Mitochondrial Genome Sequencing Reveals orf463a May Induce Male Sterility in NWB Cytoplasm of Radish

Abstract

Radish (Raphanus sativus L.) is an important root vegetable worldwide. The development of F1 hybrids, which are extensively used for commercial radish production, relies on cytoplasmic male sterility (CMS). To identify candidate genes responsible for CMS in NWB cytoplasm, we sequenced the normal and NWB CMS radish mitochondrial genomes via next-generation sequencing. A comparative analysis revealed 18 syntenic blocks and 11 unique regions in the NWB CMS mitogenome. A detailed examination indicated that orf463a was the most likely causal factor for male sterility in NWB cytoplasm. Interestingly, orf463a was identical to orf463, which is responsible for CMS in Dongbu cytoplasmic and genic male sterility (DCGMS) radish. Moreover, only structural variations were detected between the NWB CMS and DCGMS mitochondrial genomes, with no nucleotide polymorphisms (SNPs) or meaningful indels. Further analyses revealed these two mitochondrial genomes are coexisting isomeric forms belonging to the same mitotype. orf463a was more highly expressed in flower buds than in vegetative organs and its expression was differentially regulated in the presence of restorer of fertility (Rf) genes. orf463a was confirmed to originate from Raphanus raphanistrum. In this study, we identified a candidate gene responsible for the CMS in NWB cytoplasm and clarified the relationship between NWB CMS and DCGMS.

Appearance of male sterile and black radishes in the progeny of cross between <i>Raphanus raphanistrum</i> and <i>Raphanus sativus</i>

“…They observed that all six accessions of black Spanish radish possessed the orf463 gene ( Wang et al 2020 ). In addition to the cultivars mentioned above, orf463 has also been identified in R. raphanistrum ( Wang et al 2020 , Yamagishi et al 2019 ) and R. maritimus ( Wang et al 2020 ).…”

“…The cultivars had sequences that were identical to the orf463 sequence determined by Park et al (2013) ( Yamagishi et al 2019 ). Wang et al (2020) also observed that cultivars of black Spanish radish and a line of R. raphanistrum have sequences that are identical orf463 ( Wang et al 2020 ). However, the orf463 found in R. raphanistrum ( Yamagishi et al 2019 ) and in R. maritimus ( Wang et al 2020 ) had nine nucleotide substitutions, of which seven were not synonymous.…”

“…Interestingly, while orf463 was concentrated uniquely in the black radish cultivars belonging to the ‘Niger’ group, one line of the wild species, Raphanus raphanistrum , also possessed orf463 ( Yamagishi et al 2019 ). Recently, Wang et al (2020) demonstrated that all six varieties of Raphanus sativus var. niger (Black Spanish radish) possessed orf463 , and one line each of R. raphanistrum and Raphanus maritimus also possessed orf463 .…”

“…niger (Black Spanish radish) possessed orf463 , and one line each of R. raphanistrum and Raphanus maritimus also possessed orf463 . Furthermore, Wang et al (2020) demonstrated that NWB cytoplasm has a gene that is identical to orf463 , indicating that the same gene causes NWB CMS and DCGMS.…”

The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions

“…In other cases, species-specific mitochondrial open reading frames (ORFs) encoding for transmembrane proteins were found to be responsible for CMS [ 14 , 15 ]. According to the National Center for Biotechnology Information (NCBI) [ 16 ] CMS-related genes have been identified and deposited for at least 76 plant species, including cereals such as bread wheat ( Triticum aestivum ) [ 17 ], rice ( Oryza sativa ) [ 18 ], and maize ( Zea mays ) [ 19 ], and crops like stem mustard ( Brassica juncea ) [ 20 , 21 ], onion ( Allium cepa ) [ 9 ], pepper ( Capsicum annuum ) [ 5 ], radish ( Raphanus sativus ) [ 22 ], sunflower ( Helianthus annuus) [ 23 ], and carrot ( Daucus carota ) [ 11 ]. In fennel ( Foeniculum vulgare ), the presence of a naturally occurring NMS system has never been reported while several spontaneous CMS mutants have been discovered and exploited by breeders since the late 1960s [ 24 , 25 ].…”