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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The seedless trait in grapes primarily arises from pseudo-parthenocarpy, driven by early seed abortion involving programmed cell death (PCD) and autophagy. However, the specific regulatory networks governing these pathways remain poorly defined. To address this, we systematically characterized the PCD-related (vacuolar processing enzyme [VPE] and metacaspase [MC]) and autophagy-related (ATG) gene families in the seedless cultivar \u2018Jingkejing\u2019 utilizing comprehensive bioinformatic analyses, spatiotemporal transcriptomic profiling, and transient expression assays. We identified three VPE, six MC, and 33 ATG genes, whose promoters were significantly enriched in hormone-responsive and transcription factor (TF)-binding motifs. Transcriptomic profiling across critical seed abortion stages highlighted Vv\u03b3VPE and VvMC9 as key differentially expressed genes. Furthermore, protein\u2013protein interaction predictions indicated extensive crosstalk among PCD\/ATG proteins, kinases, and ubiquitin system components. Notably, transient expression assays confirmed that two core transcription factors, VvWRKY46 and VvERF71, specifically regulate downstream PCD-related targets, supporting a proposed multi-hormonal and TF-mediated regulatory network during seed abortion. These findings elucidate the molecular mechanisms underlying pseudo-parthenocarpy, providing essential candidate gene resources for the marker-assisted breeding of seedless grapes.<\/jats:p>","DOI":"10.3390\/ijms27188353","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T14:23:56Z","timestamp":1790864636000},"page":"8353","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Regulatory Network of Transcription and Hormones Controls PCD and Autophagy in Grape Seed Abortion"],"prefix":"10.3390","volume":"27","author":[{"given":"Ying","family":"Wang","sequence":"first","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1545-9610","authenticated-orcid":false,"given":"Pengcheng","family":"Zhao","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Xuxian","family":"Xuan","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Qiqi","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Ruiqiang","family":"Chao","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Yan","family":"Zhong","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Haitao","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Yuxuan","family":"Song","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Lianshuang","family":"Liang","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Leyi","family":"He","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Hui","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Zhenqiang","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Chen","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Horticulture, Nanjing Agricultural University, Nanjing 211800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"32292","DOI":"10.1074\/jbc.M305740200","article-title":"Vacuolar processing enzymes are essential for proper processing of seed storage proteins in Arabidopsis thaliana","volume":"278","author":"Shimada","year":"2003","journal-title":"J. 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