Abstract Wheat (Triticum aestivum L.) is a major crop, which is widely grown, occupying globally an area of ∼215 million hectares. The crop suffers major losses due to leaf rust caused by fungal pathogen, Puccinia triticina Eriks. and E. Henn.. When wheat plants are attacked by this fungus, hundreds of downstream genes involved in signal transduction pathways experience regulated expression. This regulation partly depends on non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In the present study, miRNAs and lncRNAs associated with wheat-leaf rust pathosystem were identified using RNA-seq data for a pair of near-isogenic lines (NILs), which differed for the gene Lr28 in the background of wheat cultivar HD2329. The study is a continuation of our earlier transcriptome study involving the same pathosystem. A total of 50 miRNAs and 1178 lncRNAs were identified through in silico analysis of RNA-seq data; of these, 16 miRNAs and 22 lncRNAs were differentially expressed (DE). Expression of as many as 8 miRNAs was induced in resistant NIL (expression of remaining DE miRNAs induced in susceptible NIL); these DE miRNAs targeted several important genes, which include disease responsive genes. As many as 49 lncRNAs were found to be the targets for miRNAs; among these, one lncRNA functioned as a precursor of two mature miRNAs, and three lncRNAs acted as target mimics (TMs, which mimic and therefore compete with the mRNA targets for miRNA) thus regulating the expression of target genes. The results were also validated using qRT-PCR analyses. Taken together, the leaf rust responsive miRNAs, their targets along with putative TMs, and the lncRNAs, identified in the present study, should improve our understanding about the role of non-coding RNAs during response to leaf rust in wheat.

中文翻译：

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Lr28 介导的小麦 (Triticum aestivum L.) 叶锈病抗性过程中 miRNA 和 lncRNA 的研究。

摘要 小麦（Triticum aestivum L.）是一种主要作物，种植广泛，全球种植面积约 2.15 亿公顷。由于真菌病原体 Puccinia triticina Eriks 引起的叶锈病，作物遭受重大损失。和 E. Henn.. 当小麦植物受到这种真菌的攻击时，数百个参与信号转导途径的下游基因的表达会受到调控。这种调节部分依赖于非编码 RNA (ncRNA)，包括微 RNA (miRNA) 和长链非编码 RNA (lncRNA)。在本研究中，使用 RNA-seq 数据对一对近等基因系 (NIL) 鉴定了与小麦-叶锈病病理系统相关的 miRNA 和 lncRNA，这对小麦品种 HD2329 背景中的基因 Lr28 有所不同。该研究是我们早期转录组研究的延续，涉及相同的病理系统。通过对RNA-seq数据进行计算机分析，共鉴定出50个miRNA和1178个lncRNA；其中，16 个 miRNA 和 22 个 lncRNA 差异表达（DE）。在抗性 NIL 中诱导了多达 8 种 miRNA 的表达（在易感 NIL 中诱导的剩余 DE miRNA 的表达）；这些 DE miRNA 靶向几个重要基因，其中包括疾病响应基因。发现多达 49 个 lncRNA 是 miRNA 的靶标；其中，1个lncRNA作为2个成熟miRNA的前体，3个lncRNA作为靶标模拟物（TMs，模拟并因此与miRNA的mRNA靶标竞争）从而调节靶基因的表达。还使用 qRT-PCR 分析验证了结果。综上所述，叶锈病反应性 miRNA、它们的靶标以及推定的 TM 和 lncRNA，