CADL-Gene Expression Atlas

A Gene Expression Atlas for Alfalfa CADL Genome v1

Alfalfa (Medicago sativa L.)


Alfalfa (Medicago sativa) is an autotetraploid (2n=4x=32), outcrossing species and is the most important forage legume in the United States. Alfalfa has the capacity for symbiotic nitrogen fixation and it is used in agricultural systems for pasture, hay or silage as a source of digestible energy and protein. The genetic diversity in cultivated and non-cultivated populations can be utilized by alfalfa breeders to develop highly productive cultivars with desirable agronomic traits through genome-assisted selection by integrating functional and translational genomics approaches.

The Gene Atlas Server


The alfalfa Gene Expression Atlas Web Server was developed to provide information about gene expression in tissue samples of contrasting alfalfa genotypes. The Medicago sativa transcriptomes generated via RNA-sequencing were annotated using gene ontology terms and evaluated for high confidence gene models based on the MAKER and SPADA pipelines. The web server includes Medicago sativa gene expression data from multiple alfalfa genotypes that were grown under a variety of abiotic stress conditions including drought and acid conditions with and without aluminum toxicity.

The website enables the user to query, visualize, compare and analyze the expression of one or more genes of interest in different genotypes and conditions. Users can search the gene expression database by gene name and/or annotation based on the gene models from the diploid alfalfa (CADL) genome, differential gene expression between pairwise comparisons and co-expression analysis using a key gene as bait to identify other genes similarly expressed. The output can be downloaded into excel format and used to generate bar graphs or line charts with the desired datasets.

Expression Profile


Search the gene expression database by gene name and/or annotation based on the gene models from the diploid alfalfa (CADL) genome.

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Differential Expression


Search the differential gene expression between pairwise comparisons.

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Co-Expression


Search the co-expression analysis using a key gene as bait to identify other genes similarly expressed.

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GO Enrichment


Search gene/mRNA names for Gene Ontology Enrichment Analysis.

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Related External Resources