2.1.5. Genes Upregulated by Both LT and Warming Treatment

Since both LT (transfer from 22 to 12 ◦C) and warming (transfer from 12 to 28 ◦C) are considered to be temperature-stress treatments, we analyzed genes responsive to LT and warming conditions (Table 1; Tables S7 and S15). We expected that genes upregulated by LT would also be upregulated by warming, but only a small number of genes in these categories overlapped: 40 and 59 genes in Chiifu and Kenshin, respectively (Table 1; Table S15). Interestingly, only one gene, *BrHSFA2* (Bra000557, an ortholog of AT2G26150), was upregulated under both conditions as well as in both inbred lines. Therefore, BrHSFA2 represents a candidate temperature-specific regulator in Chinese cabbage.

In contrast to the single upregulated gene, many genes were downregulated by both LT and warming (Table S16). Whereas no gene was upregulated under both LT and warming conditions in Chiifu, 28 genes were downregulated under both conditions in Kenshin, implying that Kenshin is more sensitive to changes in temperature. The expression levels of these 28 genes were highest under normal growth conditions and lowest at 28 ◦C. Well-known genes in this category include genes encoding HY5-homolog (*HYH*; AT3G17609; Bra022225, Bra021258), gibberellin 2-oxidase 1 (*GA2OX1*; AT1G78440; Bra008362), CONSTANS-like 1 (*COL1*; AT5G15850; Bra023541), and CONSTANS-like 2 (*COL2*; AT3G02380; Bra021464, Bra001043).
