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Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae)
Mohammad Vatanparast1, Prateek Shetty2, Ratan Chopra3
1US National Herbarium (US), Department of Botany, Smithsonian Institution-NMNH, 10th and Constitution Ave, Washington DC, 20013, USA.
Scientific Reports
|July 1, 2016
Summary
Researchers enhanced genetic resources for winged bean, an important tropical legume crop. They developed new genetic markers and identified variations, crucial for improving this underutilized plant through breeding.
Area of Science:
- Plant Genomics
- Crop Science
- Molecular Biology
Background:
- Winged bean (Psophocarpus tetragonolobus) is a tropical legume with soybean-like nutritional value.
- It is an underutilized orphan crop with limited genetic resources.
- Strengthening genetic resources is vital for its future breeding and cultivation.
Purpose of the Study:
- To generate a de novo transcriptome assembly and annotation for two Sri Lankan winged bean accessions.
- To develop novel simple sequence repeat (SSR) markers.
- To identify single nucleotide polymorphisms (SNPs) for genetic diversity analysis.
Main Methods:
- RNA sequencing of two winged bean accessions (CPP34 and CPP37).
- De novo transcriptome assembly and annotation.
- Identification and primer design for SSRs.
- SNP calling between Sri Lankan and Nigerian genotypes.
Main Results:
- A combined assembly yielded 16,115 contigs and 97,241 transcripts.
- Over 90% of contigs showed similarity to other legume sequences.
- 12,956 SSRs were identified, with primers designed for 2,594.
- 5,190 high-confidence SNPs were found between genotypes.
- Analysis of the soybean trypsin inhibitor (STI) gene family revealed Kunitz trypsin inhibitor (KTI) gene family radiation.
Conclusions:
- The generated transcriptomic data provides valuable resources for winged bean gene discovery and marker development.
- These resources will support future breeding programs for this orphan crop.
- The study provides insights into the evolution of defense genes within winged bean.
