Fig. 1

Differentially expressed genes between extracted tetraploid wheat (ETW, AABB) and natural hexaploid wheat (NHW, AABBDD). a Diagram for producing ETW from NHW, modified from those of [13, 14]. The hybrid (AABBD) between NHW and NTW was backcrossed with NHW for nine generations, followed by selfing for three generations to select AABB genotype, which was selfed for additonal five generations to maintain genome stability. The resynthesized hexaploid was made between ETW (AABB) and DD and self-pollinated for five generaitons. b Mature seed morphology of T. durum, Ae. tauschii, NHW, ETW, and resynthesized hexaploid wheat (RHW, AABBDD). Scale bar = 1 cm. c Number of differentially expressed genes (DEGs) between ETW and NHW, with the majority (blue) restored and fewer not restored (yellow) in RHW. d Gene ontology (GO) analysis of DEGs. The circle color and size indicate P value and gene number, respectively (hypergeometric test, P < 0.05). e, f Heatmaps showing expression levels (fragment per kiobase per million, FPKM) of MADS-box genes (e) and starch biosynthetic genes (f) in ETW, NHW, and RHW