title: Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping.
abstract: BACKGROUND
  Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species' ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly.
  
  
  RESULTS
  Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements.
  
  
  CONCLUSIONS
  The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other.
authors.affiliation: Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
authors.forename: Neha
authors.initials: N
authors.lastname: Gujaria-Verma
authors.affiliation: Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
authors.forename: Larissa
authors.initials: L
authors.lastname: Ramsay
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
authors.affiliation: Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
authors.forename: Lacey-Anne
authors.initials: LA
authors.lastname: Sanderson
authors.affiliation: Genetic Resources Program, International Center for Tropical Agriculture, Km 17 recta a Palmira, AA6713, Cali, Colombia.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Debouck
authors.affiliation: Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
authors.forename: Bunyamin
authors.initials: B
authors.lastname: Tar'an
authors.affiliation: Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada. k.bett@usask.ca.
authors.forename: Kirstin E
authors.initials: KE
authors.lastname: Bett
mesh_terms: D002874:Chromosome Mapping; D015723:Gene Library; D017343:Genes, Plant; D060005:Genotyping Techniques; D027805:Phaseolus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide