Additional file 1 of Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

Additional file 1: Fig. S1. The volcano plot of differentially expressed mRNAs (a, b), TUCPs (c, d) and miRNAs (e, f) between HN and LN conditions in leaf and root. Fig. S2. The TPM (Transcripts per million) (a) and length distribution of 18- to 30-nt small RNAs (b). The concentrated length distribution with the peak at 24-nt in the 12 libraries respectively. Fig. S3. Expression profiles of mRNA and miRNA during seedling under HN and LN conditions. Cluster heat map of all mRNAs (a) and miRNAs (c) expression in leaf and root. VEEN analysis of differentially expressed mRNAs (b) and miRNAs (d). Fig. S4. Characteristics of lncRNAs identified in maize seedling. Fig. S5. Functional analysis of the LN-responsive lncRNAs. The enriched Kyoto Encyclopedia of Genes (KEGG) pathways in leaf (a, c) and root (b, d). Fig. S6. Fourty-five and 232 consistent candidate genes were detected in root and leaf under LN condition (a) and LNTI (b) by combing with RNA-Seq and GWAS.

附加文件1：图S1：展示了叶片与根系中高氮（HN）、低氮（LN）处理下差异表达信使RNA（messenger RNA，mRNA，a、b组）、编码潜能不确定转录本（transcripts of uncertain coding potential，TUCPs，c、d组）以及微小RNA（microRNAs，miRNAs，e、f组）的火山图。
图S2：（a）为每百万转录本（Transcripts per million，TPM）统计结果，（b）为18~30 nt小RNA（small RNAs）的长度分布；12个文库的小RNA长度分布均呈现以24 nt为峰值的集中分布特征。
图S3：展示了高氮与低氮处理下玉米幼苗中mRNA和miRNA的表达谱；（a）为叶片和根系中所有mRNA的表达聚类热图，（c）为所有miRNA的表达聚类热图；（b）与（d）分别为差异表达mRNA和miRNA的韦恩（Venn）分析结果。
图S4：玉米幼苗中鉴定得到的长链非编码RNA（long non-coding RNAs，lncRNAs）的特征分析。
图S5：低氮响应lncRNAs的功能富集分析，分别展示了叶片（a、c组）与根系（b、d组）中富集得到的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路。
图S6：结合RNA测序（RNA-Seq）与全基因组关联分析（Genome-Wide Association Study，GWAS），在低氮（LN）处理下的根系（a组）与LNTI处理下的叶片（b组）中分别鉴定得到45个与232个一致性候选基因。