{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T05:16:31Z","timestamp":1788412591659,"version":"build-2803163510"},"reference-count":37,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32401481"],"award-info":[{"award-number":["32401481"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"award":["32401481"],"award-info":[{"award-number":["32401481"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Rind color is an important quality trait in zucchini (Cucurbita pepo). As a core transcription factor in plant pigment biosynthesis, APRR2 plays a conserved yet mechanistically diverse regulatory role in the formation of rind color in various vegetables. However, the APRR2 transcription factor regulates rind color but has not been systematically identified in C. pepo. In this study, 50 APRR2 genes were defined by the presence of the conserved REC domain verified. These genes were identified and found to be unevenly distributed across the 20 chromosomes, primarily expanded through tandem duplication events. Phylogenetic and structural analysis classified these genes into three distinct subgroups, all featuring the conserved REC domain essential for pigment regulation but exhibiting variations in motifs and intron\u2013exon structures. Promoter analysis revealed abundant light-responsive, hormone-responsive and stress-responsive elements that may contribute to environmental adaptation and photomorphogenesis. Crucially, transcriptome analysis during rind development (0 and 10 days after pollination) in green (GR) and white (WR) rind lines demonstrated profound functional divergence. Expression clusters indicated temporal shifts in metabolism and enriched \u201ccircadian rhythm-plant\u201d and \u201cphotosynthesis\u201d pathways in WR at 0 DAP. Specific APRR2 genes were tightly correlated with rind color. qPCR validation of the 24 selected APRR2 genes classified them into four trend groups based on the direction of expression change at 10 DAP. In total, 14 genes were upregulated in both GR and WR, 6 were downregulated in both lines, 1 was upregulated in GR but downregulated in WR, and 3 were downregulated in GR but upregulated in WR. Furthermore, protein\u2013protein interaction prediction and yeast two-hybrid (Y2H) assays detected a physical interaction in yeast between a core APRR2 protein and a bHLH62 transcription factor, suggesting a potential interaction that may be involved in rind color regulation, pending in planta validation. The study first identified the members of the APRR2 gene family in C. pepo and conducted a bioinformatics analysis on them. The study establishes the molecular basis of APRR2 function and offers valuable resources for breeding improved C. pepo varieties.<\/jats:p>","DOI":"10.3390\/genes17091063","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T11:33:32Z","timestamp":1788262412000},"page":"1063","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Identification of the APRR2 Gene Family and Rind Color Trait Analysis in Zucchini (Cucurbita pepo)"],"prefix":"10.3390","volume":"17","author":[{"given":"Tongsheng","family":"Liu","sequence":"first","affiliation":[{"name":"College of Agriculture, Qingdao Hengxing University of Science and Technology, Qingdao 266100, China"},{"name":"College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Li","sequence":"additional","affiliation":[{"name":"College of Agriculture, Qingdao Hengxing University of Science and Technology, Qingdao 266100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinbin","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Agriculture, Qingdao Hengxing University of Science and Technology, Qingdao 266100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyang","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqi","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Agriculture, Qingdao Hengxing University of Science and Technology, Qingdao 266100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/s00122-024-04676-z","article-title":"Fine mapping and transcriptome profiling reveal CpAPRR2 to modulate immature fruit rind color formation in zucchini Cucurbita pepo","volume":"137","author":"Ding","year":"2024","journal-title":"Theor. Appl. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/s41438-019-0176-9","article-title":"Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits","volume":"6","author":"Xanthopoulou","year":"2019","journal-title":"Hortic. Res."},{"key":"ref_3","first-page":"9","article-title":"Genetic regulation and molecular mechanism of immature cucumber peel color: A review","volume":"3","author":"Cui","year":"2023","journal-title":"Veg. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1093\/pcp\/pci087","article-title":"Pseudo-Response Regulators PRRs or True Oscillator Components TOCs","volume":"46","author":"Mizuno","year":"2005","journal-title":"Plant Cell Physiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1093\/dnares\/dsq033","article-title":"Pseudo-response regulator PRR homologues of the moss Physcomitrella patens: Insights into the evolution of the PRR family in land plants","volume":"18","author":"Satbhai","year":"2011","journal-title":"DNA Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1104\/pp.112.212654","article-title":"Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits","volume":"161","author":"Pan","year":"2013","journal-title":"Plant Physiol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Arrones, A., Mangino, G., Alonso, D., Plazas, M., Prohens, J., Portis, E., Barchi, L., Giuliano, G., Vilanova, S., and Gramazio, P. (2022). Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1025951"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Zhou, W., Yi, L., Wang, Y., Wang, H., Li, Q., Wu, N., and Dai, Z. (2025). Identification of candidate genes for green rind color in watermelon. Plants, 14.","DOI":"10.3390\/plants14010113"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2356860","DOI":"10.1080\/13102818.2024.2356860","article-title":"Development and validation of a functional molecular marker for a CaAPRR2-like gene that controls green fruit colour in pepper","volume":"38","author":"Zhang","year":"2024","journal-title":"Biotechnol. Biotechnol. Equip."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"kiaf249","DOI":"10.1093\/plphys\/kiaf249","article-title":"The transcription factor CsAPRR2 controls peel color by regulating the expression of SULFURTRANSFERASE14 in cucumber","volume":"198","author":"Fan","year":"2025","journal-title":"Plant Physiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e70496","DOI":"10.1111\/tpj.70496","article-title":"CsAPRR2 regulates cucumber immature fruit color by coordinating chloroplast biogenesis and photosynthesis-related gene expression","volume":"123","author":"Liu","year":"2025","journal-title":"Plant J."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2798","DOI":"10.1093\/plcell\/koae111","article-title":"The Y locus encodes a REPRESSOR OF PHOTOSYNTHETIC GENES protein that represses carotenoid biosynthesis via interaction with APRR2 in carrot","volume":"36","author":"Wang","year":"2024","journal-title":"Plant Cell"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1111\/tpj.16727","article-title":"Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit","volume":"118","author":"Ezura","year":"2024","journal-title":"Plant J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.molp.2017.09.003","article-title":"Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes","volume":"10","author":"Sun","year":"2017","journal-title":"Mol. Plant"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2590","DOI":"10.1016\/j.xplc.2024.100935","article-title":"Complete genome assembly provides insights into the centromere architecture of pumpkin (Cucurbita maxima)","volume":"5","author":"Zeng","year":"2024","journal-title":"Plant Commun."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2430","DOI":"10.1093\/plphys\/kiac410","article-title":"A common whole-genome paleotetraploidization in Cucurbitales","volume":"190","author":"Wang","year":"2022","journal-title":"Plant Physiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"112862","DOI":"10.1016\/j.plantsci.2025.112862","article-title":"Identification of the JAZ gene family in Cucurbita pepo and functional analysis of CpJAZ5 in drought stress response","volume":"363","author":"Xu","year":"2026","journal-title":"Plant Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/s10142-025-01744-5","article-title":"Identification of the PLATZ gene family in Cucurbita pepo and functional analysis of CpPLATZ4 in powdery mildew stress response","volume":"25","author":"Xu","year":"2025","journal-title":"Funct. Integr. Genom."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/csc2.20883","article-title":"Classification of inheritance of trichomes in different organs in zucchini (Cucurbita pepo L.)","volume":"63","author":"Lin","year":"2023","journal-title":"Crop Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1007\/s00239-025-10287-z","article-title":"MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems","volume":"94","author":"Stecher","year":"2026","journal-title":"J. Mol. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: Recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Ivica","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Gu, Y.J., Sun, J.T., Dan, F., Jiang, X., Liao, D., Yao, C., and Qi, W. (2025). Genome-wide identification and expression analysis of Wnt gene family in the forest musk deer (Moschus berezovskii) under musk secretion stage. BMC Genom., 26.","DOI":"10.1186\/s12864-025-12451-7"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Fan, Z., Yao, X., Chen, S., Gu, X., Wu, C., Li, H., Zhao, Q., and Ruan, J. (2026). Genome-wide identification, evolution, and expression pattern analysis of the LEA gene family in Tartary Buckwheat (Fagopyrum tataricum). BMC Genom., 27.","DOI":"10.1186\/s12864-026-12772-1"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"uhab057","DOI":"10.1093\/hr\/uhab057","article-title":"Cucurbitaceae genome evolution, gene function, and molecular breeding","volume":"9","author":"Ma","year":"2022","journal-title":"Hortic. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"112590","DOI":"10.1016\/j.plantsci.2025.112590","article-title":"A 13-bp insertion in CmAPRR2 gene disrupts its function in regulating the green rind formation of immature melon fruit Cucumis melo L.","volume":"359","author":"Chen","year":"2025","journal-title":"Plant Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/s10725-017-0304-1","article-title":"Identification and functional characterization of APRR2 controlling green immature fruit color in cucumber Cucumis sativus L.","volume":"83","author":"Jiao","year":"2017","journal-title":"Plant Growth Regul."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2028","DOI":"10.1111\/pce.70359","article-title":"A 13-kb Deletion in SeAPRR2 Disrupts Chloroplast Development by Dual-Targeting SeHEMA1\/SeLHCB4 for White Peel Formation in Chayote","volume":"49","author":"Cheng","year":"2026","journal-title":"Plant Cell Environ."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Fang, H., Wang, P., Wang, W., Peng, J., Zheng, J., Zhu, G., Zhong, C., and Yu, W. (2023). Fine Mapping and Identification of SmAPRR2 Regulating Rind Color in Eggplant Solanum melongena L.. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24043059"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4277","DOI":"10.1007\/s00122-022-04217-6","article-title":"Chromosomal fragment deletion in APRR2-repeated locus modulates the dark stem color in Cucurbita pepo","volume":"135","author":"Zhu","year":"2022","journal-title":"Theor. Appl. Genet."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3781","DOI":"10.1093\/jxb\/erz182","article-title":"The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon","volume":"70","author":"Oren","year":"2019","journal-title":"J. Exp. Bot."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Nguyen, T.N.P., and Sung, J. (2025). Light Spectral-Ranged Specific Metabolisms of Plant Pigments. Metabolites, 15.","DOI":"10.3390\/metabo15010001"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1093\/pcp\/pcu030","article-title":"Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana","volume":"55","author":"Mizuno","year":"2014","journal-title":"Plant Cell Physiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/treephys\/tpad089","article-title":"Transcriptomic and physiological comparison of Shatangju Citrus reticulata and its late-maturing mutant provides insights into auxin regulation of citrus fruit maturation","volume":"43","author":"Lv","year":"2023","journal-title":"Tree Physiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"0925","DOI":"10.1016\/j.postharvbio.2024.113229","article-title":"CsbHLH6 positively regulates abscisic acid-mediated citrus fruit coloration during postharvest storage","volume":"219","author":"Sun","year":"2025","journal-title":"Postharvest Biol. Technol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.hpj.2020.10.003","article-title":"Genome-wide Characterization of cis-acting Elements in the Promoters of Key Carotenoid Pathway Genes from the Main Species of Genus Citrus","volume":"6","author":"Zhu","year":"2020","journal-title":"Hortic. Plant J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1093\/pcp\/pcg078","article-title":"A Link between circadian-controlled bHLH factors and the APRR1\/TOC1 quintet in Arabidopsis thaliana","volume":"44","author":"Yamashino","year":"2003","journal-title":"Plant Cell Physiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.hpj.2025.12.003","article-title":"Identification and functional characterization of AmbHLH002 as a conserved bHLH regulator of anthocyanin biosynthesis in Antirrhinum majus","volume":"12","author":"Jiang","year":"2026","journal-title":"Hortic. Plant J."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1063\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T04:37:31Z","timestamp":1788410251000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1063"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":37,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["genes17091063"],"URL":"https:\/\/doi.org\/10.3390\/genes17091063","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,1]]}}}