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opencc-zeroJan 2022View details →

Natural variation further increases resilience of sorghum bred for chronically drought-prone environments

Moisture stress is one of the major constraints for crop production in African Sahel. Here, we explore the potential to use natural genetic variation to build on the inherent drought tolerance of an elite sorghum cultivar (Teshale) bred for Ethiopian conditions including chronic drought, evaluating a backcross nested-association mapping population using 12 diverse founder lines crossed with Teshale under three drought-prone environments in Ethiopia. All twelve populations averaged higher head exsertion and lower leaf senescence than the recurrent parent in the two highest-stress environments, reflecting new drought resilience mechanisms from the donors. 154 QTLs were detected for eight drought responsive traits – the validity of these were supported in that 113 (73.4%) overlapped with QTLs previously detected for the same traits, concentrated in regions previously associated with 'stay-green' traits. Allele effects show that some favorable alleles are already present in the Ethiopian cultivar, however the exotic donors offer rich scope for increasing drought resilience. Using model-selected SNPs associated with eight traits in this study and three in a companion study, phenotypic prediction accuracies for grain yield were equivalent to genome-wide SNPs and were significantly better than random SNPs, indicating that these studied traits are predictive of sorghum grain yield.

opencc-zeroApr 2022View details →

Plant-soil feedback of the invasive Sorghum halepense on Hainan island, China

<div> Sorghum halepense is a perennial invasive weed causing great harm worldwide, including various regions on Hainan island. In this study, using two approaches, we examined plant-soil feedback of different S. halepense populations. In the first, rhizosphere soil of S. halepense from the field was either sterilized or not to study the role of soil biota on S. halepense growth. In the second, we first let S. halepense plants condition the soil, and then regrow plants on these conditioned soil to study the role of overall changes in soil properties in plant-soil feedback. Sterilization increased the growth of S. halepense, indicating that soil biota inhibited the growth of S. halepense. Soil biota from some populations inhibited the growth of S. halepense more than that from others. In most cases, the relative response of a S. halepense population when associated with its own soil vs. when associated with other soils was similar to the relative response of other populations across the same soils. In the second approach, the effect of conditioning on most soil chemical properties were not different among populations. The interactive effect of conditioning population and replanting population on plant biomass was not significant, indicating that the performance of different S. halepense populations did not depend on the population of S. halepense that conditioned the soil. These results indicate that on Hainan island, S. halepense can outburst and proliferate despite negative feedback with soil biota, and populations of S. halepense differ little in their interactions with soil.</div>

opencc-zeroMay 2022View details →

Systematic prediction of EMS-induced mutations in a sorghum mutant population

Sorghum is a next-generation crop species with tremendous potential for discovering highly desirable agronomical traits. We described an improved method for the systematic detection of EMS-induced mutations in the previous sequencing of the M3 generation of 600 sorghum BTx623 mutants. We used both SAMtools and GATK-based variant-calling algorithms to demonstrate the general utility of the method. The approach also includes a clustering algorithm for detecting likely false-negative EMS-induced mutations. We detected 3,497,654 EMS-induced single nucleotide polymorphisms (SNPs) in 30,285 distinct sorghum genes, and cataloged 10,263 high impact and 136,639 moderate impact SNPs. We also implemented a light-weight web portal for searching the mutation database for the 600 sorghum mutants.

opencc-zeroDec 2018View details →

Data from: An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes

[No abstract entered]

opencc-by-4.0Apr 2024View details →

Sorghum bicolor SNP data

<div> <div> Sorghum diversity set was utilized for the present study. </div> </div> <div> </div>

opencc-by-4.0Sep 2024View details →

RGB images of sorghum fields gathered by UAV flights

A supplementary datase for the paper Hybrid-AI and model ensembling to exploit UAV-based RGB imagery: Evaluation of sorghum crops nitrogen content. The data set consist of RGB images of sorghum fields gathered by UAV flights and a CSV that contains laboratory measured ground-truth for Nitrogen content.

opencc-by-4.0Sep 2024View details →

Bioactive compounds, antioxidant activity, and sensory profile of sorghum tisane

This dataset provides the result of bioactive compounds, antioxidant activity, sensory acceptance, and sensory profile measurements towards sorghum tisane with different pericarp colors.

opencc-zeroAug 2021View details →

Genotyping-by-sequencing data for a Haitian sorghum breeding program

Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively intercrossed, and subjected to intense selection under SCA infestation. We conducted evolutionary population genomics analyses of 296 post-selection Haitian lines compared to 767 global accessions at 159,683 single nucleotide polymorphisms. Despite intense selection, the Haitian population retains high nucleotide diversity through much of the genome due to diverse founders and an intercrossing strategy. A genome-wide fixation (FST) scan and geographic analyses suggests that adaptation to SCA in Haiti is conferred by a globally-rare East African allele of RMES1, which has also spread to other breeding programs in Africa, Asia, and the Americas. De novo genome sequencing data for SCA resistant and susceptible lines revealed putative causative variants at RMES1. Convenient low-cost markers were developed from the RMES1 selective sweep and successfully predicted resistance in independent U.S. × African breeding lines and eight U.S. commercial and public breeding programs, demonstrating the global relevance of the findings. Together, the findings highlight the potential of evolutionary genomics to develop adaptive trait breeding technology and the value of global germplasm exchange to facilitate evolutionary rescue.

opencc-zeroApr 2023View details →

Sorghum leaf blight phenotypes for two recombinant inbred line populations

Sorghum leaf blight and northern corn leaf blight, both caused by Exserohilum turcicum, are major diseases of sorghum and maize, respectively. Examining the genetic architecture of resistance in sorghum will lead to a better understanding of the relationship between resistance in sorghum and maize, which can ultimately enhance management options in both crops. In 2018 and 2019 we evaluated two sorghum recombinant inbred line (RIL) populations for resistance to E. turcicum. The BTx623 x IS3620C and BTx623 x SC155 populations consisted of 235 and 81 RILs, respectively. Resistance in both populations was moderately to highly heritable. We identified a total of six quantitative trait loci (QTL) across the two populations. Three QTL with small to moderate effect sizes were identified in the BTx623 x IS3620C population. Three QTL, including a large-effect QTL on chromosome three that explained 24% of the variation, were identified in the BTx623 x SC155 population. We compared the identified QTL with the position of northern corn leaf blight candidate genes and found eight candidate resistance gene orthologs that colocalize with the sorghum leaf blight QTL. There were also several nucleotide-binding leucine rich repeat encoding genes within the candidate intervals. Understanding host resistance in multiple species furthers our understanding of the Exserohilum turcicum pathosystem.

opencc-by-4.0Aug 2023View details →

Passive permeability controls synthesis for the allelochemical sorgoleone in sorghum root exudate

Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: tar -zcvf sorgoleonepermeability.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf"  --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" sorgoleone-permeability, which intentionally excludes large files. The full dataset that includes trajectories is available upon request. The data is split into two directories initially "build" and "Simulations" <ul> <li>"build" directory is the part where initial system for unbiased and biased simulation were build using "resolvate.tcl" and "smd-single-build-system.tcl" respectively.</li> <li>"Simulations" directory has the different namd files for running unbiased simulation, steered molecular dynamics and replica exchange  umbrella sampling.</li> </ul> The folder structure was generated using  "gendirs*.py". The unbiased simulations were run using "run.namd". Steered molecular dynamics namd files were with name "step*.namd" and colvars configuration file are named "step*.conf". Replica exchange moleuclar dynamics (REUS) system was generated using "buildreplicas*.tcl". Replica windows size and  force constant were written into a namd configuration file using "reus-genscript*.py". REUS general configuration file containing the parameters and forcefield is  named as "base.namd". Colvars for leaflet exchange REUS are in "replicadistZcolvars.conf". Colvars for absorption into water  REUS are in  "replicadistcoordNumclovar.conf". Colvars for absorption into organic phase  REUS are in  "replica-blob-run4.conf" Umbrella sampling is performed with "umbrella.namd". For visualizing trajectories in VMD  "load*.tcl" scripts were used.

opennotspecifiedFeb 2020View details →

Fig. 3 in Stabilization of dhurrin biosynthetic enzymes from Sorghum bicolor using a natural deep eutectic solvent

Fig. 3. NADES-based stabilization of the dhurrin biosynthetic enzymes. A) Illustration of proteoliposomes comprising the POR2B, CYP79A1, CYP71E1 and UGT85B1 reconstituted in liposomes composed of phospholipids extracted from etiolated sorghum seedlings (Metabolon). B) Recovery of activity upon storage of enzymes in NADES and glycerol compared to buffer upon dilution displayed as relative conversion of tyrosine for the Metabolon samples and conversion of cyanohydrin to dhurrin for the UGT85B1 samples. Values are mean of three technical replicates± SD. C) Stability of dhurrin biosynthetic enzymes stored at room temperature in aqueous buffer, NADES and glycerol. Samples were diluted in buffer prior to activity assay. Values are mean of three technical replicates ±SD and fitted to a double exponential decay. D) Bar plot showing relative activity of the enzymes following incubation at various temperatures for 30 min in aqueous buffer, NADES and glycerol. Samples were diluted in buffer prior to activity assay. All values are mean of three independent technical replicates ± SD.

opennotspecifiedFeb 2020View details →

Fig. 2 in Stabilization of dhurrin biosynthetic enzymes from Sorghum bicolor using a natural deep eutectic solvent

Fig. 2. Dhurrin biosynthesis in the presence of different NADESs. A) Etiolated sorghum seedlings used for preparation of microsomes. B) Tyrosine conversion assay in microsomes at different NADES concentrations indicates an optimum at 5% NADES for both glucose:tartrate and glucose:malate. Values are mean of three technical replicates ± SD.

opennotspecifiedFeb 2020View details →

Fig. 1 in Stabilization of dhurrin biosynthetic enzymes from Sorghum bicolor using a natural deep eutectic solvent

Fig. 1. Formation of NADES derived from natural occurring metabolites in plants. A) Chemical structures of D-glucose, tartaric acid, malic acid, choline, glycerol and dhurrin. Mixtures of these metabolites were tested for their ability to form NADES and their potential role in stabilizing the dhurrin biosynthetic enzymes. B) Stoichiometric mixture of glucose and tartrate constitute a NADES with significantly lowered melting point compared to the individual components. C) Biosynthetic pathway of the natural product dhurrin in S. bicolor.

Fig. 6 in Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Fig. 6. Proportion of nitrogen allocated to dhurrin and nitrate (NO3) in dried, finely ground tissues of S. bicolor, S. brachypodum and S. macrospermum plants at 35 d post-germination. A) Dhurrin allocation; B) Nitrate allocation; C) C:N ratio. Graphs show mean ± 1 standard error (n = 3). Columns with different letters within each tissue are significantly different (p <0.05).

Fig. 3 in Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Fig. 3. Leaf characteristics of S. bicolor, S. brachypodum and S. macrospermum plants at six harvest points during the first 35 d post-germination. A) Total leaf number; B) Total leaf area (TLA); C) Specific leaf area (SLA); D) Leaf area ratio (LAR). Graphs show mean ± 1 standard error (n = 5), with statistically significant differences indicated at each time point: *p <0.05.

Fig. 5 in Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Fig. 5. Tissue-specific hydrogen cyanide potential (HCNp, mg HCN per g dw 1) and morphology of individual A) S. bicolor, B) S. brachypodum and C) S. macrospermum plants at six time points during seedling development. The HCNp of a section of the sheath, roots, and each individual leaf was measured at 3, 7, 14, 21, 28 and 35 days (D) post-germination. Colour scale indicates HCNp, used as a proxy for dhurrin concentration (green = low; red = high). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Fig. 4. Hydrogen cyanide potential (HCNp, mg HCN per g dw 1) and concentration of nitrate (NO) in dried, finely ground tissues of S. bicolor, S. brachypodum and 3 S. macrospermum plants at six harvest points during the first 35 d post-germination (at 35 dpg only for NO3). A) Leaf HCNp; B) Sheath HCNp; C) Root HCNp; D) Total NO3. Graphs show mean ± 1 standard error (n = 5), with statistically significant differences indicated at each time point: *p <0.05. Columns with different letters within each tissue are significantly different (p <0.05). Data for leaf HCNp at 3 days post-germination not shown as a true leaf had not emerged at this stage.

Fig. 1 in Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Fig. 1. Known geographic distribution of the two wild Sorghum species S. brachypodum and S. macrospermum and the site of collection of the accessions examined in the current study. Seeds were obtained from the Australian Grains Genebank (AGG), Horsham, Victoria. Occurrence records of S. brachypodum and S. macrospermum were obtained from the Atlas of Living Australia (ALA), htt p://www.ala.org.au. Each blue circle represents an occurrence record of S. brachypodum and each orange circle represents S. macrospermum (circled). Collection localities of individual accessions examined here are marked by darker coloured circles. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedAug 2020View details →

Fig. 7 in Identification and functional characterization of two acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) genes from forage sorghum (Sorghum bicolor) embryo

Fig. 7. Flow cytometer analysis of LB accumulation in yeast cells. (A) Cytogram of BODIPY fluorescence vs. side scatter of cells expressing forage sorghum SbDGAT1- 1 variants. (B) Mean intensity of P3/fluorescent population (represents BODIPY uptake) events transformed with different variants of forage sorghum SbDGAT1-1 genes. The error bars represent the SD of three biological replicates. Asterisks indicates significant differences according to student t-test results where * = p <0.05.