DOI: 10.5281/zenodo.3941962
title: Supplementary dataset to "A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses"

description: SUPPLEMENTARY DATASETS TO: <strong>A new genome allows the identification of genes associated with natural variation in aluminium tolerance in <em>Brachiaria </em>grasses</strong> <strong>Supplementary File 1:</strong> Cumulative root length (RL), root biomass (RB), and root tip diameter (RD) during Al<sup>3+</sup> stress (A) and control (C) conditions, and the ratio (R) between stress and control values, in the interspecific progeny between CIAT 606 and BXR 44-02. <strong>Supplementary File 2: </strong>Gene annotation in GFF3 format. <strong>Supplementary File 3: </strong>Functional annotation of the genes, including GO terms and homologous proteins in NCBI nr database, Uniprot, <em>A. thaliana</em>, rice, <em>P. halli</em>, <em>S. italica</em> and <em>S. viridis</em><em>.</em> <strong>Supplementary File 4: </strong>Assignment of the proteins in the Poaceae family to eggNOG orthologous groups to identify shared clusters of proteins among these species. <strong>Supplementary File 5:</strong> Anchoring 21,145 <em>Brachiaria ruziziensis</em> scaffolds longer than 10 Kbp or with at least one annotated gene (533.9 Mbp) in <em>S. italica </em>nine chromosomes. <strong>Supplementary File 6:</strong> Chromosomal position of the 41,974 transcripts in <em>Brachiaria ruziziensis</em> based on the synteny with the <em>S. italica</em> genome. In BED5 format. <strong>Supplementary File 7: </strong>Genetic map with 4,427 markers placed at LOD 10 in 18 linkage groups, including the position of each marker in the genetic map and genome assembly. <strong>Supplementary File 8:</strong> Functional annotation of the 84 DE genes within QTLs. <strong>Supplementary File 9:</strong> Enrichment analysis of the GO terms (full ontology) over-represented among DE genes in each species with the biological processes (BP) and molecular functions (MF). <strong>Supplementary File 10:</strong> Enrichment analysis of the GO SLIM terms (reduced ontology) over-represented among DE genes in each species with the biological processes (BP) and molecular functions (MF). Margaret Worthington<sup>1#</sup>, Juan Guillermo Perez<sup>1</sup>, Saule Mussurova<sup>2</sup>, Alexander Silva-Cordoba<sup>1</sup>, Valheria Castiblanco<sup>1</sup>, Juan Andres Cardoso Arango<sup>1</sup>, Charlotte Jones<sup>3</sup>, Narcis Fernandez-Fuentes<sup>3</sup>, Leif Skot<sup>3</sup>, Sarah Dyer<sup>2&</sup>, Joe Tohme<sup>1</sup>, Federica Di Palma<sup>2</sup>, Jacobo Arango<sup>1</sup>, Ian Armstead<sup>3</sup>, Jose J De Vega<sup>2</sup> 1. International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia. 2. Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. 3. Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK.
description: Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as forage in the tropics because of their resilience and low demand for nutrients, show greater tolerance to high concentrations of aluminium cations (Al3+) than most other grass crops. In this work, we explored the natural variation in tolerance to Al3+ between high and low tolerant Brachiaria species and characterised their transcriptional differences during stress. We identified three QTLs (quantitative trait loci) associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we identified 30 genes putatively responsible for Al3+ tolerance in Brachiaria. We observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition and vesicle location genes homologous to aluminium-induced proteins involved in limiting uptake or localising the toxin. However, there was limited regulation of malate transporters in Brachiaria, which suggests that exudation of organic acids and other external tolerance mechanisms, common in other grasses, might not be relevant in Brachiaria. The contrasting regulation of RNA translation and response signalling suggests response timing is critical in high Al3+ tolerant Brachiaria.