The comparative genomics approach has enabled us to identify SNPs and other variable regions in Pae that offer candidate molecular markers for large scale phylogenetic analyses.
However, analyses of large data sets of eastern [ 31, 32] and northern Asian complete mtDNA sequences [ 19- 21, 30, 33, 34] have significantly refined the topology of the mtDNA phylogeny, providing new informative markers for large scale population studies.
Additionally, this study meets all the criteria proposed for evaluating the use of molecular markers for large scale germplasm diversity analyses [ 35]; a large number of markers, thorough representation of these markers on a genetic linkage map of the species and the selection of monolocus probes.
The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs.
Thus, when Pi9-Pro serves as a base marker for large-scale screening of Pi2 in MAS breeding programs, Pi2-LRR can be used as a supplementary marker for confirmative screening, enabling more precise selection of Pi2 in rice breeding populations.
Overall, this work provides the first set of oat-based SNP markers, and a pipeline for large scale development of a much-needed genomic resource.
These markers will be essential for large scale backcross breeding efforts to produce a tree of primarily American chestnut origin but with a combination of Chinese chestnut chromosomal segments that confer necessary biotic resistance loci.
Fortunately, with the development of biotechnology, the next-generation sequencing (NGS) technology makes it feasible for large scale SNP marker discovery.
Ninety-four percent of the PCR primers amplified products with anticipated sizes (data not shown), demonstrating a high fidelity and efficiency for large scale SSR marker development by the GS-FLX sequencing approach.
Based on these results, 103 clones with a mean marker retention of 23.8% were selected for large scale culture to produce DNA in sufficient quantities for the genotyping of numerous markers.
