ARS | Publication request: ASSESSMENT OF THE GENETIC DIVERSITY AND PHYLOGENETIC RELATIONSHIPS OF A TEMPERATE BAMBOO COLLECTION BY USING TRANSFERRED EST-SSR MARKERS

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 8, 2005
Publication Date: August 1, 2005
Citation: Barkley, N.L., Newman, M.L. aka Harrison Dunn, M.L., Wang, M.L., Hotchkiss, M.W., Pederson, G.A. 2005. Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred est-ssr markers. Genome. 48:731-737

Interpretive Summary: Classifying bamboo germplasm can be quite cumbersome since many bamboos flower so infrequently. Vegetative characters are commonly used to classify bamboo; however, these characters can be unreliable because they are often influenced by the environment. Due to the unusual life cycle of bamboo, many bamboos have been classified and subsequently reclassified. DNA marker technology is a powerful tool to fingerprint germplasm and to evaluate inter- and intraspecific relationships. Unfortunately, minor grass species such as bamboo do not have many publicly available markers for research. However, many markers are available from major grass crops such as wheat, corn, rice and sorghum. Since DNA marker development is costly and time consuming, we utilized markers from major grass crops to evaluate their transferability to bamboo. These markers allowed us to examine the genetic diversity and phylogenetic relationships of a temperate bamboo collection. The molecular data allowed us to determine that a few of the plots in the field were contaminated. This information was not previously known and thus is extremely valuable for future curation of this crop.

Technical Abstract: EST-SSR markers derived from major cereal crops were utilized to assess their transferability to bamboo. The EST-SSR markers derived from sorghum produced the most polymorphic fragments and demonstrated the highest transfer rate (67%). The maize markers were not successful at amplifying fragments in bamboos and thus the transfer rate for maize markers was only 38%. The markers that were determined to be polymorphic from screening eight bamboo accessions were selected to assess genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pair wise combinations (UPGMA) and assessing differences in character data (parsimony). These dendrograms clustered the accessions into two main clades which corresponded to accessions characterized as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their taxonomic classification. These markers were also beneficial in identifying contaminated and misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.