Identification of novel miRNA related to low nitrogen stress in sorghum and prediction of their target genes
To explore the regulatory role of microRNAs(miRNAs)in the sorghum response to low-nitrogen stress,sorghum seedlings were treated with short-term(8 h)and long-term(15 d)low-nitrogen stress,and their small RNAs were sequenced on an Illumina HiSeqTM2000.The Mireap software was used to predict novel miRNAs and analyze their expression differences.Cluster analysis of expression patterns and quantitative real-time RT-PCR were performed for the differentially expressed miRNAs.The TargetFinder software was used to predict target genes and Gene Ontology(GO)annotation classification.A total of 123 novel miRNAs were identified using high-throughput sequencing,of which 40 novel miRNAs had significant or extremely significant expression differences.Differentially expressed miRNAs were from the roots after short-term low-nitrogen stress,six of which were upregulated,and 10 miRNAs were downregulated.In roots under long-term low-nitrogen stress,three differentially expressed miRNAs were upregulated,and three miRNAs were downregulated.In sorghum leaves,differentially expressed miRNAs were identified after short-term low-nitrogen stress,four of which were upregulated,and 22 miRNAs were downregulated.Two miRNAs were upregulated and nine were downregulated,respectively,under long-term low-nitrogen stress.The expression patterns of these novel differentially expressed miRNAs in the roots and leaves were different,and they were grouped into three types:Ⅰ,Ⅱ,and Ⅲ.The differentially expressed novel miRNAs were unevenly distributed on different chromosomes,with the highest distribution on chromosome 2,followed by chromosomes 4,1,and 7.The target genes of the differentially expressed novel miRNAs were predicted and eight target genes were identified.These target genes are involved in many biological processes such as material metabolism,stimulus-response,biological regulation,reproduction,and development.This study identified 40 novel miRNAs that were differentially expressed under low-nitrogen stress in sorghum and predicted eight target genes.Our results identified relevant miRNAs and candidate genes for studying the regulatory mechanisms of low-nitrogen stress in sorghum.
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