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Using Oryza sativa ssp. japonica Nipponbare and ssp. indica 9311, we generated reciprocal F1 hybrids and their genome-doubled segmental allotetraploids, and profiled leaf and root transcriptomes under normal, cold, and low-nitrogen conditions. For each tissue and condition, an in silico 1:1 mixture of parental transcriptome reads was used as a reference for parental expression state. Reciprocal F1 hybrids consistently reduced parental homeologous expression differences and maintained narrow, near-equal homeolog expression across tissues and conditions, consistent with trans-regulatory buffering. Segmental allotetraploids augmented parental homeologous expression bias with strong tissue and condition dependence, as well as maternally biased parent-of-origin effects. In F1 hybrids, most expression-biased homeolog pairs inherited the parental bias direction, whereas segmental allotetraploids underwent extensive de novo reprogramming. Condition-dependent homeolog expression-biased gene sets showed more detectable functional enrichments in segmental allotetraploids than in F1 hybrids, highlighting stress- and signaling-related functions under cold in leaves and transport- and energy-related processes under low nitrogen in roots. Representative cloned cold- and nitrate-related genes showed locus-, tissue-, and genotype-dependent homeologous expression and total-expression patterns, with only partial concordance with stress-related phenotypes. Together, our results provide insights into how hybridization and WGD exert contrasting effects on homeolog regulation and suggest that regulatory flexibility may contribute to subsequent allopolyploid evolution.<\/jats:p>","DOI":"10.1093\/plphys\/kiag620","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:06:30Z","timestamp":1789473990000},"source":"Crossref","is-referenced-by-count":0,"title":["Pervasive and context-dependent homeologous expression remodeling in intersubspecific diploid F1 hybrids and segmental allotetraploids of rice"],"prefix":"10.1093","volume":"202","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2799-0898","authenticated-orcid":false,"given":"Guo","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University , Changchun 130024 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