The new Sorghum bicolor mRNA-Seq platform

20 Jan 2021

Sorghum RNA-Seq platform


Sorghum bicolor (L.) Moench is a model C4 grass species with a small diploid genome and highly heterogeneous germplasm. It is the fifth most widely grown cereal crop worldwide after rice, wheat, maize, and barley. Sorghum originated from northeast Africa and is well adapted to growth in hot and dry regions, where it serves as a staple food and primary source of human nutrition. Sorghum exhibits high phenotypic and morphological diversity reflected in the crop’s multiple agronomic uses. For instance, early flowering Sorghum with short stature is grown mostly for its grain, while tall and late maturing genotypes are used to produce sugar, forage, or bioenergy. Various applications for cultivated Sorghum and its resilience to difficult conditions make it a growing interest crop among farmers and breeders. The vast genetic pool of sorghums offers a great scope of possibilities for genetic enhancement of its traits and their transfer to other crop species.

The new Sorghum bicolor mRNA-Seq platform

The new Sorghum mRNA-Seq platform in GENEVESTIGATOR currently has 793 curated samples from 20 experiments focusing on vegetative and reproductive development and response to stress. Almost 30 anatomical parts are covered, ranging from cells to tissues and organs. The detailed annotation allows gene expression analysis in 15 cultivated Sorghum genotypes: from local landraces to inbred lines representing grain, sweet, and bioenergy types of Sorghum.

post thumb Figure 1: The content of the Sorghum bicolor mRNA-Seq platform in GENEVESTIGATOR is represented as a number of samples from highlighted research topics and genotypes. Our database’s mRNA Seq samples are from Sorghum plants of 15 different genotypes. Important traits such as crop type and photoperiod sensitivity are manually assigned to each genotype by the curators at NEBION. The “Plot groups” command in the “Samples tool” helps getting an overview of the relations between Sorghum lines, their characteristics, and your gene of interest.


A TRANSCRIPTOME MAP OF INFLORESCENCE TISSUES IN SORGHUM - FROM MERISTEM TO GRAIN

Inflorescence and seed development are important aspects of Sorghum research, as most of this crop is grown for grain used in the food and feed production. Understanding the molecular regulation of grain yield and quality requires investigation of genes influencing reproductive tissues’ development and seed traits.

The new Sorghum platform contains 10 mRNA-Seq experiments with 131 samples of inflorescence, seed, and their parts. Our “Anatomy” tool in the “GENE SEARCH” toolset allows the identification of genes specifically expressed in single or multiple organs. e.g., in the panicle, microspore, or endosperm. Such a list of genes can be saved for further analysis with other GENEVESTIGATOR tools or exported to secondary software.

post thumb Figure 2: The Anatomy tool under GENE SEARCH generates a list of genes showing elevated mRNA levels in panicle, spikelet, and floret samples. The flexibility of the tool allows for multiple combinations of anatomy selection.


To learn more about our curated plant data and licensing conditions for GENEVESTIGATOR, contact us at sales@nebion.com.


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