Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize.
Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize.
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DOI：
10.1186/s12870-021-02847-4
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发表时间：
2021-02-12
影响因子：
5.3
通讯作者：
Gao S
中科院分区：
文献类型：
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作者：
Ma P;Zhang X;Luo B;Chen Z;He X;Zhang H;Li B;Liu D;Wu L;Gao S;Gao D;Zhang S;Gao S
长链非编码rna （lncRNAs）在重要的生物学过程中发挥着重要作用。然而，我们对lncRNAs作为竞争内源性rna （ceRNAs）及其对氮胁迫反应的理解仍然有限。本研究利用lncRNA-Seq和小RNA-Seq技术，对玉米自交系P178幼苗期叶片和根系在高氮（HN）和低氮（LN）条件下的lncrna和mirna进行了分析。共鉴定出894个差异表达的lncrna和38个不同的mirna。共表达分析发现，2个lncrna和4个lncrna -target分别可以与ZmmiR159和ZmmiR164竞争性结合。为了剖析lncrna可能使其适应有限氮供应的遗传调控，一个包含高密度单核苷酸多态性（SNP）阵列（56,110个SNP）的关联图谱与从水培中获得的可变LN耐受性相关表型相结合，用于全基因组关联研究（GWAS）。通过GWAS和RNA-Seq的结合，在显著标记范围内筛选出170个不同表达的lncrna。此外，还鉴定出了40个与谷氨酰胺生物合成和根系氮素获取有关的一致响应基因。在烟叶中的瞬时表达实验表明，LNC_002923可以在zmmir159引导下切割Zm00001d015521。这些lncrna含有与性状相关的显著snp，可以认为与根系发育和养分利用有关。综上所述，我们的研究结果可以为lncrna对LN胁迫的潜在调控作用提供新的见解，并为进一步筛选候选基因以及提高玉米对LN胁迫的抗性提供有价值的信息。在线版本包含补充材料，可在10.1186/s12870-021-02847-4获得。
Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress. The online version contains supplementary material available at 10.1186/s12870-021-02847-4.
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