Organelle genome-based markers in deciphering mitonuclear conflict displaying floral malformations and distinguishing cytoplasm types in snowball cauliflower

Snowball cauliflower (Brassica oleracea var. botrytis L.) is an important member of the cole group of vegetables. The cultivation of hybrids is remunerative in cauliflower and cytoplasmic male sterility (CMS) is an important genetic mechanism for hybrid breeding. The CMS in angiosperms is mainly the consequence of mitonuclear intergenomic conflict and different cytoplasms are associated with an array of floral deformities. Therefore, it is essential to distinguish different cytoplasm types in cauliflower. The mitotype-specific mt-DNA markers are instrumental in differentiating cytoplasm types in angiosperms. The prevalence of autoplasmic and alloplasmic mitonuclear intergenomic incompatibilities yields complex floral malformations. In this context, the utility of mitochondrial DNA markers was illuminated in determining cytoplasm types in snowball cauliflowers and revealed epistatic effects of mitonuclear conflict affecting floral phenotypes. The genomic DNA isolation of cauliflower cytolines was done by the CTAB method. The PCR amplification with the primers specific to orf-138 revealed the presence of Ogura cytoplasm in the CMS lines of Indian cauliflower. The mt-SSRs (BnTR4 and orf125) depicted the polymorphism within the orf-138 sequence. The InDels (insertion/deletions) of 51 nucleotides were found to be linked with such cytoplasmic genetic variations as revealed by polymorphic sequence analysis. The influence of the cytoplasm on varying nuclear-genetic backgrounds caused floral deformities like reduction in the size of petals and sepals, fused flowers, splitting of style, flowers devoid of non-functional stamens, and conversion of stamens to petaloid structures. These deformities caused dysplasia of floral reproductive organs and reduced the nectar volume and seed yield. The current investigation has identified useful marker to identify the cytoplasmic lines with floral malformations. The study opened new horizons to develop ideal CMS lines and making hybrid breeding in cole vegetables remunerative to improve the economic status of farmers.