IntroductionWith the development of society, the consumption demand for edible oil is increasing rapidly. Most vegetable oils are produced by four major crops, including soybean, oil palm, rape and sunflower (Dyer and Mullen, 2008). Rapeseed (Brassica napus L. ) contributes more than 15% of the world’s edible oil supply (Usda, 2014). Rapeseed is the most significant oilseed crop and a primary source of edible oil in China, Canadian, and the European Union. As people’s demand for edible oil increases year by year, enhancing seed oil content and oil production per unit area of land is one of the most important goals in the breeding of rapeseed.The seed oil content is a complicated quantitative trait that is easily affected by environmental factors and varies from 35% to 55% in rapeseed depending on ecological zones and climate conditions (Zhou et al., 2018). Low temperature increases polyunsaturated fatty acid content in plants, contributing to maintaining the fluidity of biological membranes (Los and Murata, 1998). Bellaloui et al. (2013) demonstrated that high temperature altered oil production and composition, which could be partially related to the limited availability and movement of carbohydrates from leaves to seeds. Zhou et al. (2018) suggested that temperature affects storage lipids and gene expression changes in lipid metabolism in low and high oil content rapeseed cultivars. Some research has suggested that temperature directly affects the expression instability of the FAD2 and FAD3 genes in the process of lipid accumulation (Román et al., 2012; Zhu et al., 2012; Li et al., 2015). Meanwhile, light intensity is an essential factor in determining the efficiency of photosynthesis. Light intensity affects gene expression in lipid metabolism, which regulates the seed oil content in developing seeds (Vuorinen et al., 2014; Zhu et al., 2020). The expression of WRINKLED1 , an important lipid synthesis regulatory gene in developing seeds, is associated with silique wall photosynthetic activity (Hua et al., 2012). Although the molecular mechanism by which temperature and light regulate fatty acid accumulation is not well known, uncovering environment-insensitive genes in lipid metabolism may be a better way to further improve the stability of oil content and fatty acid composition.Environmental and genotypic interactions lead to gene expression pattern differences that result in phenotypic diversity. With the development of next-generation sequencing, gene expression variation can be measured quantitatively, and DEGs related to phenotypes and/or environments can be explored. Transcriptome analysis has been applied to uncover the DEGs involved in rapeseed oil content (Tan et al., 2019; Yu et al., 2023). A large number of DEGs could be identified in short times by this application. However, the transcriptome was only interpreted as phenotypic variation in terms of gene expression and failed to fully interpret genetic variations (van Dam et al., 2015). Meanwhile, numerous differentially expressed genes make explaining transcriptome results and enacting breeding strategies more difficult. GWAS is an application that studies complex phenotypes by investigating genetic variations in the whole genome and has been extensively applied in rapeseed (He et al., 2017; Zhou et al., 2018b; Chen et al., 2019). Therefore, combining transcriptome analysis and GWAS to identify differentially expressed genes and explore genetic variations is a novel strategy. For example, Zhang et al. (2018) used GWAS combined with transcriptome analysis to reveal that HCTs and WRKYs interact to regulate the defence response of poplar. Xiao et al. (2019) identified a few key genes of the lipid biosynthesis pathway controlling oil content by combining GWAS and transcriptome analysis in Brassica napus . A combination of genome-wide and transcriptome-wide association studies identified three thermal tolerance-associated loci that contained 75 protein-coding genes and 27 long noncoding RNAs (Ma et al., 2021).In this study, we performed transcriptome sequencing of two HOC and LOC accessions at 35 DAP across three different environments. Meanwhile, a GWAS was performed to detect candidate genes significantly associated with seed oil content in three different environments. Our aimed to identity environment-insensitive genes in the process of oil accumulation. These results will provide useful molecular markers for the improvement of high and stability oil content varieties.