Co-expression complementary effect between a transposon-related gene and its ancestral syntenic gene.
(A) The homologous relationship between the transposon-related gene (GRMZM2G004617) and its ancestral syntenic gene GRMZM2G154301. The blue dotted lines and the light blue area show the homologous region between the two genes. The grey boxes represent the coding regions, while the open boxes indicate the untranslated regions. The transposon annotation was done using CENSOR (http://www.girinst.org/censor/index.php). The blue triangle and diamond represent helitron element and CACTA-like element, respectively. (B) The negative co-expression correlation between the two genes. (C) The validation of RT-PCR and genomic DNA PCR of the transposon-related gene (GRMZM2G004617), which exhibits unexpected expression patterns in the RILs. (D) Two-marker interaction (M3735 located in chromosome 4 is designated as locus A and M5604 in chromosome 7 is denoted as locus B, neither of which are linked to the differentially expressed genes) was significantly associated with the transcriptomic variation of type I gene GRMZM2G004617 in the RILs (P = 1.3E-07). aabb shows the genotype of B73, while AABB represents Mo17 genotype. The numbers close to the genotype show the number of RILs with the same genotype. The y-axis shows the normalized expression levels (RPKM). The blue triangle indicates the expression level in B73, while the red diamond indicates the expression level in Mo17.