Transcription profiling of soybean soybean line PI200492 resistant to P. pachyrhizi
ABSTRACT: Affymetrix soybean genome arrays were used to identify genes differentially expressed in the immune resistance response at 6, 12, 24, and 48 hours after inoculation with Phakopsora pachyrhizi isolates TW72-1 or HW94-1; soybean + HW94-1 = resistant; soybean + TW72-1 = susceptible Experiment Overall Design: For each of 4 time points (6, 12, 24 and 48 hours post inoculation) a soybean PI200492 plant was inoculated with 2 treatments: HW94-1, or TW72-1. A mock inoculation was performed and sampled at time 0. There were three biological replicates of the entire experiment, for a total of 27 samples. During data analysis two samples failed the quality control metrics and were removed from the analysis, leaving 25 samples in the final data set.
This article describes specific procedures for conducting quality assessment of Affymetrix GeneChip(R) soybean genome data and for performing analyses to determine differential gene expression using the open-source R programming environment in conjunction with the open-source Bioconductor software. We describe procedures for extracting those Affymetrix probe set IDs related specifically to the soybean genome on the Affymetrix soybean chip and demonstrate the use of exploratory plots including im ...[more]
Project description:To investigate the molecular mechanism of nonhost resistance of M. truncatula against soybean rust, we performed integrated tanscriptome and metabolome analyses using samples derived from M. truncatula leaves inoculated with soybean rust. To identify host signaling pathways triggered by soybean rust infection, we carried out microarray analysis to monitor the expression profiles associated with nonhost resistance including pre-invasive (12 hai) and apoplastic defense (24 hai) using Affymetrix GeneChip® Medicago Genome Array (Affymetrix).
Project description:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. BARC-2 (Rj4/Rj4)) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to the seed pack (Seed Pack; Daiki rika Kogyo Co., Ltd., Shiga, Japan) watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61 or its type III secretion mutant BErhcJ. Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 2 and 4 days after inoculation. Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BErhcJ was measured 2 and 4 days after inoculation. Three independent experiments were performed at each inoculation.
Project description:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to a plant box (CUL-JAR300; Iwaki, Tokyo, Japan) containing sterile vermiculite watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation. Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment) was measured 8 days after inoculation. Three independent experiments were performed at each inoculation.
Project description:We deep sequenced a degradome library constructed from different soybean tissues. As a result, 19,830,257 represented 5,337,590 distinct signatures were obtained. 70.98% of the signatures were assigned to one soybean cDNA sequence and 24.05% matched with two cDNA sequences. 428 potential targets of small RNAs and 25 novel miRNA families were identified in soybean. A total of 211 potential miRNA targets including 150 conserved miRNA targets and 69 soybean-specific miRNA targets were identified. The signatures distribution on soybean primary miRNAs (pri-miRNAs) showed that most of the pri-miRNAs had the characteristic pattern of Dicer processing. The TAS3 small RNAs (siRNAs) biogenesis was conserved in soybean and nine Auxin Response Factors (ARFs) were identified as the TAS3 siRNA targets. The global identification of miRNAs targets would contribute to the functional research of the miRNA in soybean. one sample, We deep sequenced a degradome library constructed from different soybean tissues.
Project description:Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are negative regulators to target endogenous genes and repetitive sequences in plants. Although miRNAs and trans-acting or phased siRNAs (tasiRNAs or phasiRNAs) were found to target hundreds of disease related genes in Medicago, their role in plant-pathogen interactions in the legumes, particularly the R genes mediated interaction of soybean and the pathogen Phytophthora sojae is poorly understood. A deep sequencing was performed on nine soybean near isogenic lines (NILs) each carrying an Rps (Resistance to Phytophthora sojae) gene and their recurrent parent “Williams”, with sampling performed both pre- and post-inoculation with P. sojae. From these data, 44 known MIRNA loci with new miRNA variants, 78 novel miRNAs corresponding to 108 precursors, and 208 phasiRNA-producing (PHAS) loci were identified. Our data showed that overall the expression levels of miRNAs, phasiRNAs and siRNAs were extensively down-regulated after pathogen-inoculation. Moreover, the down-regulation levels in the nine resistant NILs were significantly higher than that detected in the susceptible Williams, and variations of small RNA expression within the resistant NILs were also observed, suggesting the molecular responses of different Rps lines are distinct. Surprisingly, the expression level changes of 21-nt phasiRNAs were significantly positively correlated with that of the corresponding mRNA level of the PHAS genes, suggesting the cascade effects of miRNA triggers on the downstream PHAS genes and phasiRNAs. Our data provided a comprehensive picture regarding small RNA based regulation of target genes, particularly NB-LRRs, involved in the responses to the pathogen. 20 samples were sequenced, 10 inoculated with P. sojae, the other 10 were mock-inoculated
Project description:Gene expression profiles in the bacterial pustule-resistant soybean cultivars To investigate the differential action between resistance and susceptible cultivars, we examined genome wide expression levels at five time points after X. axonopodis pv. Glycines (Xag) inoculation using microarray.
Project description:Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation. We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation. Soybean seeds were sowed on sterile agar medium and grown for 3 days in a growth chamber before being treated with H2O (mock-inoculated) or B. japonicum (inoculated). Soybean root hair cells were isolated at different time points (6hr, 12hr, 18hr, 24hr, 36hr, 48hr) after treatment. For each time point and condition, 3 or 4 independent biological replicates were produced.
Project description:The present study highlights the phytotoxicity of nanoparticles (NPs) to soybean roots and leaves at proteome level. The effect of three NPs Al2O3, ZnO, and Ag suspensions on soybean was evaluated.