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.

BackgroundThe medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions.ResultsOne-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways.ConclusionsThe M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.

Winged bean, Psophocarpus tetragonolobus (L.) DC., is analogous to soybean in yield and nutritional quality, proving a valuable alternative to soybean in tropical regions of the world. The presence of anti-nutritional factors and high costs associated with indeterminate plant habit have been major concerns in this crop. But occurrence of good genetic variability in germplasm collections offers precious resources for winged bean breeding. However, lack of germplasm characterization is hindering such efforts. From a genomic standpoint, winged bean has been little studied despite rapid advancement in legume genomics in the last decade. Exploiting modern genomics/breeding approaches for genetic resource characterization and the breeding of early maturing, high yielding, determinate varieties which are disease resistant and free of anti-nutritional factors along with developing consumer friendly value-added products of local significance are great challenges and opportunities in the future that would boost cultivation of winged bean in the tropics. We review past efforts and future prospects towards winged bean improvement.

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Xanthomonas campestris pv. dieffenbachiae, the causal agent of anthurium bacterial blight, is a major concern of the anthurium industry worldwide. This pathogen has many hosts in the family Araceae (e.g., Anthurium, Dieffenbachia, Syngonium, Aglaonema, Philodendron, Xanthosoma, Caladium, and Colocasia). Most anthurium cultivars are susceptible to bacterial blight, making it very difficult to manage the disease once introduced to a production area. Therefore, sanitation and exclusion of the pathogen through pathogen-free propagative stock are vital aspects of anthurium cultivation. The anthurium industry is expanding in India, and as many new cultivars are being imported, the plant material is subject to thorough quarantine inspection at the port of arrival. During routine inspections on three separate occasions, Anthurium andreanum plants imported from The Netherlands had watersoaked spots at leaf margins bordered by chlorotic or necrotic zones. Xanthomonas-like colonies were isolated from four different cultivars with semiselective media (2). Bacteriological tests confirmed that the cultures were X. campestris. Pathogenicity tests, performed by rubbing leaves with a cotton swab dipped into a suspension of the bacteria (approx. 107 CFU/ml), resulted in production of leafspots in 6 days and early blight symptoms in 10 to 12 days. The bacterium was further identified as X. campestris by carbon source utilization (similarity coefficient = 0.582; Biolog, Hayward, CA). Enzyme-linked immunosorbent assay reaction patterns with a panel of monoclonal antibodies for X. campestris pv. dieffenbachiae designated as Xcd1 (clone 72E-E3-B9-C5, isotype IgG2a), Xcd2 (clone 97-2-1-01, isotype IgM), Xcd3 (clone 72B-F9-B6-E9, isotype IgM), Xcd7 (clone72D-E10-C2-D9, isotype IgM), T1 (clone 92-16, isotype IgM), and T2 (clone 92-59-1-1, isotype IgG) showed that the intercepted strain belong to the serogroup 5 of X. campestris pv. dieffenbachiae (1). This pathogen is not known to occur in India, and there is high probability of risk of introduction through large-scale import of anthurium plants with either visible or latent infections. References: (1) R. L. Lipp et al. Phytopathology 82:677, 1992. (2) D. J. Norman and A. Alvarez. Plant Dis. 73:654, 1989.