Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements’ (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimers pipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.

麻疯树是潜在的生物柴油作物，对各种农业气候条件的适应性强。在这项研究中，我们利用了转座元件（TE）重复连接（RJs），它是基因组的重要组成部分，由于其在植物的基因组研究中的使用而形成了全基因组的分子标记平台。我们使用RJPrimers管道软件筛选了先前生成的大小为265 Mbp的麻风树杂种基因组，并鉴定出总共1274个TE接头。对于预测的RJ，我们设计了基于2868聚合酶链反应（PCR）的RJ标记（RJM），位于连接区的两侧。除了标记设计之外，还使用已鉴定的RJ来检测整个基因组中的225,517个TE。不同类型的转座重复元件主要分散在Retro，LTR，科皮和吉普赛类别。通过利用随机选择的RJM子集测试设计标记的功效。我们已经验证了32种J. curcas基因型中96种随机选择的RJ引物，超过90％的标记被有效增强为扩增子。其中，在估计32个麻疯树品系之间的遗传多样性时，显示10个引物具有多态性。UPGMA聚类分析表明，形成了两个聚类，例如A和B，它们的相似系数分别为85.5％和87％。在这项研究中确定的各种RJM可用作麻疯树功能基因组学的重要资产，包括基因组确定，作图和标记辅助选择。