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BMC Genomics. 2019 May 21;20(1):392. doi: 10.1186/s12864-019-5770-6.

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

Chen H1,2,3, Yang Q1,2,3, Chen K1,2,3, Zhao S1,2,3, Zhang C1,2,3, Pan R4, Cai T1,2,3, Deng Y1,2,3, Wang X5, Chen Y1,2,3, Chu W1,2,3, Xie W1,2,3, Zhuang W6,7,8.

Author information

1
State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
2
Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
3
College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
4
Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan.
5
Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
6
State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. weijianz@fafu.edu.cn.
7
Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. weijianz@fafu.edu.cn.
8
College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. weijianz@fafu.edu.cn.

Abstract

BACKGROUND:

Peanut 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.

RESULTS:

In 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.

CONCLUSIONS:

Both 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.

KEYWORDS:

Calcium; Embryo abortion; Hormone; Peanut; miRNA

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