Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches.

Mengya Shi,Xu Hou,Xue Yuan,Yu Wei,Xiao Hu,Jun Liu,Yueping Liu

doi:10.3390/ijms18122599

Abstract

Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA). Our analyses identified 24 evolutionarily conserved miRNA genes as well as 16 predicted genes. Experimental verification showed that the expression levels of miR398 and miR408b were significantly upregulated after NAA treatment, whereas those of miR156, miR160, miR166, miR167, miR390, miR393, miR482, miR535 and miR2118 were significantly downregulated. Degradome sequencing coupled with miRNA target prediction analyses detected 119 significant cleavage sites on several mRNA targets, including SQUAMOSA promoter binding protein–like (SPL), ARF, (NAM, ATAF1/2 and CUC2) NAC, Arabidopsis thaliana homeobox protein (ATHB), the homeodomain-leucine zipper transcription factor revoluta(REV), (teosinte-like1, cycloidea and proliferating cell factor1) TCP and auxin signaling F-box protein (AFB) family genes. Our systematic profiling of miRNAs and the degradome in peach fruit suggests the existence of a post-transcriptional regulation network of miRNAs that target auxin pathway genes in fruit development.

Highlights

Peach trees are one of the most widely planted Rosaceae trees owing to their economic and ecological importance
To explore the molecular regulation of auxin in peach fruit development, we treated the fruit of the peach cultivar Jing-Yan/Beijing24 (JY, Prunus persica, 2n = 16) at the hard core stage with 2 mM of the synthetic auxin naphthylacetic acid (NAA) and mock solution (NAA omitted) and collected samples three days after
We found that miR165/miR166 can target REV, ATHB8, ATHB14 and ATHB15 in the peach fruit with high prediction confidence (Figure 3). miR156 is known to target SQUAMOSA promoter binding protein–like (SPL) (Figure 3), but in our study, we found additional targets for miR156, including ATHB13, auxin-repressed protein (ARP), and inhibitor of growth protein 5 (ING5), suggesting that miR156 may have direct functions in modulating auxin response in the peach fruit. miR393 regulates expression of the auxin receptor gene TIR1 and the F-box genes AFB1, AFB2 and AFB3 [38,39]

Summary

Introduction

Peach trees are one of the most widely planted Rosaceae trees owing to their economic and ecological importance. Due to its relatively small genome (265 Mb), short breeding season and abundant cultivars with various phenotypes, peach is a model Rosaceae plant species for studies of plant development, evolution and comparative genomics [2]. Genomic studies uncovered that the expression of some peach miRNAs was preferentially induced in roots, leaves, flowers and/or fruit in response to stress conditions [7,8,9]. 180 mature miRNAs and 214 miRNA precursors have been collected in peach in the miRBase20.0 database [10]. Most of these miRNAs are evolutionarily conserved

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Discussion

Conclusion