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Abstract
BackgroundCommon 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.ResultsTranscript-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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2499-3) contains supplementary material, which is available to authorized users.
Highlights
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
Large scale single nucleotide polymorphism (SNP) discovery and validation To capture a diverse subset of the genic nucleotide diversity in the common bean and tepary bean genomes, a set of six common bean and two tepary bean accessions were selected for targeted 3’-cDNA transcript profiling using 454 pyrosequencing technology
The current molecular marker resources for tepary bean are restricted to a few SSRs and SNPs from common bean and AFLPs, neither of which is ideal for genetic studies nor for breeding purposes
Summary
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. There has been a resurgence in interest in this crop recently as it is viewed as a potential source of genes for stress tolerance for common bean breeding, with a view to making common bean more resilient in the face of climate instability. It has the potential as a crop in its own right but Gujaria-Verma et al BMC Genomics (2016) 17:239 currently suffers from a lack of breeding activity directed towards larger seed size and increased yield
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