Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages

Abstract

Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food. miRNAs are tiny riboregulator of gene expression by either decreasing and/or increasing the expression of their corresponding target genes. Despite several works on identification and functional characterization of plant miRNAs, the role of miRNAs in the regulation of isoflavones metabolism is still a virgin field. In the present study, we identified a total of 31 new miRNAs along with their 245 putative target genes from soybean seed-specific ESTs using computational approach. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates metabolism and genetic information processing. Out of that, a total of 5 miRNAs (Gma-miRNA12, Gma-miRNA24, Gma-miRNA26, Gma-miRNA28, and Gma-miRNA29) were predicted and validated for their probable role during isoflavone biosynthesis. We also validated their five target genes using RA-PCR, which is as good as 5'RLM-RACE. Temporal regulation [35 days after flowering, 45, 55, and 65 DAF] of miRNAs and their targets showed differential expression schema. Differential expression of Gma-miR26 and Gma-miRNA28 along with their corresponding target genes (Glyma.10G197900 and Glyma.09G127200) showed a direct relationship with the total isoflavone content. Therefore, understanding the miRNA-based genetic regulation of isoflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isoflavone yield.

Genome‐wide discovery of tissue‐specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

“…38.9-and 101.4-fold, 5.9 and 84.3-fold, respectively (Figure 12b,c). In agreement with the previous studies, our results also showed the lower accumulation of RA-Mid region than the RA 3 0 region signifying that these target genes are potentially cleaved by corresponding regulatory miRNAs (Oh et al, 2008;Gupta et al, 2017). Our combinatorial approach of fusing two different miRNA identification softwares with two types of deep-sequencing data from same platform in clusterbean provides a systematic overview on novel and known miRNAs expression profiling involved in galactomannan biosynthesis.…”

“…38.9‐ and 101.4‐fold, 5.9 and 84.3‐fold, respectively (Figure b,c). In agreement with the previous studies, our results also showed the lower accumulation of RA‐Mid region than the RA 3′ region signifying that these target genes are potentially cleaved by corresponding regulatory miRNAs (Oh et al ., ; Gupta et al ., ).…”

“…Typically, miRNAs are known to negatively regulate the expression of genes at the post-transcriptional level by binding to their mRNA targets via the RISC complex, leading to major variations in the activities of metabolic pathways (Gupta et al, 2017;Wu et al, 2016). They are known to regulate cell signalling (Yang et al, 2007), oxidative stress (Sunkar et al, 2006), abiotic and biotic stress responses (Khraiwesh et al, 2012), and the development of different tissues, including leaf, stem, root (Kidner and Martienssen, 2005), anther (Millar and Gubler, 2005) and flower (Yang et al, 2007).…”

“…Deep-sequencing technologies quickly reveal the hidden information of a genome. Prediction and characterization of miRNAs using in silico approaches are emerging as faster, and trustworthy methods as compared to laboratory-based cloning (Gupta et al, 2017;Nigam et al, 2015). So far, genomewide discovery and characterization of miRNA have been reported for leguminous plants such as G. max, M. truncatula and P. vulgaris (Formey et al, 2015).…”

Cytosine Methylation of Isoflavone Synthase Gene in the Genic Region Positively Regulates Its Expression and Isoflavone Biosynthesis in Soybean Seeds

“…The methodologies for quantification and data analysis of different isoforms of isoflavone were adopted from our previous publication (Gupta et al, 2017).…”