Cold temperatures can be detrimental to crop survival and productivity. Breeding progress can be improved by understanding the molecular basis of low temperature tolerance. We investigated the key routes and critical metabolites related to low temperature resistance in cold-tolerant and -sensitive common bean cultivars 120 and 093, respectively. Many potential genes and metabolites implicated in major metabolic pathways during the chilling stress response were identified through transcriptomics and metabolomics research. Under chilling stress, the expression of many genes involved in lipid, amino acid, and flavonoid metabolism, as well as metabolite accumulation increased in the two bean types. Malondialdehyde (MDA) content was lower in 120 than in 093. Regarding amino acid metabolism, 120 had a higher concentration of acidic amino acids than 093, whereas 093 had a higher concentration of basic amino acids. Methionine accumulation was clearly higher in 120 than in 093. In addition, 120 had a higher concentration of many types of flavonoids than 093. Flavonoids, methionine and malondialdehyde could be used as biomarkers of plant chilling injury. Transcriptome analysis of hormone metabolism revealed considerably greater, expression of abscisic acid (ABA), gibberellin (GA), and jasmonic acid (JA) in 093 than in 120 during chilling stress, indicating that hormone regulation modes in 093 and 120 were different. Thus, chilling stress tolerance is different between 093 and 120 possibly due to transcriptional and metabolic regulation.

Melatonin plays important roles in multiple stress responses; however, the downstream signaling pathway and molecular mechanism remain unclear. This study aimed to elucidate the transcriptional regulation of melatonin-induced salt stress tolerance in Phaseolus vulgaris L. and identify the key downstream transcription factors of melatonin through transcriptomic and metabolomic analyses. The melatonin-induced transcriptional network of hormones, transcription factors, and functional genes was established under both control and stress conditions. Among these, eight candidate transcription factors were identified via gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, one gene related to transmembrane transport of salts (Phvul.004G177300). These genes may play a role in maintaining the cell structure and excreting sodium ions outside the cell or transporting them to the vacuoles for storage. Melatonin regulates the Phvul.009G210332 gene and metabolites C05642 (N-acetyl-N-2-formyl-5-methoxycanurine), C05643 (6-hydroxymelatonin), C05660 (5-methoxyindoleacetic acid) involved in tryptophan metabolism. The metabolites C05642 and C05643 were identified as decomposition products of tryptophan, indicating that exogenous melatonin entered the P. vulgaris tissue and was metabolized. Melatonin promotes the synthesis and metabolism of tryptophan, which is crucial to plant metabolism, growth, maintenance, and repair.

Background: Lipoxygenases (LOXs) catalyze polyunsaturated fatty acid oxygenation and regulate plant stress responses and oxylipin biosynthesis. This study provides comprehensive genome-wide characterization of the soybean LOX gene family, revealing unprecedented expansion and functional diversification. Methods: We identified unique GmLOX gene loci through systematic database searches and domain analysis, selecting representative isoforms to avoid transcript redundancy. Phylogenetic analysis compared 43 GmLOX with 6 AtLOX proteins. Protein structures, conserved domains, promoter cis-regulatory elements (2,000 bp upstream), and synteny relationships were characterized. Expression profiling under four abiotic stresses (alkaline, drought, heat, salt) across six time points (0–24 h) was performed using qRT-PCR. Results: Genes distribute unevenly across 10 chromosomes, with highest densities on Gm10 (11 genes), Gm08 (9 genes), and Gm07 (8 genes). Phylogenetic analysis revealed six evolutionary clades with soybean-specific expansion. Structural analysis showed 92% encode full-length proteins (average 887 amino acids) with conserved PLAT/LH2 (97%) and catalytic domains. Promoter analysis identified 23 regulatory element categories, including hormone-responsive (auxin 97%, gibberellin 89%, ABA 94%), stress-responsive (95%), and light-responsive elements (100%). Synteny analysis demonstrated ancient whole-genome duplications and recent tandem duplications drove expansion. Expression profiling revealed five functional categories: alkaline-specific, drought-dominant, heat-specific, salt-responsive, and multi-stress responsive genes. GmLOX16 showed exceptional multi-stress responsiveness (40-fold salt, 38-fold alkaline), GmLOX13 displayed strongest heat response (20-fold), and GmLOX17 exhibited peak drought sensitivity (7-fold). Conclusion: Soybean possesses the largest crop LOX family with remarkable functional diversification maintained under strong selective pressure (92% functional retention). Key stress-responsive genes, particularly GmLOX16 and GmLOX13 , represent valuable targets for molecular breeding to enhance climate resilience, providing critical genetic resources for sustainable crop improvement.

Pod color is a major economic trait of snap beans (Phaseolus vulgaris L.), among which the pod with a purple stripe is more attractive to people. A stable purple mutant with purple stripes on the pods was obtained by artificial mutagenesis with the high generation snap bean inbred line ‘A18-1’. In order to reveal the genetic factors and pathways responsible for the purple appearance in snap bean, we performed transcriptome and metabolome analyses using the green stem and yellow pod cultivar ‘A18-1’ and its purple mutant ‘pv-pur’ via ⁶⁰Co-γ radiation. Transcriptome analysis showed that three genes in the anthocyanin biosynthetic pathway were differentially expressed, among which the expression level of F3′5′H (Phvul.006G018800) was increased in the mutant ‘pv-pur’, while expression of F3′H (Phvul.004G021200) and ANS (Phvul.002G152700) was downregulated. Anthocyanin-targeted metabonomics analysis showed significant differences in the contents of 10 metabolites between the wild type and mutant plants. Combined analysis of transcriptome and metabolomics showed that one differential metabolite, delphinidin, was related to the differential expression of Phvul.006G024700, Phvul.002G152700, and Phvul.006G018800. Based on the levels of six anthocyanins in wild type and mutant plants, we speculative that the purple appearance of the mutant ‘pv-pur’ is caused by the increased expression of F3′5′H (Phvul.006G018800), the key enzyme in the transformation from dihydroflavanol (DHK) to dihydromyricetone (DHM) in the anthocyanin biosynthetic pathway. The results lay a foundation for further studies on the molecular mechanism of anthocyanin synthesis in snap bean, and provide a framework for breeding different colors of snap bean.