Project description:Background: Sorghum bicolor is a remarkably drought tolerant cereal crop. Its natural biodiversity that enables this tolerance has developed in sub-Saharan Africa. The sequencing of the sorghum genome in 2009 has expedited research of this crop which has also been proposed as a model C4 cereal crop for genomics. In this study, the genetic response mechanisms involved in sorghums’ tolerance to progressive water deficit and moderate re-watering were investigated in three previously uncharacterized South African landraces (designated: LR5, LR6 and LR35) using cDNA microarrays comprising 35 899 transcript probes. Results: Across the three landraces, significant differential expression of 1 797 genes, including 264 genes with currently unknown functions, were altered in response to progressive water stress and re-watering. The modulated sorghum genes had homology to proteins involved in growth, regulation, and protection. Gene ontology analysis identified significant enrichment of 26 genes involved in the ‘response to abiotic stimulus’ GO category in LR6 during severe stress. The expression of USP responded to progressive water stress and moderate re-watering in LR6 and LR35. Moreover, our results indicate a putative role for β-alanine betaine biosynthesis in drought tolerance of sorghum. Conclusions: This study identified the drought responsive gene complement of three previously uncharacterized South African sorghum landraces. Each landrace is a distinct genotype and similar responses to water deficit and re-watering were not expected. Functional characterizations of some of the differentially expressed genes found in this study may be used as possible targets for marker-assisted breeding or transgenic initiatives for sorghum and, other closely related crop species.
Project description:Sorghum (Sorghum bicolor) is the fifth most important cereal crop in the world. It is an annual C4 crop having a high biomass, used widely, and has a strong resistance to stress. Obviously, there are many benefits of planting sorghum on marginal soils such as saline-alkali land.
Project description:This dataset contains raw spectral data captured from sorghum roots collected from four Sorghum bicolor L. Moench genotypes grown in an arid field setting in Maricopa, Arizona in water-replete and water-limited conditions. We used these data to examine the root metabolome of field-grown sorghum in Arizona, USA, and related metabolomic data to microbial responses to stress.
Project description:This study utilized next generation sequencing technology (RNA-Seq) to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) to elucidate those genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. We examined the mRNA of 9 day old Sorghum bicolor (BTx623) from 2 tissue types (roots and shoots) for 2 treatments (20 uM ABA and 20% PEG) with corresponding controls (0.2M NaOH and H2O) for 27 hrs prior to harvesting, each done in triplicate biological replicates - resulting in 24 unique runs
Project description:Two alfalfa varieties, 'Chilean' (M. sativa ssp. sativa var. Chilean, drought sensitive) and 'Wisfal' (M. sativa ssp. falcata var. Wisfal, drought tolerant), with contrasting water use efficiency were subjected to water withholding for 11 days followed by re-watering. Samples were taken for well-watered plants and plants after five, eight, eleven days of drought stress as well as plants after recovery for one day following drought stress. Roots and shoots were sampled and analyzed separately by expression profiling using Affymetrix Medicago GeneChip.
Project description:This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification
Project description:This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation We examined the mRNA of various Sorghum bicolor (BTx623) tissues (flowers, vegitative and floral meristems, embryos, roots and shoots) and bisulfite treated DNA from two root samples
Project description:This study explores the changes in histone modifications of sorghum bicolor through developmental stages and in response to drought stress in two sorghum genotypes. We analyzed the leaves of 48 plants using top-down mass spectrometry and identified 26 unique histone proteins and 677 unique histone proteoforms. We detected trimethylation on nearly all H2B N-termini where acetylation is commonly expected. In addition, an unexpected modification on H2A histones was assigned to N-pyruvic acid 2-iminylation based on its unique neutral loss of CO2.
Project description:We developed a commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) and generated this dataset to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.
