Transcriptome Dynamics of Common Bean Roots Exposed to Various Heavy Metals Reveal Valuable Target Genes and Promoters for Genetic Engineering

Abstract

Understanding the gene regulatory basis of plant response to heavy metals (HMs) is fundamental for the management of food safety and security. However, a comprehensive and comparative view of the plant responses to different HMs is still lacking. Here, we compared root transcriptomes in common bean under 9 HM treatments at 50 μM for three time points each. Cd, Cr, Co, Ni, and Pb caused most severe morphological and/or biochemical retardations. A total of 448 genes were found to be responsive to all nine HMs, which were mostly involved in photosynthesis, oxidization–reduction, and ion binding. Cd and Cu triggered the greatest number of unique differentially expressed genes (DEG)s, which were predominantly related to cellular transport/localization in the former and RNA binding in the latter. Short-term and prolonged HM treatments shaped very different DEG patterns. Weighted gene co-expression network analysis identified six co-expression modules showing exceptionally high transcripts abundance in specific HM × time scenarios. We experimentally verified the promoter activity of the gene GIP1 and the novel function of XTH23 under Cu/Cd stress. Collectively, the transcriptomic atlas provides valuable resources for better understanding the common and unique mechanisms of plant response to different HMs and offers a mass of candidate target genes/promoters for genetic engineering.

Selective penetration of fullerenol through pea seed coats mitigates osmosis‐repressed germination via chromatin remodeling and transcriptional reprograming

“…Pairwise comparisons of gene expressions were made between samples, and genes having an FPKM of 1 or more in all replicates of at least one sample in a comparison and a coefficient of variant (CV) less than 0.2 among the replicates were considered 25 . Differentially expressed genes (DEGs) were identified using R DESeq2 with the criteria of |log 2 Fold Change| ≥ 1 and false discovery rate ( q ‐value) less than 0.05.…”

“…Pairwise comparisons of gene expressions were made between samples, and genes having an FPKM of 1 or more in all replicates of at least one sample in a comparison and a coefficient of variant (CV) less than 0.2 among the replicates were considered. 25 Differentially expressed genes (DEGs) were identified using R DESeq2 with the criteria of |log 2 Fold Change| ≥ 1 and false discovery rate (q-value) less than 0.05. The Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes ontology (KO) pathway analysis were carried out using Goatools (https://github.com/tanghaibao/Goatools).…”

A molecular toolkit to boost functional genomic studies in transformation-recalcitrant vegetable legumes

“…Pictures are reproduced from Fang et al . [ 4 ]. f , n , t Representative images of stomata (scale bars = 10 μm) from the control and ABA3 -silenced common bean, cowpea, and pea plants, respectively, and the relative expression of ABA3 and ABA pathway downstream genes as well as stomatal apertures.…”

“…This method is also highly valuable for validating gene functions involved in abiotic stress, as recently reported by Fang et al . [ 4 ] for a heavy-metal responsive gene, PvXTH23 , encoding xyloglucan endo-transglycosylase ( Fig. 1e ).…”