{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:10:36Z","timestamp":1790097036864,"version":"4.0.1"},"reference-count":41,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005046","name":"Heilongjiang Province Collaborative Innovation Promotion System\u2014Snap Bean System","doi-asserted-by":"publisher","award":["LH2024C097"],"award-info":[{"award-number":["LH2024C097"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>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 \u03b2-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.<\/jats:p>","DOI":"10.3390\/ijms27188380","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:32:12Z","timestamp":1790083932000},"page":"8380","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic and Targeted Carotenoid Metabolomic Dissection of Pod Color Difference Between Wild Type and an EMS-Induced Stable pcm Mutant in Snap Bean (Phaseolus vulgaris L.)"],"prefix":"10.3390","volume":"27","author":[{"given":"Qiuhui","family":"Mu","sequence":"first","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Hongning","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Guojun","family":"Feng","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Xiaoxu","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"}]},{"given":"Dajun","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Zhishan","family":"Yan","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Taifeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"}]},{"given":"Chang","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Liu, C., Yang, X., Yan, Z., Liu, D., and Feng, G. (2022). Identification and Characterization of a Mutant PV-PUR Gene Responsible for the Purple Phenotype of Snap Bean (Phaseolus vulgaris L.). Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031265"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Sun, H., Zhang, Y., Zhang, L., Wang, X., Zhang, K., Cheng, F., and Chen, S. (2025). Genetic Regulation of Chlorophyll Biosynthesis in Pepper Fruit: Roles of CaAPRR2 and CaGLK2. Genes, 16.","DOI":"10.3390\/genes16020219"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1093\/jxb\/erp097","article-title":"Light-induced vegetative anthocyanin pigmentation in Petunia","volume":"60","author":"Albert","year":"2009","journal-title":"J. Exp. Bot."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Junko, Y. (2017). Carotenoids Database: Structures, chemical fingerprints and distribution among organisms. Database J. Biol. Databases Curation, 2017.","DOI":"10.1093\/database\/bax004"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/978-3-319-39126-7_6","article-title":"Regulation of Carotenoid Biosynthesis During Fruit Development","volume":"79","author":"Lado","year":"2016","journal-title":"Subcell. Biochem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1111\/j.1365-313X.2004.02263.x","article-title":"The tomato carotenoid cleavage dioxygenase 1 genes contribute to the formation of the flavor volatiles beta-ionone, pseudoionone, and geranylacetone","volume":"40","author":"Simkin","year":"2004","journal-title":"Plant J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s43897-022-00023-2","article-title":"Plant carotenoids: Recent advances and future perspectives","volume":"2","author":"Sun","year":"2022","journal-title":"Mol. Hortic."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1111\/tpj.12451","article-title":"The tomato mutation nxd1 reveals a gene necessary for neoxanthin biosynthesis and demonstrates that violaxanthin is a sufficient precursor for abscisic acid biosynthesis","volume":"78","author":"Neuman","year":"2014","journal-title":"Plant J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.abb.2018.07.014","article-title":"Cis-carotene biosynthesis, evolution and regulation in plants: The emergence of novel signaling metabolites","volume":"654","author":"Alagoz","year":"2018","journal-title":"Arch. Biochem. Biophys."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Liu, Y., Zhou, B., Qi, Y., Chen, X., Liu, C., Liu, Z., and Ren, X. (2017). Expression Differences of Pigment Structural Genes and Transcription Factors Explain Flesh Coloration in Three Contrasting Kiwifruit Cultivars. Front. Plant Sci., 8.","DOI":"10.3389\/fpls.2017.01507"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Huo, J., Zhang, N., Gong, Y., Bao, Y., Li, Y., Zhang, L., and Nie, S. (2024). Effects of different light intensity on leaf color changes in a Chinese cabbage yellow cotyledon mutant. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1371451"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Gupta, P., and Hirschberg, J. (2022). The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.806184"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1105\/tpc.105.039966","article-title":"A chromoplast-specific carotenoid biosynthesis pathway is revealed by cloning of the tomato white-flower locus","volume":"18","author":"Galpaz","year":"2006","journal-title":"Plant Cell"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Garc\u00eda-Fern\u00e1ndez, C., Campa, A., Garz\u00f3n, A.S., Miklas, P., and Ferreira, J.J. (2021). GWAS of pod morphological and color characters in common bean. BMC Plant Biol., 21.","DOI":"10.1186\/s12870-021-02967-x"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/s11032-023-01362-8","article-title":"Fine mapping and characterisation of a PV-PUR mediating anthocyanin synthesis in snap bean (Phaseolus vulgaris L.)","volume":"43","author":"Liu","year":"2023","journal-title":"Mol. Breed."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.1007\/s00122-021-03928-6","article-title":"Identification and fine genetic mapping of the golden pod gene (pv-ye) from the snap bean (Phaseolus vulgaris L.)","volume":"134","author":"Yang","year":"2021","journal-title":"Theor. Appl. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5243","DOI":"10.1093\/jxb\/eru288","article-title":"SlNCED1 and SlCYP707A2: Key genes involved in ABA metabolism during tomato fruit ripening","volume":"65","author":"Ji","year":"2014","journal-title":"J. Exp. Bot."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1111\/tpj.15102","article-title":"Plant apocarotenoids: From retrograde signaling to interspecific communication","volume":"105","author":"Moreno","year":"2021","journal-title":"Plant J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.scienta.2018.08.030","article-title":"Changes in the content of chlorophylls and carotenoids in the rind of Fino 49 lemons during maturation and their relationship with parameters from the CIELAB color space","volume":"243","author":"Conesa","year":"2019","journal-title":"Sci. Hortic."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2137","DOI":"10.1016\/j.hpj.2024.06.008","article-title":"BoaCRTISO regulates the color and glossiness of Chinese kale through its effects on pigment, abscisic acid, and cuticular wax biosynthesis","volume":"11","author":"Zhang","year":"2025","journal-title":"Hortic. Plant J."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"G\u00f3mez-Mart\u00edn, C., Capel, C., Gonz\u00e1lez, A.M., Lebr\u00f3n, R., Yuste-Lisbona, F.J., Hackenberg, M., Oliver, J.L., Santalla, M., and Lozano, R. (2020). Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.). Plants, 9.","DOI":"10.3390\/plants9040545"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Stanley, L., and Yuan, Y.W. (2019). Transcriptional Regulation of Carotenoid Biosynthesis in Plants: So Many Regulators, So Little Consensus. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.01017"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1007\/s000180050186","article-title":"Zinc-finger transcription factors in plants","volume":"54","author":"Takatsuji","year":"1998","journal-title":"Cell Mol. Life Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13068-023-02299-y","article-title":"Integrated metabolic and transcriptional analysis reveals the role of carotenoid cleavage dioxygenase 4 (IbCCD4) in carotenoid accumulation in sweetpotato tuberous roots","volume":"16","author":"Zhang","year":"2023","journal-title":"Biotechnol. Biofuels Bioprod."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Ma, X., Luo, X., Wei, Y., Bai, T., Shi, J., Zheng, B., Xu, W., Li, L., Wang, S., and Zhang, J. (2021). Chromosome-Scale Genome and Comparative Transcriptomic Analysis Reveal Transcriptional Regulators of \u03b2-Carotene Biosynthesis in Mango. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.749108"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Zhang, L., Du, W., Tu, J., Zhu, H., and Li, X. (2025). Light-mediated activation of PpPSY enhances \u03b2-carotene accumulation in pear fruit peel. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1542830"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1007\/s11032-011-9591-9","article-title":"Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening","volume":"29","author":"Gady","year":"2012","journal-title":"Mol. Breed."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1111\/j.1365-313X.2006.02666.x","article-title":"Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family","volume":"45","author":"Auldridge","year":"2006","journal-title":"Plant J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1126\/science.1218094","article-title":"The path from \u03b2-carotene to carlactone, a strigolactone-like plant hormone","volume":"335","author":"Alder","year":"2012","journal-title":"Science"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Zheng, X., Yang, Y., and Al-Babili, S. (2021). Exploring the Diversity and Regulation of Apocarotenoid Metabolic Pathways in Plants. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.787049"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Kim, H.M., Park, S.H., Ma, S.H., Park, S.Y., Yun, C.-H., Jang, G., and Joung, Y.H. (2020). Promoted ABA Hydroxylation by Capsicum annuum CYP707As Overexpression Suppresses Pollen Maturation in Nicotiana tabacum. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.583767"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4527","DOI":"10.1093\/jxb\/eru316","article-title":"Transcriptional control of fleshy fruit development and ripening","volume":"65","author":"Karlova","year":"2014","journal-title":"J. Exp. Bot."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1146\/annurev-genet-110410-132507","article-title":"Genetics and control of tomato fruit ripening and quality attributes","volume":"45","author":"Klee","year":"2011","journal-title":"Annu Rev. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Gottwald, S., Bauer, P., Komatsuda, T., Lundqvist, U., and Stein, N. (2009). TILLING in the two-rowed barley cultivar \u2019Barke\u2019 reveals preferred sites of functional diversity in the gene HvHox1. BMC Res. Notes, 2.","DOI":"10.1186\/1756-0500-2-258"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1746-4811-5-13","article-title":"Implementation of two high through-put techniques in a novel application: Detecting point mutations in large EMS mutated plant populations","volume":"5","author":"Gady","year":"2009","journal-title":"Plant Methods"},{"key":"ref_36","first-page":"9","article-title":"Formulae and program to determine total carotenoids and chlorophylls A and B of leaf extracts in different solvents","volume":"2","author":"Welburn","year":"1984","journal-title":"Adv. Agric. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_39","unstructured":"Kolde, R. (2026, September 14). Pheatmap: Pretty Heatmaps. R Package Version 1.0.13. Available online: https:\/\/CRAN.R-project.org\/package=pheatmap."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"RESEARCH0034","DOI":"10.1186\/gb-2002-3-7-research0034","article-title":"Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes","volume":"3","author":"Vandesompele","year":"2002","journal-title":"Genome Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8380\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:33:08Z","timestamp":1790094788000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8380"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,20]]},"references-count":41,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27188380"],"URL":"https:\/\/doi.org\/10.3390\/ijms27188380","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,20]]}}}