Background: Common bean (Phaseolus vulgaris) is an essential crop with high economic value. The growth of this plant is sensitive to environmental stress. Heat shock factor (Hsf) is a family of antiretroviral transcription factors that regulate plant defense system against biotic and abiotic stress. To date, few studies have identified and bio-analyzed Hsfs in common bean. Results: In this study, 30 Hsf transcription factors (PvHsf1–30) were identified from the PFAM database. The PvHsf1–30 belonged to 14 subfamilies with similar motifs, gene structure and cis-acting elements. The Hsf members in Arabidopsis, rice (Oryza sativa), maize (Zea mays) and common bean were classified into 14 subfamilies. Collinearity analysis showed that PvHsfs played a role in the regulation of responses to abiotic stress. The expression of PvHsfs varied across different tissues. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PvHsfs were differentially expressed under cold, heat, salt and heavy metal stress, indicating that PvHsfs might play different functions depending on the type of abiotic stress. Conclusions: In this study, we identified 30 Hsf transcription factors and determined their location, motifs, gene structure, cis-elements, collinearity and expression patterns. It was found that PvHsfs regulates responses to abiotic stress in common bean. Thus, this study provides a basis for further analysis of the function of PvHsfs in the regulation of abiotic stress in common bean.

Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and clarify the relationship between DNA methylation status and continuous cropping stress adaptability in soybean. We generated a genome-wide map of cytosine methylation induced by this kind of comprehensive stress in a tolerant soybean variety (Kang Xian 2, KX2) and a sensitive variety (He Feng, HF55) using whole-genome bisulfite sequencing (WGBS) technology. The expression of DNA demethylase genes was detected using real-time quantitative PCR (qRT-PCR). The functions of differentially methylated genes (DMGs) involved in stress response in biochemical metabolism and genetic information transmission were further assessed based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results showed that genomic DNA demethylation was closely related to continuous cropping comprehensive stress adaptability in soybean, which was further verified by the increasing expression of DNA demethylases ROS1 and DML. The demethylation of mCpG and mCpHpG (mCpApG preferred) contexts was more critical, which mainly occurred in gene-regulatory regions at the whole-chromosome scale. Moreover, this kind of stress adaptability may be related to various stress responders generated through strengthened glucose catabolism and amino acid and fatty acid anabolism, as well as fidelity transmission of genetic information. Genomic DNA demethylation was closely associated with continuous cropping comprehensive stress adaptability, highlighting the promising potential of screening continuous cropping-tolerant cultivars by DNA methylation index and further exploring the application of DNA demethylases in soybean breeding.

Cytokinin oxidase/dehydrogenase (CKX) irreversibly degrades cytokinin, regulates growth and development, and helps plants to respond to environmental stress. Although the CKX gene has been well characterized in various plants, its role in soybean remains elusive. Therefore, in this study, the evolutionary relationship, chromosomal location, gene structure, motifs, cis-regulatory elements, collinearity, and gene expression patterns of GmCKXs were analyzed using RNA-seq, quantitative real-time PCR (qRT-PCR), and bioinformatics. We identified 18 GmCKX genes from the soybean genome and grouped them into five clades, each comprising members with similar gene structures and motifs. Cis-acting elements involved in hormones, resistance, and physiological metabolism were detected in the promoter regions of GmCKXs. Synteny analysis indicated that segmental duplication events contributed to the expansion of the soybean CKX family. The expression profiling of the GmCKXs genes using qRT-PCR showed tissue-specific expression patterns. The RNA-seq analysis also indicated that GmCKXs play an important role in response to salt and drought stresses at the seedling stage. The responses of the genes to salt, drought, synthetic cytokinin 6-benzyl aminopurine (6-BA), and the auxin indole-3-acetic acid (IAA) at the germination stage were further evaluated by qRT-PCR. Specifically, the GmCKX14 gene was downregulated in the roots and the radicles at the germination stage. The hormones 6-BA and IAA repressed the expression levels of GmCKX1, GmCKX6, and GmCKX9 genes but upregulated the expression levels of GmCKX10 and GmCKX18 genes. The three abiotic stresses also decreased the zeatin content in soybean radicle but enhanced the activity of the CKX enzymes. Conversely, the 6-BA and IAA treatments enhanced the CKX enzymes’ activity but reduced the zeatin content in the radicles. This study, therefore, provides a reference for the functional analysis of GmCKXs in soybean in response to abiotic stresses.

Salt stress is a common abiotic stress that negatively affects crop growth and yield. However, there have been significant differences found on the effect degree and management mechanism in plants under neutral salt stress and alkaline stress. In this study, two soybean cultivars, Heihe 49 (HH49, saline-alkali stress tolerant) and Henong 95 (HN95, saline-alkali stress sensitive), were hydroponically cultured and treated with salt solutions of 25, 50, and 75 mM Na⁺ in the form of NaCl, Na₂SO₄, NaHCO₃, and Na₂CO₃. Plants treated with alkaline stress (NaHCO₃ and Na₂CO₃) showed a greater decrease in root growth and root activity of both soybean cultivar seedlings than that under neutral salt stresses (NaCl and Na₂SO₄) with 25–75 mM Na⁺ concentration. Alkaline stress (25–50 mM Na⁺ content) activated a higher ability of antioxidant defense (by enhancing the activists of superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX)) and increased the content of soluble sugars to a higher level than that under neutral salt stresses. However, 75 mM Na⁺ content salt treatments reduced antioxidant enzyme activities and osmotic regulating substance content. Furthermore, alkaline salt and neutral salt stress was able to induce DNA damage and cell cycle arrest in HH49 and HN95 seedling roots. Treatment with Na₂CO₃ induced the least random amplification polymorphic DNA (RAPD) polymorphism in soybean seedling roots among all salt treatments, which could have been related to the early cell cycle arrest.

Common bean (Phaseolus vulgaris) seeds are important legume crops and an important source of dietary proteins and carbohydrates. Therefore, it is important to develop strategies to improve salt tolerance in common beans. In this study, transcriptome and metabolome analyses were conducted on local common bean variety under salt stress at the sprout stage for a period of 0, 12, and 24 h. Results showed that phenylpropanoid pathways (including phenylpropanoid biosynthesis and phenylalanine metabolism) and flavonoid pathways (including flavonoid biosynthesis and flavone and flavonol biosynthesis) played an important role in controlling responses to salt stress as evidenced by analysis of differentially expression genes, common expression patterns, WCGNA, and differentially altered metabolites (DAMs) analyses. In addition, exploration of the activities of 4‐coumarate‐CoA ligase (4CL), caffeoyl‐CoA O‐methyltransferase (CCoAOMT), peroxidase (POD), chalcone isomerase (CHI), dihydroflavonol‐4‐reductase (DFR), and flavonol synthase (FLS) further showed that phenylpropanoid and flavonoid pathways participate in plant responses to salt stress. Moreover, the phenylpropanoid pathways and flavonoid pathways were found to be potential pathways regulating plant response to salt stress based on transcriptome and metabolome analysis. The activities of 4CL, CCoAOMT, POD, CHI, DFR, and FLS revealed that these pathways are crucial to the regulation of plant responses to salt stress. These findings provided theoretical basis for further improvement of salt tolerance in common bean.