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Updated: Jul 12, 2026
Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development
Published on: March 5, 2017
Small RNA sequencing unveils predominant expression patterns and miRNA-target modules associated with seed
Rubi Jain1, Garima Yadav2, Namrata Dhaka2
1School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
None:
Sorghum is a prominent cereal crop of global importance. Advancements in seed research are essential to enhance 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 a total of 226 miRNAs, of which 72 were known and 154 were novel. Based on the predominant expression patterns, these miRNAs were 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 promising candidates for grain size control. Notably, 13 modules co-localized with previously known grain size quantitative trait loci (QTLs) in sorghum. Additionally, we identified 12, 5, 3, and 3 candidate modules that were associated with starch content, seed dormancy, seed vigor, and seed shattering, respectively. By integrating miRNA expression profiles and their targets with comparative genomic data, we obtained significant insights into the putative roles of miRNAs in regulating seed development and associated agronomic traits.
Supplementary Information:
The online version contains supplementary material available at 10.1007/s12298-026-01765-9.
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