Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement.
Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement.
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DOI：
10.3390/genes6041164
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发表时间：
2015-11-02
期刊：
影响因子：
3.5
通讯作者：
Chung JW
中科院分区：
文献类型：
--
作者：
Kim TS;Raveendar S;Suresh S;Lee GA;Lee JR;Cho JH;Lee SY;Ma KH;Cho GT;Chung JW
箭舌豌豆（Vicia sativa）是世界上最重要的一年生豆科牧草之一，具有多种用途和高营养价值。尽管有这些农学上的好处，许多缺点，包括氰基丙氨酸毒素，降低了豌豆品种的农学价值。在这里，我们使用454技术对两个V. sativa亚种（ssp. sativa和ssp. nigra），为野豌豆研究界丰富功能信息和遗传标记资源。总共86，532和47，103个读段分别产生了35，202和18，808个单一基因，其中V.sativa和V.sativa nigra的平均长度分别为735和601 bp。利用Gene Ontology注释和正向同源基因类聚类对野豌豆转录组的功能进行了注释。然后，利用蚕豆转录组序列进行简单重复序列（SSR）和单核苷酸多态性（SNP）标记。约13%和3%的野豌豆单基因组中分别含有推定的SSR和SNP序列。在这些SSR中，选择了100个用于验证和多态性测试，使用野豌豆种质集。因此，我们的方法利用转录组学数据的效用，以加快野豌豆育种计划。
The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.