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.

Snap bean (Phaseolus vulgaris L.) is low in fat and high in nutrients; however, it also contains toxigenic factors such as phytohemagglutinin (PHA), which is poisonous to humans. Here, we aimed to determine the distribution of PHA in natural populations of snap bean by analyzing a candidate gene (PHA-E) related to PHA content. Functional genome-wide single nucleotide polymorphisms (SNPs) were then scanned to identify SNPs related to PHA content. A total of 150 snap bean varieties were examined. PHA content and PHA-E expression levels were determined 10, 14, 18, 22, 26 and 30 days after anthesis. Then, association analyses were carried out to identify causal SNPs in PHA-E via genotyping and association tests. PHA-E expression was positively-correlated with PHA content. Among 59 detected SNPs, the ratio of synonymous to nonsynonymous changes was 1:8. P190 was identified as a novel SNP associated with PHA content. The allele carrying the GG genotype at P190 was detected in 130 varieties, of which 86 had an above-average PHA content, while the allele carrying the AA genotype at P190 was detected in 20 varieties, of which 17 (85%) had a low PHA content. Analyses of the PHA content and gene expression in fresh pods of 150 snap bean cultivars revealed population-level distribution and genetic variation, providing a unique measure for screening of low-level or nontoxic cultivars and aiding future breeding of new cultivars. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1985613.

Snap bean leaves are the primary site of photosynthesis. Mutant leaf color provides valuable tools for investigating leaf color changes, their role in photosynthesis, and pigment metabolic pathways. In this study, we found that the seedling leaves of ‘ytg-2’ exhibited a yellow phenotype characterized by reduced chlorophyll content compared with ‘A18’. Blockage of the uroporphyrinogen III (Urogen III) to the fecal porphyrinogen III (Coprogen III) synthesis pathway primarily affected the synthesis of chlorophyll intermediate metabolites. As the plants matured, their leaves transformed from yellow to light green, accompanied by an increase in the total chlorophyll content. Transcriptome analysis revealed that the significantly down-regulated expression of four genes in the HemE gene family (Phvul.008G059400.1, Phvul.010G110900.1, Phvul.008G147200.1, and Phvul.010G069500.1), which blocked the Urogen III to Coprogen III conversion, was the primary cause of the yellow phenotype in ‘ytg-2’ seedlings. Additionally, the down-regulation of POR (Phvul.004G113000.1) and NOL (Phvul.004G163900) genes during the chlorophyll cycle explained the reduced total chlorophyll content in ‘ytg-2’ and the gradual normalization of the chlorophyll a/b ratio in ‘ytg-2’ yellow leaves. The ex‍pression of PAO (Phvul.004G163900.1), a key enzyme in chlorophyll degradation, further confirmed that the yellow-to-green transition in ‘ytg-2’ leaves was linked to chlorophyll degradation processes.

Pod color is an essential economic trait of snap bean (Phaseolus vulgaris L.), and golden-yellow pods are more commercially popular than light-yellow varieties. Exploring the molecular regulatory mechanism underlying deep-yellow pod formation is essential for snap bean quality improvement. In this study, the wild-type cultivar Jinguan and the EMS-derived deep-yellow pod mutant pcm were used as materials. Integrative analyses of photosynthetic pigment quantification, genetic analysis, transcriptome sequencing, and targeted carotenoid metabolomics were performed to identify key genes and metabolic pathways governing pod color variation. Genetic analysis revealed that the deep-yellow pod trait of the pcm is stably inherited and controlled by a nuclear recessive gene. Transcriptome screening identified three differentially expressed key genes, PSY (Phvul.006G024100g), CCD4 (Phvul.002G120600g), and CYP707A (Phvul.002G122200g), whose expression patterns were strongly correlated with carotenoid accumulation. Metabolomic results demonstrated that the pcm presented reduced upstream β-carotene content, while the synthesis and accumulation of downstream chromogenic carotenoids, including zeaxanthin and capsorubin, were significantly enhanced, resulting in elevated total carotenoid content. Collectively, the differential expression of these genes remodels carotenoid metabolism and ultimately contributes to the deep-yellow pod phenotype. This study explores the regulatory mechanism of carotenoid metabolism in pod color formation, providing valuable theoretical support and genetic resources for quality breeding of snap beans.

Background and aims: Snap bean is a widely planted legume vegetable crop in the world, with tender pods as its edible organ. In the actual production process, excessive fiber content in bean pods can lead to a deterioration in their taste after cooking, seriously affecting their edible quality. In order to better study the mechanism of fiber formation in bean pod walls, we selected a bean pod fiber mutant (bfm) from the bean mutant library. Methods: Fiber content determination, cytological observation, and transcriptome and metabolome analysis were performed on the pod walls of mutant bfm and its wild-type at different developmental stages. Key results: The results showed that the crude fiber content of the bfm pod wall tissue was significantly higher than that of the wild type during the mature commercial pod stage, and cellulose may be the main factor causing the increase in fiber content in the bean pod wall. During the mature commercial pod stage, the number of cells in the pod wall tissue of bfm increased significantly compared to the wild type, with an increase in phloem fibers and thicker cell walls. It is speculated that this situation led to changes in fiber content in the mutant bfm. The combined analysis of transcriptome and metabolome showed that differentially expressed genes and metabolites were enriched in metabolic pathways and secondary metabolite biosynthesis pathways. Several metabolites, including glycine, L-glutamine, D-arabinitol, and D-ribose, were associated with the expression of Phvul.007G077800 (CTL) and Phvul.003G089600 (KOR). Conclusions: These genes and metabolites may participate in coordinated metabolic pathways that influence the availability of substrates and energy required for cellulose biosynthesis, thereby potentially contributing to cellulose accumulation in the pod wall. This study provides theoretical research on the mechanism of fiber synthesis in bean pod walls, and also to provide some reference for bean breeding improvement and application practice.