Utilization of the Fluidigm Integrated Fluidic Chip (IFC) for SNPs Genotyping and BAC Clone Identification in Amaranthus

The grain amaranths (Amaranthus sp.) are important pseudo-cereals native to the New World. The genus also includes several well-known weedy species, collectively referred to as "pigweeds", which are arguably the most damaging weeds in the U.S. Notwithstanding their importance as an alternative crop species and as a weed species with significance global importance, few genomic tools have been developed for this genus.  Here we describe the identification of >27,000 Single Nucleotide Polymorphisms (SNPs) and the development of >400 functional SNP marker assays for the species as well as the first complete genetic linkage map in the genus. The SNP assays are based on genotyping KASPar^TM chemistry and were detected using the Fluidigm dynamic array platform. We also describe the utilization of the Fluidigm dynamic array platform for rapid screening of a super pooled 10X A. hypochondriacus Bacterial Artificial Chromosome (BAC) library.