Table 1. Classification of additive and non-additive gene expression pattern in allotetraploids.
| Group | Description | Classification criteria* |
|---|---|---|
| a | Additive expression with no parental differentiation | Cgi = xij = Coi |
| b | Partial ELD or additive expression with parental differentiation | (Cgi <xij < Coi) or (Coi <xij < Cgi) or (Cgi ≠ Coi and xij = Cgi and xij = Coi) |
| c | Up-regulated ELD toward Cg2 | xij = Cgi and xij >Coi |
| d | Down-regulated ELD toward Cg2 | xij = Cgi and xij <Coi |
| e | Up-regulated ELD toward Co2 | xij = Coi and xij >Cgi |
| f | Down-regulated ELD toward Co2 | xij = Coi and xij <Cgi |
| g | Up-regulated TRE with no parental differentiation | Cgi = Coi and xij >Cgi and xij >Coi |
| h | Up-regulated TRE with parental differentiation | Cgi ≠ Coi and xij >Cgi and xij >Coi |
| i | Down-regulated TRE with no parental differentiation | Cgi = Coi and xij <Cgi and xij <Coi |
| j | Down-regulated TRE with parental differentiation | Cgi ≠ Coi and xij <Cgi and xij <Coi |
*
Cgi: expression level of gene i in the Cg2 group; Coi: expression level of gene i in the Co2 group; xij: expression level of gene i in allotetraploid group j, and j∈(Sd, Sh, Cbp); ELD: expression level dominance; TRE: transgressive expression; The significance of differential expression between groups were determined by results of differential expression analysis on unphased gene expression, with a threshold of fold-change >2 and false discovery rate <0.05.