Functional Biology of Alfalfa

Jeffrey J. Volenec

Department of Agronomy, Purdue University,

West Lafayette, IN 47907-1150, jvolenec@purdue.edu

Functional genomics and proteomics are tools that may aid crop improvement efforts, including those focusing on alfalfa (Medicago sativa L.). Effective use depends, in part, on knowing what genomic information is available for use, and how best to apply it. GenBank was searched for all Medicago sativa sequences deposited between its inception through June 1, 2000. A total of 476 accessions were found, but surprisingly 152 accessions (32%) were duplicate submissions. Another 52 accessions (11%) were fragments. The remaining 272 accessions (57%) were used in this analysis. Since the first sequence was submitted to GenBank, submissions have risen from 2/year to about 60/year in 1997, 1999, and 2000 (projected total) (Fig. 1). At this annual rate of progress, and assuming 50,000 genes in the alfalfa genome, it will take over 800 years to sequence and characterize the alfalfa genome. Most alfalfa GenBank submissions are cDNAs made from mRNA. Therefore, tissue-specific sequences are likely to be found. Cultured cells (>70) and nodules (>50) are tissues most frequently analyzed (Fig. 2). Fewer than 10 GenBank accessions have been reported for crowns, seeds, pollen, stems, and crown meristems of alfalfa. Cultivar effects may influence sequences obtained. About one-half of the GenBank entries failed to identify the cultivar used in the analysis. Thirty three cultivars (mainly fall dormant) were identified in the remaining entries. Apollo was the most commonly used cultivar (14 of the 17 entries for Apollo were cultured cells). The nature of the alfalfa genes in GenBank will be discussed. In addition, the utility of sequence information derived from the Medicago truncatula genomics initiative in alfalfa improvement will be discussed. A limitation is that we know so little regarding alfalfa biology that we will have difficulty using the vast array of molecular data becoming available. Understanding the functional biology of alfalfa must emerge as a priority in the future.