Mitochondrial genomes between a cytoplasmic male-sterile line and its restorer line in G.hirsutum

As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton, the mitochondrial genome of CMS line SI3A and its restorer line 0-613-2R were sequenced and de novo assembled. Remarkable variations in the genome structure and gene transcripts between SI3A and 0-613-2R were detected. The mitochondrial genome of SI3A has three circle molecules, including one main circle and two sub-circles, while 0-613-2R only has one circle. RNA-seq and qPCR analysis proved that orf606a and orf109a, which have a chimeric structure and transmembrane domain, were highly expressed in abortive anthers of SI3A. In addition, combining a comparative analysis of RNA-seq and full-length transcripts revealed that the complex I gene nad4 was at a lower expression level in SI3A than in its restorer and contained an intron retention splicing pattern. We think these differential genes might be the causable genes for sterility of the CMS line SI3A. In summary, we released the complete mitochondrial genome and full-length transcripts of the cotton CMS line SI3A and its restorer line in this study. Combining the comparative analysis of RNA-seq and full-length transcripts revealed the CMS-associated genes. We think this study provides new insight into the molecular basis of the nuclear-cytoplasmic interaction mechanism, and the identified CMS genes are important sources for cross-breeding of cotton by precise design in the future.