ARS | Publication request: Alfalfa Biomass Germplasms: SFP Detection and Transcriptome Analysis

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 9, 2008
Publication Date: January 10, 2009
Citation: Yang, S.H., Xu, W.W., Tesfaye, M., Lamb, J.F., Jung, H.G., Samac, D.A., Vance, C.P., Gronwald, J.W. 2009. Alfalfa Biomass Germplasms: SFP Detection and Transcriptome Analysis [abstract]. XVII Plant and Animal Genome Conference Proceedings, January 10-14, 2009, San Diego, California. Abstract W167.

Technical Abstract: Advances in alfalfa [Medicago sativa (L.) subsp. sativa] breeding, molecular genetics, and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32) with complex polysomic inheritance. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve this crop as a cellulosic ethanol feedstock. We selected two alfalfa genotypes (252, 1283) that differ in cellulose and Klason lignin concentration in stem cell walls. Analysis of GeneChip expression data files of alfalfa stem internodes of genotypes 252 and 1283 at two growth stages (elongating, post-elongation) revealed 10,887 single-feature polymorphisms (SFPs) in 8,230 probe sets. Validation analysis by PCR-sequencing of a random sample of SFPs indicated a 12% false discovery rate. Functional classification and over-representation analysis showed that both genotypes were highly enriched in SFP-harboring cell wall genes. We mapped 5,833 of the 8,230 SFP-harboring genes onto putative orthologous loci on Medicago truncatula chromosomes. Clustering and over-representation of SFP-harboring genes within the same functional class (e.g., cell wall genes) was observed on some chromosomes. Prior to analysis of expression data for the two alfalfa genotypes, SFP probes were masked to reduce false positives and false negatives. The combination of SFP and gene expression analysis provide a list of candidate cell wall genes that can be used as molecular markers in a breeding program to improve alfalfa as a cellulosic feedstock. The results of this study will also be useful in advancing understanding of genome organization in alfalfa and for comparative genomics research with other legume species.