Small RNA sequencing unveils predominant expression patterns and miRNA-target modules active during seed development in sorghum

Sorghum is a prominent cereal crop of global importance. Advances in seed research are essential for the enhancement of seed yield and nutritional value in sorghum. Here, we report small RNA profiling from five stages of sorghum seed development depicting miRNA dynamics during pollination, fertilization, early seed development, grain filling, and maturation. We identified 226 miRNAs, 72 of which were known while 154 are novel. Based on the predominant expression patterns, all miRNAs could be classified into five distinct groups. Target prediction unveiled 6640 miRNA-target modules of which 1507 were predicted to regulate grain size. Based on the experimentally verified functions of the orthologs of miRNAs and their targets, 83 modules comprising 16 miRNA families and 24 target genes were shortlisted as high-priority candidates for grain size control. Among these, 13 modules co-localized with previously known grain size quantitative trait loci (QTLs) in sorghum. Furthermore, a total of 12, 5, 3, and 3 candidate modules were implicated in regulating starch content, seed dormancy, seed vigor, and seed shattering, respectively. By integrating the expression profiles of miRNAs and their targets with the comparative genomic data, we could gain global insights into the specific roles of miRNAs in regulating seed development and associated agronomic traits.