Summary of Differentially Expressed Genes.

Note: 6400, 5200, and 1200 are S0��1 generation lines and 6450, 5250, and 1250 are corresponding S5��6 lines.aGenetic changes included total number of RFLP and SSR marker fragment losses (Gaeta et al., 2007).bDEG = Statistically significant differentially expressed genes using FDR (0.05) under per-gene or common gene variance models.c% differentially expressed genes that were also differential between the diploid progenitors under the given variance model. The proportion of genes that demonstrated nonadditive expression in the allopolyploids that were also differential between the parents was significantly greater than would be expected by random chance. We performed Chi-square tests of equal proportions using R statistical software, Pd% differentially expressed genes that were also differential between the diploid progenitors under the given variance model. The proportion of genes that demonstrated nonadditive expression in the allopolyploids that were also differential between the parents was significantly greater than would be expected by random chance. Tests involving these proportions required a Fisher Exact Test using R statistical software because of low cell counts, P

备注：6400、5200与1200为S₀₋₁代株系，6450、5250及1250为对应的S₅₋₆代株系。
a. 遗传变异包含限制性片段长度多态性（RFLP, Restriction Fragment Length Polymorphism）与简单序列重复（SSR, Simple Sequence Repeat）标记的总片段缺失数量（Gaeta等，2007）。
b. 差异表达基因（DEG, Differentially Expressed Gene）指在单基因方差模型或通用基因方差模型下，使用错误发现率（FDR, False Discovery Rate）阈值0.05筛选得到的具有统计学显著性的差异表达基因。
c. 本百分比指在指定方差模型下，同时在二倍体祖先种间存在表达差异的差异表达基因占比。异源多倍体中表现出非加性表达的基因，同时在亲本间存在表达差异的比例，显著高于随机概率下的预期值。我们使用R统计软件进行了等比例卡方检验。
本百分比指在指定方差模型下，同时在二倍体祖先种间存在表达差异的差异表达基因占比。异源多倍体中表现出非加性表达的基因，同时在亲本间存在表达差异的比例，显著高于随机概率下的预期值。由于单元格计数较低，针对此类比例的检验需使用R统计软件进行费希尔精确检验，P