Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae).
Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae).
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DOI：
10.1038/srep29070
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发表时间：
2016-06-30
影响因子：
4.6
通讯作者：
Egan AN
中科院分区：
文献类型：
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作者：
Vatanparast M;Shetty P;Chopra R;Doyle JJ;Sathyanarayana N;Egan AN
四棱豆（Psophocarpus tetragonolobus (L.) DC.）的产量和营养价值与大豆相似，但在热带条件下更容易生存。在这里，我们通过对两个斯里兰卡品种（本文表示为 CPP34 [PI 491423] 和 CPP37 [PI 639033]）进行从头转录组组装和注释、开发简单序列重复 (SSR) 标记以及鉴定地理上分离的基因型之间的单核苷酸多态性 (SNP) 来加强这种孤儿作物的遗传资源。基于来自两个种质的 804,757 个读数的组合组装产生了 16,115 个重叠群，N50 为 889bp，其中超过 90% 与其他豆科植物具有显着的序列相似性。将重叠群与单例相结合产生了 97,241 个转录本。我们鉴定了 12,956 个 SSR，包括设计引物的 2,594 个重复序列以及斯里兰卡和尼日利亚基因型之间的 5,190 个高可信度 SNP。这里生成的转录组数据集为这种孤儿作物的基因发现和标记开发提供了新的资源，并且对于未来的植物育种工作至关重要。我们还在相关豆类中分析了大豆胰蛋白酶抑制剂（STI）基因家族（重要的植物防御基因），并发现了四棱豆内库尼茨胰蛋白酶抑制剂（KTI）基因家族辐射的证据。
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.