Phaseolus vulgaris 454 Sequencing & SNP Discovery Project

Phaseolus vulgaris 454 Sequencing & SNP Discovery Project

Eight germplasm were chosen for this project:CDC WM-2, BAT 93, Expresso, Higuera-E, Jalo EEP-558, PI 430219, SMARC1N-PN1, and W6-15578. Tissue was collected from multiple plants at various developmental stages for RNA extraction which led to the generation of 3'-anchored cDNA libraries using the method described in Parkin et al., 2010. Each line was sequenced using the Roche 454 Titanium sequencing protocol. Sequencing reads were aligned directly to the Phaseolus vulgaris genomic build v0.9 using GMap. Then loci which were polymorphic between at least two of the lines were identified resulting in 133,108 SNPs.  All SNPs were re-mapped to the published genome assembly 1.0 (Phytozome.org; Schmutz et al. 2014).