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The Alfalfa Gene Index and Expression Atlas Database    
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Alfalfa is the fourth most widely grown crop in the United stated and the most widely cultivated forage legume around the world. In addition to its value as a livestock feed, cultivation of alfalfa provides numerous agro-ecological services by reducing soil erosion and nutrient loss, enhancing soil carbon sequestration, and increasing soil nitrogen fertility.

Using Illumina RNA-seq technology, we developed a de novo transcriptome assembly from two subspecies, Medicago sativa ssp. sativa (B47) and Medicago sativa ssp. falcata (F56). These two genotypes have proven to be important parents in USDA-ARS alfalfa breeding programs. The two subspecies have with distinct phenotypes and geographic origins, but are easily hybridized. The de novo transcriptome assembly was developed using transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes and assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences.

Statistical analyses identified 20,447 transcripts differentially expressed between subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Single nucleotide polymorphisms (SNPs) differing between subspecies (110,721) and SNPs common to both subspecies (20,833) were also identified.

This web-accessbile database is intended to provide the Alfalfa researchers with the MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs identified in this study.

Data & bioinformatic resources were generated by the laboratory of Dr. Carroll P. Vance, USDA-ARS, St. Paul, MN, Dr. Patrick X. Zhao at the Samuel Roberts Noble Foundation, and many international collaborators.