Development of DArT Marker Platforms and Genetic Diversity Assessment of the U.S. Collection of the New Oilseed Crop Lesquerella and Related Species

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 germplasm 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 germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a 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.

QTLs for iron concentration in seeds of the cultivated lentil (Lens culinaris Medic.) via genotyping by sequencing

“…Ltd., Canberra, Australia) following the protocol of Raman et al (2014). DArTseq takes advantage of a DArT complexity reduction method and combines it with next generation sequencing platforms, providing a less complex representation of sequencing (Altshuler et al, 2000;Kilian et al, 2012;Courtois et al, 2013;Cruz et al, 2013;Ward et al, 2013). Similarly to DArT methods based on array hybridization, the technology was optimized for each organism and application by selecting for the most appropriate complexity reduction method (both the size of the representation and the fraction of a genome selected for assays).…”

Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

“…The company developed a method named DArTseq. DArTseq combines genome complexity reduction methods and next-generation sequencing platforms (Courtois et al, 2013;Cruz et al, 2013;Raman et al, 2014;Kilian et al, 2016). Therefore, DArTseq represents a new implementation of sequencing of complexity-reduced representations (Huang et al, 2014) and more recent applications of this concept on the nextgeneration sequencing platforms (Sonah et al, 2013;Bastien et al, 2014).…”

“…The many advantages of DArTseq include no prior knowledge about sequencing of the plant genome and the capacity to produce high-density results, scoring thousands of unique genomic-wide DNA fragments in one single experiment with low-cost genotype information (Jaccoud et al, 2001;Kilian et al, 2016). The DArTseq method is used to discriminate diverse species for population studies, genetic diversity studies, germplasm characterization (Cruz et al, 2013), association studies (Courtois et al, 2013;Phuong Phung et al, 2014), and genetic mapping (Ren et al, 2015). To date, DArTseq genotyping has also been used for genetic analysis in species genomes, including Sorghum bicolor (Mace et al, 2008), rye (Bolibok-Brągoszewska et al, 2009), Lesquerella and related species (Cruz et al, 2013), japonica rice (Courtois et al, 2013), watermelon (Ren et al, 2015), and pineapple (Kilian et al, 2016).…”

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

“…Sequences were then loaded into the DArT Toolbox for quality filtering (average phrade score > 10 in sliding windows of 15 bp) of adapter removed sequences according to the protocol developed by Cruz et al (2013). Quality filtered sequences were then blasted against the NCBI GenBank and DArTdb Custom databases to check for microbial contamination, and contaminant sequences removed if present.…”