Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Seed Expansion in Peanut (Arachis hypogaea L.).

Xingli Ma,Xingguo Zhang,Jialin He,Zeyu Xin,Kunkun Zhao,Dongmei Yin,Longlong Ning,Fapeng Li,Ke Li

doi:10.3389/fpls.2018.00349

Abstract

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. We 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, we identified 1,082 miRNAs in developing peanut seeds including 434 novel miRNAs. We 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. We 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 our 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.

Highlights

As one of the most important oil crops in the world, peanut (Arachis hypogaea L.) is grown on six continents but mainly in Asia, Africa, and America (Zhang et al, 2012; Zhao et al, 2015)
The expression analysis of the 12 representative target genes by qPCR showed negative correlations with the levels of their corresponding miRNAs (Figure 5). These results show that several miRNAs may be directly or indirectly involved in peanut seed expansion by regulating expression of their target gene(s)
The results showed that these two miRNAs may be involved in the seed expansion process in peanut by negatively regulating NAC100 and scarecrowlike protein 22 (SCL22)

Summary

Introduction

As one of the most important oil crops in the world, peanut (Arachis hypogaea L.) is grown on six continents but mainly in Asia, Africa, and America (Zhang et al, 2012; Zhao et al, 2015). Yield of peanut is determined primarily by two vital factors; (1) seed expansion, and (2) subsequent seed filling (Stanciel et al, 2000; Ramakrishna et al, 2006). Compared to other food crops, peanuts show a distinct pattern of seed development. A new organ called the peg differentiates from the ovary (Brennan, 1969). Little mitotic division occurs in the embryo or endosperm during active geotropic peg growth until the peg penetrates the soil. Roles of microRNAs in Seed Expansion in Peanut

Methods

Results

Discussion

Conclusion