Cytoplasmic male sterility (CMS) is a complex phenomenon in plants, rendering them unable to produce functional pollen. In general, this is caused by an abnormal or dysfunctional mitochondrial genome. In wheat, however, the systematic structural characteristics of the mitochondrial genome from the CMS line, vis-à-vis its maintainer line, are rarely reported. Here, we identified the morphological characteristics, sequenced, assembled, and characterized the complete mitogenomes of the wheat B-type CMS line (B) and its maintainer line (YS9). The morphological results indicated that the B likely undergoes binucleate microspore abortion. The B and YS9 genomes were assembled into a typical circular molecule 452,794 and 452,453 bp in length, respectively, comprising 34 protein-coding genes (PCGs), 3 ribosomal RNA genes (rRNAs), and 16 transfer RNA genes (tRNAs). The codon usage analysis revealed leucine (Leu) and serine (Ser) as the most frequently used amino acid residues in the B and YS9 mitochondrial proteins. In particular, we uncovered a specific ORF2718, whose length of 501 bp was more 30 bp than that of the atp8 gene in the B genome, which perhaps could affect normal function of ATP8. Further, the existence of SNPs at the atp6 gene is probably associated with the CMS mechanism. This study suggests that sequencing and comparing the genomic features of the B and YS9 mitogenomes provides not only an important opportunity to conduct further genomic breeding studies, but also valuable information for future evolutionary and molecular studies of CMS in wheat.

The multi-ovary trait of wheat inbred line DUOII is controlled by a dominant gene whose expression can be suppressed by the heterogeneous cytoplasm of TeZhiI (TZI), another inbred line with the nucleus of common wheat and the cytoplasm of Aegilops. DUOII (♀) × TZI (♂) shows multi-ovary trait, while TZI (♀) × DUOII (♂) shows mono-ovary. To elucidate the molecular mechanism regulating heterogeneous cytoplasmic suppression of the multi-ovary gene, we performed an untargeted metabolomic analysis of 2–6 mm young spikes of reciprocal crosses between DUOII and TZI at the critical stage of additional pistil primordium development. We identified 198 annotated differentially expressed metabolites and analyzed them according to their biological functions. The results showed that these metabolites had obvious functional pathways mainly implicated in amino acid, carbohydrate, nicotinate and nicotinamide, and purine metabolism and isoquinoline alkaloid biosynthesis. We also found that shikimate, phosphoglycolic acid, nicotinamide, guanine, and xanthine might play essential roles in cytoplasmic suppression of multi-ovary trait. Chloroplast metabolism was also implicated in the nuclear-cytoplasmic effect of the multi-ovary gene. The findings provide solid theoretical and empirical foundations for future studies elucidating the mechanisms controlling heterogeneous cytoplasmic suppression of the nuclear multi-ovary gene in wheat.