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342 results for “sorghum”
Stress amelioration response of glycine betaine and Arbuscular mycorrhizal fungi in sorghum under Cr toxicity
<p>In search of the solution to Cr toxicity a two-year pot experiment (completely randomized design with three replications), in three genetically different varieties of sorghum (SSG 59-3, HJ 513 and HJ 541) under Cr toxicity (2 and 4 ppm) was conducted to determine the effect of glycine betaine (50 and 100mM) and <i>Arbuscular mycorrhizal fungi</i> (AMF) on the antioxidant system (enzymes <i>viz.</i> superoxide dismutase, ascorbate peroxidase, catalase, glutathione reductase, peroxidase and metabolites <i>viz.</i> glutathione, ascorbate, proline, β-carotene) along with Cr accumulation and indices of oxidative stress parameters (polyphenol oxidase, hydrogen peroxide and malondialdehyde) at two growth stages (vegetative and grain filling). According to results; Cr stress (2 & 4 ppm) increased its accumulation and indices of oxidative stresses significantly (<i>p≤0.05</i>) in all varieties of sorghum at both growth stages. However, soil application of glycine betaine (GB) and AMF decreased Cr accumulation and indices of oxidative stress by increasing antioxidant enzymes and metabolites activities at both growth stages in all varieties. The combination of 100mM GB with AMF was observed most significant (<i>p≤0.05</i>) in decreasing oxidative stress and improved the antioxidant system's activities. The SSG 59-3 cultivar showed the lowest Cr accumulation indices of oxidative stress and highest antioxidant system's activity among these three cultivars at both growth stages. Thus, SSG 59-3 was found most tolerant cultivars followed by HJ 513 and then HJ 541. These findings suggest that both GB and AMF, either individually or combined can play a positive role to reduce oxidative stress and increased antioxidant attributes under Cr toxicity in sorghum.</p>
Data extracted from APSIM simulations for Sorghum
<p>The data are supplemental material for paper entitled APSIM-powered framework for effective post-rainy sorghum agri-system design in India.</p> <p>The APSIM sorghum model was run using environmental data spanning 30 years with a total of 13,824 Genotype × Management combinations per grid. To cover the Indian rabi sorghum production tract 311 grid items were used resulting in a total of 4299264 simulations. The computation took approximately 14 days including several downtime periods and generated 14.6 TB of output data. APSIM natively generates the data in raw text format, therefore for follow-up processing it was necessary to conduct extraction and parsing of relevant pieces of information. For the purposes of extraction and transformation into .csv file format a program was written in C# language to select only the relevant data.</p>
Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies
<p><strong>Background</strong></p> <p>Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene—the main provitamin A carotenoid—is below the target concentration in sorghum grain, therefore, biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors.</p> <p><strong>Results</strong></p> <p>In this study, we characterized carotenoids in 447 accessions from the sorghum association panel and carotenoid panel using high-performance liquid chromatography, finding high carotenoid accessions not previously identified. Genome-wide association studies confirmed that zeaxanthin epoxidase is a major gene underlying variation for not only zeaxanthin but also lutein and β-carotene. High carotenoid lines were found to have limited genetic diversity and originated predominantly from only one country. Potential novel genetic diversity for carotenoid content was identified through genomic predictions in 2,495 accessions of unexplored germplasm. Oligogenic variation of carotenoids was confirmed, as well as evidence for polygenic variation, suggesting both marker-assisted selection and genomic selection can facilitate breeding efforts.</p> <p><strong>Conclusions</strong></p> <p>Sorghum vitamin A biofortification could be beneficial for millions of people who rely on it as a dietary staple. Carotenoid content in sorghum is low, but high heritability suggests that increasing concentrations through breeding is possible. Low genetic diversity among high carotenoid lines might be the main limitation for breeding efforts, therefore further germplasm characterization is needed to assess the feasibility of biofortification breeding. Based on germplasm here evaluated, most countries' germplasm lacks high carotenoid alleles, thus prebreeding will be needed. An SNP marker within the zeaxanthin epoxidase gene was identified as a good candidate for use in marker-assisted selection. Due to the oligogenic and polygenic variation of sorghum grain carotenoids, both marker-assisted selection and genomic selection can be employed to accelerate breeding efforts.</p>
Data from: Sorghum bicolor TX08001 nodal root tissue development gene expression profiling
<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> <p>Bioenergy sorghum's large nodal root system enables deposition of soil organic carbon deep in soil profiles aiding production of low carbon intensity biofuels from this crop. During bioenergy sorghum's long growing season, plants produce ~175 nodal roots In review bearing lateral roots that take up water and nutrients from >2 m deep in soil profiles, and aerial roots that support a complex phyllosphere. In the current study, nodal root bud development, a slow process spanning ~40 days, was characterized using microscopy and transcriptome analysis. A first ring of 10-15 nodal root buds was initiated in the stem pulvinus of phytomer 7 near sub-epidermal vascular bundles. A second ring of buds formed above the first ring much later in phytomer development. Nascent nodal root buds from phytomer 7 exhibited relatively high expression of pericycle marker genes (PFA) and genes involved in auxin transport (ABCB19, PIN4, LAX2), cytokinin signaling (TSO, MYB3R1), and cell proliferation (CYCB2;4, CDKB2;1, REM1).</p> <p>Following initiation, expression of genes involved in cell proliferation and cytokinin-signaling decreased while expression of genes involved in proliferative arrest, ABA-signaling, dormancy and stress tolerance increased. Further bud development was correlated with increased expression of WOX11 and PLT5 followed by PLT2, PLT4 and genes encoding RGF peptides that regulate PLT-expression and bud development. Expression of the ARF7-regulated LBD29, a gene required for nodal root formation, increased in parallel with increasing bud size to a maximum late in NRB development. Appearance of the nodal root bud cap late in development coincided with expression of SMB and FEZ, whereas genes such as WOX5 and two MYB36 family members were expressed at higher levels in outgrowing aerial roots. Genes involved in gibberellin, brassinosteroid, strigolactone, ethylene, jasmonate, salicyclic acid, and eATP signaling showed complex patterns of expression during nodal root bud formation. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for molecular analysis of networks that regulate nodal root development.</p> </div> </div> </div> </div>
Stress amelioration response of glycine betaine and Arbuscular mycorrhizal fungi in sorghum under Cr toxicity
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Adaptation and plasticity of yield in hybrid and inbred sorghum
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Sorghum phenotypic data in drought and irrigated conditions in Haiti
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Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies
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Multi-locus genome-wide association study for grain yield and drought tolerance indices in sorghum accessions
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Data from: Extended grain filling has potential to improve yield in grain sorghum
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Supplementary table, figures and DNA sequences of sorghum gene models SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and indels created
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Optimum seeding rate for biomass sorghum in response to harvesting and planting dates in the Mid-Atlantic regions
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Data from: Sorghum bicolor TX08001 nodal root tissue development gene expression profiling
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Data from: Globally-deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but being bolstered by RMES2
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Data from: Precise colocalization of sorghum’s major chilling tolerance locus with Tannin1 due to tight linkage drag rather than antagonistic pleiotropy
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Data from: Genomic signatures of adaptation to a precipitation gradient in Nigerian sorghum
Evolution of plants under climatic gradients may lead to clinal adaptation. Understanding the genomic basis of clinal adaptation in crops species could facilitate breeding for climate resilience. We investigated signatures of clinal adaptation in the cereal crop sorghum (Sorghum bicolor L. [Moench]) to the precipitation gradient in West Africa using a panel (n = 607) of sorghum accessions from diverse agroclimatic zones of Nigeria. Significant correlations were observed between common-garden phenotypes of three putative climate-adaptive traits (flowering time, plant height, and panicle length) and climatic variables. The panel was characterized at >400,000 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). Redundancy analysis indicated that a small proportion of SNP variation can be explained by climate (1%), space (1%), and climate collinear with space (3%). Discriminant analysis of principal components identified three genetic groups that are distributed differently along the precipitation gradient. Genome-wide association studies were conducted with phenotypes and three climatic variables (annual mean precipitation, precipitation in the driest quarter, and annual mean temperature). There was no overall enrichment of associations near a priori candidate genes implicated in flowering time, height, and inflorescence architecture in cereals, but several significant associations were found near a priori candidates including photoperiodic flowering regulators SbCN12 and Ma6. Together, the findings suggest that a small (3%) but significant proportion of nucleotide variation in Nigerian sorghum landraces reflects clinal adaptation along the West African precipitation gradient.
Data from: Repeat variants for the SbMATE transporter protect sorghum roots from aluminum toxicity by transcriptional interplay in cis and trans
Acidic soils, where aluminum (Al) toxicity is a major agricultural constraint, are globally widespread and are prevalent in developing countries. In sorghum, the root citrate transporter SbMATE confers Al tolerance by protecting root apices from toxic Al3+, but can exhibit reduced expression when introgressed into different lines. We show that allele-specific SbMATE transactivation occurs and is caused by factors located away from SbMATE. Using expression-QTL mapping and -GWAS, we establish that SbMATE transcription is controlled in a bipartite fashion, primarily in cis but also in trans. Multi-allelic promoter transactivation and ChIP analyses demonstrated that intermolecular effects on SbMATE expression arise from a WRKY and a zinc finger-DHHC transcription factor (TF) that bind to and trans-activate the SbMATE promoter. A haplotype analysis in sorghum RILs indicate that the TFs influence SbMATE expression and Al tolerance. Variation in SbMATE expression likely results from changes in tandemly repeated cis sequences flanking a transposable element (MITE) insertion in the SbMATE promoter, which are recognized by the Al3+-responsive TFs. According to our model, repeat expansion in Al-tolerant genotypes increases TF recruitment and, hence, SbMATE expression, which is, in turn, lower in Al-sensitive genetic backgrounds due to lower TF expression and fewer binding sites. We thus show that even dominant cis regulation of an agronomically-important gene can be subjected to precise intermolecular fine-tuning. These concerted cis/trans interactions, which allow the plant to sense and respond to environmental cues, such as Al3+ toxicity, can now be used to increase yields and food security on acidic soils.
Data from: Influence of ethnolinguistic diversity on the sorghum genetic patterns in subsistence farming systems in eastern Kenya
Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ. To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests. The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers' varieties and the structure of both genetic and morphological diversity highlight the effects of the social organization of communities on the diffusion of seed, practices, and variety nomenclature.
Data from: Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal
Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.
Sustainable Development of Sorghum through the Promotion of Microbial Symbiosis and Disease Resistance: Supplemental Data
<p>Supplemental data for Chapter 3 of the dissertation titled: "Sustainable Development of Sorghum through the Promotion of Microbial Symbiosis and Disease Resistance"</p>
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