Identification of Key Gene Networks and Deciphering Transcriptional Regulators Associated With Peanut Embryo Abortion Mediated by Calcium Deficiency

Abstract

Peanut embryo development is easily affected by a variety of nutrient elements in the soil, especially the calcium level. Peanut produces abortive embryos in calcium-deficient soil, but underlying mechanism remains unclear. Thus, identifying key transcriptional regulators and their associated regulatory networks promises to contribute to a better understanding of this process. In this study, cellular biology and gene expression analyses were performed to investigate peanut embryo development with the aim to discern the global architecture of gene regulatory networks underlying peanut embryo abortion under calcium deficiency conditions. The endomembrane systems tended to disintegrate, impairing cell growth and starch, protein and lipid body accumulation, resulting in aborted seeds. RNA-seq analysis showed that the gene expression profile in peanut embryos was significantly changed under calcium deficiency. Further analysis indicated that multiple signal pathways were involved in the peanut embryo abortion. Differential expressed genes (DEGs) related to cytoplasmic free Ca2+ were significantly altered. DEGs in plant hormone signaling pathways tended to be associated with increased IAA and ethylene but with decreased ABA, gibberellin, cytokinin, and brassinosteroid levels. Certain vital genes, including apoptosis-inducing factor, WRKYs and ethylene-responsive transcription factors, were up-regulated, while key regulators of embryo development, such as TCP4, WRI1, FUS3, ABI3, and GLK1 were down-regulated. Weighted gene co-expression network analysis (WGCNA) identified 16 significant modules associated with the plant hormone signaling, MAPK signaling, ubiquitin mediated proteolysis, reserve substance biosynthesis and metabolism pathways to decipher regulatory network. The most significant module was darkolivegreen2 and FUS3 (AH06G23930) had the highest connectivity among this module. Importantly, key transcription factors involved in embryogenesis or ovule development including TCP4, GLK1, ABI3, bHLH115, MYC2, etc., were also present in this module and down regulated under calcium deficiency. This study presents the first global view of the gene regulatory network involved in peanut embryo abortion under calcium deficiency conditions and lays foundation for improving peanut tolerances to calcium deficiency by a targeted manipulation of molecular breeding.

Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters

“…These studies could be verified by chromatin immunoprecipitation-sequencing (ChIP-seq) of DNA fragments that are associated with particular proteins [ 93 ]. Finally, regulatory networks of TFs and other proteins playing a pivotal role in the response to certain external factors could be built using transcriptomic RNA sequencing, and weighted gene co-expression network analysis (WGCNA) [ 94 , 95 ].…”

The Expression Profiles of the Salvia miltiorrhiza 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase 4 Gene and Its Influence on the Biosynthesis of Tanshinones

“…The role of specific TFBSs in the response of HMGR4 to abiotic or biotic factors could be verified by its mutagenesis [ 69 ]. TF networks that play a key role in the regulation of HMGR4 gene expression could be explored through transcriptomic RNA sequencing and weighted gene co-expression network analysis (WGCNA) [ 70 , 71 ].…”

Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars

“…Zhang et al also found that calcium application could improve disease resistance to soil-borne pathogens by enriching them with speci c dominant bacteria [9]. Chen et al identi ed that multiple signal pathways involved in embryo abortion under calcium de ciency, which induced increased IAA and ethylene but decreased ABA, gibberellin, cytokinin and brassinosteroid levels [10].…”

“…The "WGCNA" package implemented in R was developed to perform analyses in explaining molecular mechanisms such as tomato growth and development [13], banana maturity [14], sugar accumulation in sugarcane [15] as well as peanut embryo abortion under calcium de ciency [10]. The WGCNA study in peanut embryo identi ed modules associated with plant hormone signaling, MAPK signaling, ubiquitin mediated proteolysis, reserve substance biosynthesis and metabolism pathways to decipher regulatory network involved in embryo abortion under calcium de ciency [10].…”

“…Despite the global view of peanut transcriptome under calcium de ciency, previous studies only reported differentially expressed genes (DEGs) between calcium de cient and su cient conditions in the same cultivar [4,6,[8][9][10], and few of them made comparisons between different cultivars with different seed size, which showed tolerance inconsistency under calcium de ciency. The pod fullness was reported to be in uenced by seed calcium concentration, which is affected by seed size, absorption ability of cultivars and soil calcium fertility during seed development stage [16].…”