title: Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae).
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.
authors.affiliation: US National Herbarium (US), Department of Botany, Smithsonian Institution-NMNH, 10th and Constitution Ave, Washington DC, 20013, USA.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Vatanparast
authors.affiliation: Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.
authors.forename: Prateek
authors.initials: P
authors.lastname: Shetty
authors.affiliation: United States Department of Agriculture, Agriculture Research Service, 3810 4th St., Lubbock, TX, 79415, USA.
authors.forename: Ratan
authors.initials: R
authors.lastname: Chopra
authors.affiliation: Section of Plant Breeding &Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA.
authors.forename: Jeff J
authors.initials: JJ
authors.lastname: Doyle
authors.affiliation: Department of Botany, Sikkim University, 5th Mile, Tadong, Gangtok, Sikkim, 737102, India.
authors.forename: N
authors.initials: N
authors.lastname: Sathyanarayana
authors.affiliation: US National Herbarium (US), Department of Botany, Smithsonian Institution-NMNH, 10th and Constitution Ave, Washington DC, 20013, USA.
authors.forename: Ashley N
authors.initials: AN
authors.lastname: Egan
mesh_terms: D020224:Expressed Sequence Tags; D007887:Fabaceae / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics*; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome / Q000235:genetics*; D014360:Trypsin Inhibitor, Kunitz Soybean / Q000235:genetics
chemical_list: D014360:Trypsin Inhibitor, Kunitz Soybean