Transcriptomic analysis of maize kernel row number-associated miRNAs between a single segment substitution line and its receptor parent

摘要

To detect microRNAs (miRNAs) involved in determining kernel row number in maize, next generation deep sequencing was performed on an elite inbred line Zong3 (row number 14-16) of maize in China and a single segment substitution line (SSSL) SSL-10 (row number 8-10) derived from the same genetic background. In SSL-10, the single segment is inserted in chromosome 1 between molecular marker bnlg1953 and bnlg1811. Twenty-eight miRNAs belonging to 11 conserved miRNA families in maize showed expression differences >2-fold in the two lines, among which 14 members from four miRNA families were up-regulated and 14 members from 7 miRNA families were repressed in SSL-10. A genome wide degradome was sequenced to validate the miRNA target genes in solid experiment. In addition, novel miRNAs associated with ear development were predicted using a series of strict criteria, and 29 miRNAs representing eight families were predicted as novel miRNAs. Among the novel miRNAs, only one showed an expression difference >2-fold. The conserved and novel miRNAs with >2-fold expression differences were treated as candidate miRNAs involved in maize kernel row number determination. MiRNA-dependent gene expression regulation and physiological and morphological effects on ear development may explain why the SSSL changed kernel row number compared with its recurrent parent. Based on the interaction of miRNAs and their target genes, a possible miRNA-dependent pathway leading to the given DNA fragment inducing a change in kernel row number was proposed.