A single base deletion in exon 2 of Hd1 delineates monogenic recessive photoperiod insensitivity in an aromatic Joha rice mutant.

Abstract A photoperiod-insensitive mutant was isolated from a gamma rays-induced M₂ population of a Joha rice landrace, Kon Joha. The mutant was found to be unique, and the induced photoperiod insensitivity was conditioned by a single recessive gene. Towards mutant gene tagging, 402 SSR and InDel markers were screened, and later polymorphic markers were used in bulk segregant analysis (BSA) in the F₂ population of 'mutant x Kalijeera (distant parent)'. BSA identified an association of an SSR marker RM527 with this mutant trait. This marker is present in chromosome 6 of the rice genome. Including chromosome 6 specific SSR markers in polymorphic screening and BSA later identified another associated marker, RM19725, for the mutant trait. The genomic interval of RM527 and RM19725 harboured a photoperiod-insensitive gene, Hd1, in chromosome 6. Cloning and sequencing of Hd1 genomic fragments from parent and mutant revealed a single base deletion in exon 2, leading to a frameshift mutation in the Hd1 protein. Designing allele-specific primer pairs for the above mutation was crucial to detect a tight association of the Hd1 with the mutant trait in the homozygous mutant/parent type plants in the F₃ generation of the 'mutant x parent' population. The mutation in exon 2 leads to severe structural abnormalities in the CCT domain of the Hd1 protein that is critical in the interaction of repressing complex with conserved response element in the florigen gene under long-day conditions.