Skip to main content
ARS Home » Research » Publications at this Location » Publication #158824


item He, Chunlin
item Xia, Zheng-Lian
item Campbell, Travis
item Bauchan, Gary

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/30/2003
Publication Date: 11/30/2003
Citation: He, C.N., Xia, Z., Campbell, T.A., Bauchan, G.R. 2003. Isolation and characterization of SSR markers in alfalfa [abstract]. Plant and Animal Genome Conference Proceedings. P242.

Interpretive Summary:

Technical Abstract: Simple sequence repeat (SSR) or microsatellite markers are codominant, abundant and hypervariable molecular markers from eukaryotic genomes that are being widely used in genetic mapping, phylogenetic studies and marker-assisted selection. Currently, the number of available SSR markers is still very limited for use in alfalfa. Thus, this study was conducted to develop microsatellites from alfalfa genomic libraries for use in genomic mapping and marker-assisted selection, and to determine the level of polymorphism of the isolated SSR markers using a set of 16 alfalfa germplasms. Genomic DNA was extracted from the alfalfa variety, W10, and the libraries were constructed with the vector pUC19 following restriction digest. Probes containing simple sequence repeats of dinucleotides (AC, AT, CT) and trinucleotides (CTT, GAT, GGT) were used for screening the colonies carrying inserts from the genomic libraries. A total of 158 colonies with positive signals were identified and sequenced. Of the 158 alfalfa DNA sequences, 81 sequences that contained SSRs with sufficient flanking DNA sequences were used for primer design for PCR screening. After PCR testing, the vast majority of the PCR primer pairs amplified the expected PCR fragments. These primers were used to screen 10 historically recognized alfalfa germplasm sources and germplasm collected in the wild to detect genetic variation. Based on the primers screened, 70.6% of the primer pairs generated polymorphisms and the number of alleles generated from the SSR primers among the germplasm ranged from 1-10. The polymorphic primers for the SSR loci with dinucleotide and trinucleotide repeats were used for genetic analysis and a dendrogram was constructed for 16 Medicago germplasms. The relationship among the germplasm revealed by the SSR markers is also discussed in this study.