_15 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A network-enabled pipeline for gene discovery and validation in non-model plant species.
Cell Rep Methods
January 2025
MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA. Electronic address:
Identifying key regulators of important genes in non-model crop species is challenging due to limited multi-omics resources. To address this, we introduce the network-enabled gene discovery pipeline NEEDLE, a user-friendly tool that systematically generates coexpression gene network modules, measures gene connectivity, and establishes network hierarchy to pinpoint key transcriptional regulators from dynamic transcriptome datasets. After validating its accuracy with two independent datasets, we applied NEEDLE to identify transcription factors (TFs) regulating the expression of cellulose synthase-like F6 (CSLF6), a crucial cell wall biosynthetic gene, in Brachypodium and sorghum.
View Article and Find Full Text PDFUtilizing FRET-based Biosensors to Measure Cellular Phosphate Levels in Mycorrhizal Roots of .
Bio Protoc
January 2025
Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, USA.
Arbuscular mycorrhizal (AM) fungi engage in symbiotic relationships with plants, influencing their phosphate (Pi) uptake pathways, metabolism, and root cell physiology. Despite the significant role of Pi, its distribution and response dynamics in mycorrhizal roots remain largely unexplored. While traditional techniques for Pi measurement have shed some light on this, real-time cellular-level monitoring has been a challenge.
View Article and Find Full Text PDFHalotolerant bacterial endophyte s CBE mediates abiotic stress tolerance with minimal transcriptional modifications in .
Front Plant Sci
January 2025
Institute of Biological, Environmental and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, United Kingdom.
Nitrogen and water are the primary resources limiting agricultural production worldwide. We have demonstrated the ability of a novel halotolerant bacterial endophyte, s CBE, to induce osmotic stress tolerance in under nitrogen-deprived conditions. Additionally, we aimed to identify the molecular factors in plants that contribute to the beneficial effects induced by CBE in .
View Article and Find Full Text PDFExogenous dsRNA triggers sequence-specific RNAi and fungal stress responses to control Magnaporthe oryzae in Brachypodium distachyon.
Commun Biol
January 2025
Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany.
In vertebrates and plants, dsRNA plays crucial roles as PAMP and as a mediator of RNAi. How higher fungi respond to dsRNA is not known. We demonstrate that Magnaporthe oryzae (Mo), a globally significant crop pathogen, internalizes dsRNA across a broad size range of 21 to about 3000 bp.
View Article and Find Full Text PDFEvaluation of spp. System Model Against .
J Fungi (Basel)
January 2025
Instituto de Biología Funcional y Biotecnología (BIOLAB)-INBIOTEC-CONICET-CICBA, Facultad de Agronomía, Universidad Nacional del Centro de la Provincia de Buenos Aires, Av. República de Italia # 780, Azul 7300, BA, Argentina.
Cereal crops are affected by one of the most devastating diseases worldwide, known as Fusarium head blight (FHB), with being the most isolated causal pathogen. Another species associated with this disease is . This species has been considered a relatively weak pathogen compared to , but its importance has increased due to its occurrence in cereal grains worldwide.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!