Project description:The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping by sequencing (GBS)
Project description:Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the worldâs most important legume crop and is sensitive to O3. Current ground-level O3 are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated O3 using RNA-Sequencing.
Project description:Soybean fast neutron mutant lines were maintained to an advanced generation (ranging between approximately M6 and M11) and compared to their wild-type parent (M92-220-Long) using CGH to identify sequence deletions and duplications in the mutant plants.
Project description:An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean Four small RNA sequence populations from high throughput deep sequencing-by-synthesis and representing different tissues/organs of the soybean were characterized into small RNA classes, level of expresion, genes of origin and putative targeted genes
Project description:We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in soybean (Glycine max) which is sytenic with legume (Medicago truncatula). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types. Keywords: RNA Both the barrel medic and soybean tiling arrays were produced on the Maskless Array Synthesizer platform. Briefly, tiling-paths consisting of 36-mer oligonucleotides offset by five nucleotides were designed to represent both DNA strands of the selected barrel medic and soybean genome sequence. Probes were synthesized at a feature-density of 390,000 probes per array in a âchess boardâ design. Microarray production and storage were carried out. Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturerâs recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated. The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two μg dye-labeled targets were used for hybridization.
Project description:This SuperSeries is composed of the following subset Series: GSE10055: Transcriptional Analysis of 1M Regions in Medicago truncatula Using Tiling Microarrays GSE10056: Transcriptional Analysis of 1M Regions in Glycine max Using Tiling Microarrays Keywords: tiling array, transcriptional analysis Both the barrel medic and soybean tiling arrays were produced on the Maskless Array Synthesizer platform. Briefly, tiling-paths consisting of 36-mer oligonucleotides offset by five nucleotides were designed to represent both DNA strands of the selected barrel medic and soybean genome sequence. Probes were synthesized at a feature-density of 390,000 probes per array in a âchess boardâ design. Microarray production and storage were carried out. Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturerâs recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated. The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two μg dye-labeled targets were used for hybridization.
Project description:RNA-seq was used to characterize gene expression in soybean from a wide range of tissues. The primary focus of the project was small RNAs, and the identification of microRNAs and phased siRNA-generating loci, but RNA-seq data were generated from the same samples. This project was supported by the United Soybean Board.
Project description:Intercropping is a sustainable agricultural practice widely used around the world for enhancing resource use efficiency. However, short crops often grow in shade condition underneath the canopy of tall crops. Soybean is one of the most important oil crops and usually is planted in intercropping patterns. However, little is known about the acclimation responses of soybean leaves to shade in intercropping condition at the transcriptome level.