Small RNA expression pattern in multiply inbred lines and their hybrids of maize embryo

Abstract

Heterosis, also known as hybrid vigor or transgression, is the phenomenon wherein an F1 hybrid produced from crossing two cultivars of the same or different species shows superior phenotypes. Heterosis in maize has been found and applied in breeding for more than one hundred years. However, its underlying molecular mechanisms are still poorly understood. To investigate whether small RNAs (sRNAs) participate in the regulation of heterosis, we profiled the sRNA expression patterns in the germ seeds of five inbred lines and theirs three F1 hybrids using high-throughput sequencing technology. The sequencing result show maize sRNAs are enriched in 22-nt length. Nearly 90% of 22-nt small RNA dominated clusters (SRCs) are in repeat regions, which mainly originated from Gypsy and Copia in retrotransposon. About 25% differentially expressed SRCs exist between parents, and hybrid gain almost all differentially expressed 22-nt SRCs. Twenty-four-nt sRNA also enriched in maize, which showed great sequence diversity and overall low expression across the genome. More than half of 24-nt SRCs originate from repeat, and 80% of them come from DNA transposon. Nearly 30% of 24-nt SRCs located in genes or their flanking regions, especially in flanking regions of \"lipid metabolic process\" and \"macromolecule modification\" related genes. Several thousands 24-nt SRCs are paternal or maternal specific expressed, and hybrids gain only half of differentially expressed 24-nt SRCs. Hundreds of 24-nt SRCs show high parent or above high parent expression pattern in different hybrids, and them mainly from Tourist, haT, and CACTA in DNA transposon and enrich nearby \"tRNA aminoacylation for protein translation\" related genes. Also, some 21-nt SRCs show conserved expression pattern in low parent. They were enriched in anti-sense region of some genes, which functions are about oxidative phosphorylation and translation. miRNAs have a global downregulated tendency in hybrids. zma-miR408-5p, zma-miR1432-5p and zma-miR528-5p are significant downregulated in each hybrid, and this phenomenon may cause their target genes more stable and contribute to hybrid vigor. Taken together, our results illustrated that sRNAs may contribute to heterosis at the very early stage of seed germination through repressing of retrotransposon activity, regulation gene activity at gene and genic flanking regions, and promotion some gene expressions by downregulated miRNAs.