{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T05:05:07Z","timestamp":1789621507685,"version":"build-2803163510"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Winter rapeseed (\n                    <jats:italic>Brassica rapa<\/jats:italic>\n                    L.) is exposed to recurrent low-temperature episodes, yet cultivar differences and reference-genome choice can complicate the interpretation of transcriptomic variation. Here, we reanalyzed 24 growth-point RNA-seq samples from the cold-tolerant cultivar \u2018Longyou-7\u2019 and the cold-sensitive cultivar \u2018Lenox\u2019 under control conditions (CK), after 3 and 24\u00a0h at 4\u00a0\u00b0C, and after 24\u00a0h of recovery at 22\u00a0\u00b0C. Transcriptome analysis was performed using the chromosome-level Longyou-7 reference genome and compared with results obtained using Chiifu v1.5. Functional analyses revealed stage-dependent transcriptional changes involving photosynthesis, lipid metabolism, hormone signaling, circadian regulation, sulfur and amino acid metabolism, and other stress-related processes. Glutathione metabolism was represented among the top-ranked pathways in several within-genotype contrasts, and genotype-specific co-expression networks linked glutathione-related transcription with antioxidant enzyme activities, soluble sugar, and ROS-associated traits. Biochemical measurements further showed stage-dependent changes in GSH and GSSG contents and GST activity, with \u2018Longyou-7\u2019 maintaining a higher GSH\/GSSG ratio and higher GST activity than \u2018Lenox\u2019 during cold treatment. qRT-PCR analysis of 22 candidate genes showed overall concordance with RNA-seq (\n                    <jats:italic>R<\/jats:italic>\n                    \u00b2 = 0.736), and 17 candidates contained conserved GST_N and GST_C domains, including nine Tau and eight Phi GSTs. Relative to Chiifu v1.5, the Longyou-7 reference increased uniquely mapped read rates by 1.28\u20131.69 percentage points in Longyou-7 samples, whereas differences in \u2018Lenox\u2019 ranged from \u22120.26 to 0.30 percentage points, while shared DEG responses remained highly concordant between the two reference backgrounds. Together, these results reveal stage-dependent transcriptional and biochemical adjustment during cold treatment and recovery and identify GSH\/GST-related genes as candidates for further functional analysis in winter rapeseed.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1947775","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T04:50:04Z","timestamp":1789620604000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Temporal and genotype-dependent transcriptomic responses to cold treatment and recovery in winter rapeseed (Brassica rapa L.)"],"prefix":"10.3389","volume":"17","author":[{"given":"Yifan","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyi","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengnan","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijun","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tun","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junyan","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gang","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wancang","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"B2","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1038\/s41477-020-0733-0","article-title":"Plant pan-genomes are the new reference","volume":"6","author":"Bayer","year":"2020","journal-title":"Nat. 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