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The composition of saline\u2013alkali land is a variety of salt and alkali mixed with the formation of alkaline salt. Hydrogen sulfide (H2S) has been reported to have positive effects on plant responses to abiotic stresses. Our previous study showed that H2S pretreatment alleviated the damage caused by alkaline salt stress to Malus hupehensis Rehd. var. pingyiensis Jiang (Pingyi Tiancha, PYTC) roots by regulating Na+\/K+ homeostasis and oxidative stress. In this study, transcriptome analysis was used to investigate the overall mechanism through which H2S alleviates alkaline salt stress in PYTC roots. Simultaneously, differentially expressed genes (DEGs) were explored. Transcriptional profiling of the Control-H2S, Control-AS, Control-H2S + AS, and AS-H2S + AS comparison groups identified 1618, 18,652, 16,575, and 4314 DEGs, respectively. Further analysis revealed that H2S could alleviate alkaline salt stress by increasing the energy maintenance capacity and cell wall integrity of M. hupehensis roots and by enhancing the capacity for reactive oxygen species (ROS) metabolism because more upregulated genes involved in ROS metabolism and sulfur-containing compounds were identified in M. hupehensis roots after H2S pretreatment. qRT-PCR analysis of H2S-induced and alkaline salt-response genes showed that these genes were consistent with the RNA-seq analysis results, which indicated that H2S alleviation of alkaline salt stress involves the genes of the cell wall and sulfur-containing compounds in PYTC roots.<\/jats:p>","DOI":"10.3390\/ijms232314848","type":"journal-article","created":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T01:52:20Z","timestamp":1669773140000},"page":"14848","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["H2S Enhanced the Tolerance of Malus hupehensis to Alkaline Salt Stress through the Expression of Genes Related to Sulfur-Containing Compounds and the Cell Wall in Roots"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4133-2629","authenticated-orcid":false,"given":"Huan","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengyuan","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianfei","family":"Song","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuansheng","family":"Ning","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8792-7612","authenticated-orcid":false,"given":"Hongqiang","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Street, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,27]]},"reference":[{"key":"ref_1","first-page":"91","article-title":"Degeneration and conservation of aneurolepidium chinense grassland in Northern China","volume":"37","author":"Kawanabe","year":"1991","journal-title":"J. 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