W739 Utilization of the Fluidigm Integrated Fluidic Chip (IFC) for SNPs Genotyping and BAC Clone Identification in Amaranthus

Date: Tuesday, January 17, 2012
Time: 11:00 AM
Room: Pacific Salon 4-5 (2nd Floor)
Jeff Maughan , Brigham Young University, Provo, UT
Scott Smith , Brigham Young University, Provo, UT
David B. Harker , Brigham Young University, Provo, UT
Eric N. Jellen , Brigham Young University, Provo, UT
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 KASParTM 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.