Dataset Information

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.

SUBMITTER: Gujaria-Verma N

PROVIDER: S-EPMC4793507 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Publications

Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping.

Gujaria-Verma Neha N Ramsay Larissa L Sharpe Andrew G AG Sanderson Lacey-Anne LA Debouck Daniel G DG Tar'an Bunyamin B Bett Kirstin E KE

BMC genomics 20160315

<h4>Background</h4>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 po ...[more]

PMID: 26979462

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Project description:The tepary bean (Phaseolus acutifolius Gray) is a US-Mexico frontier native crop, produces high yields in agriculture, and needs to be reconsidered because of its nutritional and functional properties. This study aimed to determine the technological and nutritional properties of flours and protein concentrates of tepary bean, besides determining an in silico agonist effect of tepary bean lectin to peroxisome proliferator-activated receptor gamma (PPAR-γ). We evaluated the technological properties of raw samples (tepary flour and tepary protein concentrate) and cooked samples (tepary flour and tepary protein concentrate). The flours present a significant difference (p < 0.05) concerning protein concentrates in water absorption and oil absorption capacity. The raw samples' emulsifying capacity was higher than that reported in the literature for other legumes, but not the cooked samples. The samples' foaming capacity had no significant difference in treatments (p > 0.05), and cooked tepary bean protein concentrate presented complete gelation at a lower concentration (2%). Nutritionally, raw samples present a protein percentage of 23.46 ± 0.06 and 71.38 ± 0.44 and cooked samples present a protein percentage of 25.27 ± 0.04 and 62.69 ± 0.14; a chemical score of 72, 86, 82, and 72; in vitro protein digestibility (%) = 48.20 ± 0.31, 49.80 ± 0.80, 61.77 ± 1.70, and 63.61 ± 4.19; and C-PER = 0.86, 1.34, 1.93, and 1.81, respectively. All the samples showed methionine + cysteine as the limiting amino acid. All these nutritional data are very similar to the common bean (Phaseolus vulgaris). SDS-PAGE preserves the lectin fraction in both protein concentrates. The in silico study of tepary lectin (PDB: 6tt9) shows that there were seven peptides that presented values below -120 kcal/mol: PEW, VSVGF, PSQK, TTPW, ATSF, ITY, and TSF, with VSVGF, PSQK, and PEW having the highest affinity for active sites of the PAPRγ receptor (binding energies from -5.32 to -7.04 kcal/mol). These peptides could show antiadipogenic or antidiabetic activity based on the intermolecular bond energies and open an interesting research item.

Project description:BackgroundExpressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes.ResultsA set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes.ConclusionThe SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation between species allowed synteny comparisons to be made to sequenced genomes. This synteny analysis may support positional cloning of target genes in common bean through the use of genomic information from these other legumes.

Dataset Information

Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping.

Publications

Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping.

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