Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae).

Mohammad Vatanparast,Prateek Shetty,Ratan Chopra,Jeff J Doyle,N Sathyanarayana,Ashley N Egan

doi:10.1038/srep29070

Abstract

Winged bean, Psophocarpus tetragonolobus (L.) DC., is similar to soybean in yield and nutritional value but more viable in tropical conditions. Here, we strengthen genetic resources for this orphan crop by producing a de novo transcriptome assembly and annotation of two Sri Lankan accessions (denoted herein as CPP34 [PI 491423] and CPP37 [PI 639033]), developing simple sequence repeat (SSR) markers, and identifying single nucleotide polymorphisms (SNPs) between geographically separated genotypes. A combined assembly based on 804,757 reads from two accessions produced 16,115 contigs with an N50 of 889 bp, over 90% of which has significant sequence similarity to other legumes. Combining contigs with singletons produced 97,241 transcripts. We identified 12,956 SSRs, including 2,594 repeats for which primers were designed and 5,190 high-confidence SNPs between Sri Lankan and Nigerian genotypes. The transcriptomic data sets generated here provide new resources for gene discovery and marker development in this orphan crop, and will be vital for future plant breeding efforts. We also analyzed the soybean trypsin inhibitor (STI) gene family, important plant defense genes, in the context of related legumes and found evidence for radiation of the Kunitz trypsin inhibitor (KTI) gene family within winged bean.

Highlights

Since the 1975 publication by the US National Academy of Sciences of The Winged Bean: A High Protein Crop for the Tropics[6], considerable effort has been focused on studying the nutritional quality and climatic and ecological tolerances of the plant[7,8]
The advent of genomic technologies has brightened the prospects for such orphan crops[20,25,26], with recent research focusing on lentil (Lens culinaris Medik.27), chickpea[28], grass pea (Lathyrus sativus L.29), and a number of Vigna species[30,31], among others
Winged bean represents a promising alternative to protein-rich soybean for tropical regions of the world that house nearly 40% of the world population, of which nearly one third is protein deficient, and many of whom are women and children[32]

Summary

Introduction

Since the 1975 publication by the US National Academy of Sciences of The Winged Bean: A High Protein Crop for the Tropics[6], considerable effort has been focused on studying the nutritional quality and climatic and ecological tolerances of the plant[7,8]. Processing using moist heat or soaking has been shown to safely eliminate these substances Research efforts concerning such anti-nutritional components have yielded significant knowledge concerning trypsin, a serine protease that acts to hydrolyze proteins as part of vertebrate digestion, and trypsin inhibitors, proteins that stop the action of trypsin, thereby interfering with digestion. Studies show involvement in defense against insects that suck the phloem sap and against bacteria that invade upon wounding[11] In biomedical research, these modes of action have made trypsin and trypsin inhibitors vital components of molecular cell research where they are widely used in cell culture to detach cells from tissue culture plates. We compared Sri Lankan accessions to a Nigerian winged bean transcriptome previously sequenced on the Illumina platform (e) to identify Single Nucleotide Polymorphisms (SNPs) evident between the geographically separated genotypes and (f) to present an analysis of the Kunitz trypsin inhibitor gene family in the context of related legumes

Methods

Results

Conclusion