Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

Hua Chen,Weijian Zhuang,Tiecheng Cai,Wenping Xie,Xingjun Wang,Ronglong Pan,Kun Chen,Yuting Chen,Chong Zhang,Shanshan Zhao,Ye Deng,Qiang Yang,Wenting Chu

doi:10.1186/s12864-019-5770-6

Abstract

BackgroundPeanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortion in peanut, which provides an opportunity to determine the mechanism underlying this important event. MicroRNA (miRNA)-guided target gene regulation is vital to a wide variety of biological processes. However, whether miRNAs participate in peanut embryo abortion under calcium deficiency has yet to be explored.ResultsIn this study, with the assistance of a recently established platform for genome sequences of wild peanut species, we analyzed small RNAs (sRNAs) in early peanut embryos. A total of 29 known and 132 potential novel miRNAs were discovered in 12 peanut-specific miRNA families. Among the identified miRNAs, 87 were differentially expressed during early embryo development under calcium deficiency and sufficiency conditions, and 117 target genes of the differentially expressed miRNAs were identified. Integrated analysis of miRNAs and transcriptome expression revealed 52 differentially expressed target genes of 20 miRNAs. The expression profiles for some differentially expressed targets by gene chip analysis were consistent with the transcriptome sequencing results. Together, our results demonstrate that seed/embryo development-related genes such as TCP3, AP2, EMB2750, and GRFs; cell division and proliferation-related genes such as HsfB4 and DIVARICATA; plant hormone signaling pathway-related genes such as CYP707A1 and CYP707A3, with which abscisic acid (ABA) is involved; and BR1, with which brassinosteroids (BRs) are involved, were actively modulated by miRNAs during early embryo development.ConclusionsBoth a number of miRNAs and corresponding target genes likely playing key roles in the regulation of peanut embryo abortion under calcium deficiency were identified. These findings provide for the first time new insights into miRNA-mediated regulatory pathways involved in peanut embryo abortion under calcium deficiency.

Highlights

Peanut embryo development is a complex process involving a series of gene regulatory pathways and is affected by various elements in the soil
Calcium deficiency significantly affects peanut pod development peanut pods at 15, 20 and 30 days after pegging (DAP) between calcium deficiency and sufficiency conditions did not differ in size (Fig. 1), the seed coat color started to become black, and the embryos tended rot under calcium deficiency, eventually producing empty pods
The biological characteristics examined at harvest indicated that no obvious differences in vegetative growth-related characteristics were observed between calcium deficiency and sufficiency conditions (Table 1)

Summary

Introduction

Peanut embryo development is a complex process involving a series of gene regulatory pathways and is affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortion in peanut, which provides an opportunity to determine the mechanism underlying this important event. Whether miRNAs participate in peanut embryo abortion under calcium deficiency has yet to be explored. A typical geocarpic plant, is a complex process involving the activity of a series of gene regulatory pathways at both the transcriptional and posttranscriptional levels and is affected by a variety of elements in the soil, especially calcium (Ca2+). Severe calcium deficiency in the soil induces early peanut embryo abortion. The molecular basis of peanut embryo development, especially embryo abortion, under calcium deficiency conditions is still unknown

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Discussion

Conclusion