Small RNA and degradome sequencing reveals the roles of microRNAs in seed expansion in peanut

Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. Researchers at Henan Agricultural University examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut eighth-generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, they identified 1,082 miRNAs in developing peanut seeds including 434 novel miRNAs. They identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. The researchers validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of this study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.

Clustering of partially differentially expressed miRNAs in the two peanut RILs

(A). Biological Process GO categories of the predicted target genes of the differentially expressed miRNAs (B). KEGG pathways related to plant hormone signal transduction targeted by differentially expressed miRNAs (C).

Ma X, Zhang X, Zhao K, Li F, Li K, Ning L, He J, Xin Z, Yin D. (2018) Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Seed Expansion in Peanut (Arachis hypogaea L.). Front Plant Sci 9:349. [article]

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