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Title: Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of new oilseed crop lesquerella and relative species

Author
item Cruz, von Mark
item KILIAN, ANDRZEJ - Diversity Arrays Technology
item Dierig, David

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2013
Publication Date: 5/28/2013
Citation: Cruz, V.V., Kilian, A., Dierig, D.A. 2013. Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of new oilseed crop lesquerella and relative species. PLoS One. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064062.

Interpretive Summary: Lesquerella is a promising new oilseed crop for the U.S. Southwest. It is a source of novel hydroxy fatty acids that have direct uses in the automotive, cosmetic, and biofuel industries. There is little information known about the genetic diversity of the lesquerella germplasm collection in the U.S. National Plant Germplasm System. Two molecular marker platforms based on microarray technology were developed and successfully utilized to examine the genetic variability in several species of lesquerella and their relative species. The relationships among the germplasm accessions were determined to be in agreement with geographic groupings and the results supported the known taxonomic classification in the species. The new molecular marker platforms will be useful in further understanding the genetics of lesquerella to hasten crop improvement efforts, as well as help streamline germplasm preservation activities on the species.

Technical Abstract: The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of the collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the Physaria germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa. Hopefully, the study will encourage similar analysis of diversity in other minor and new oilseed crop species.