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Title:   Author  item
                                            O`Rourke, Jamieitem
                                            FU, FENGLI - University Of Minnesotaitem
                                            Bucciarelli, Brunaitem
                                            YANG, SAM - University Of Minnesotaitem
                                            Samac, Deborah

                                                         - *Debby*item
                                            Lamb, Joannitem
                                            MONTEROS, MARIA - Samuel Roberts Noble Foundation, Incitem
                                            Graham, Michelleitem
                                            GRONWALD, JOHN - Retired ARS Employeeitem
                                            KROM, NICK - Samuel Roberts Noble Foundation, Incitem
                                            LI, JUN - Samuel Roberts Noble Foundation, Incitem
                                            DAI, XINBIN - Samuel Roberts Noble Foundation, Incitem
                                            ZHAO, PATRICK - Samuel Roberts Noble Foundation, Incitem
                                            Vance, Carroll
  Submitted to: BioMed Central (BMC) Genetics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 6/24/2015
                                    Publication  Date: 7/7/2015
                                    Citation: O'Rourke, J.A., Fu, F., Bucciarelli, B., Yang, S.S., Samac, D.A., Lamb, J.F., Monteros, M., Graham, M.A., Gronwald, J.W., Krom, N., Li, J., Dai, X., Zhao, P.X., Vance, C.P. 2015. The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BioMed Central (BMC) Genetics. 16:502. DOI: 10.1186/s12864-015-1718-7.Interpretive Summary: Alfalfa is the fourth most widely produced crop in the United States, contributing $10 billion to the U.S. economy.  Alflafa is primarily used as feed in dairy cow, sheep, and beef production systems but is also important for restoring nitrogen to soils. In recent years, there has been increased interest in using alfalfa as a biofuel.  Alfalfa grown in the U.S. is a tetraploid, with each cell having four copies of every chromosome.  Due to the complicated genetics, there are few resources available for alfalfa improvement.  To develop resources for alfalfa improvement and better understand the differences between alfalfa used for biofuel production and forage production systems we captured the sequences of all genes active in roots, nitrogen-fixing root nodules, leaves, flowers, elongating stems and post elongating stems.  Using these sequences we built a transcriptome representing the majority of genes in the alfalfa genome.  Using these sequences we then measured the expression of the genes in different tissues of biological interest and compared their expression activity between the two alfalfa lines.  Specifically we examined expression differences in genes involved in cold tolerance, cell wall development, flower color, and nodule development.  In addition, we used the assembly to identify sequence changes between the two alfalfa lines that could be used for marker development by breeders to improve alfalfa production.  We have developed a website, the Alfalfa Gene Index and Expression Database – AGED, for the alfalfa community to utilize this important resource.  The database is available at http://plantgrn.noble.org/AGED/.
                                Technical Abstract: Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement. A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,721) were identified. The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by nine-fold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/, a publicly available genomic resource for alfalfa improvement and legume research.


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