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Hybridization involving non-aromatic HYVs improves yield with concomitant loss of quality. In this context, mutation breeding, a sustainable approach where genetic mutations are induced to create desirable traits, often provides useful allelic variation in specific morpho-agronomic traits. The present study delves into the genetic characterization of a photoperiod-insensitive mutant. As part of our mutation breeding programme, this mutant was isolated from a gamma ray-induced M<jats:sub>2<\/jats:sub> population of a\u00a0<jats:italic>Joha<\/jats:italic>\u00a0rice landrace,\u00a0<jats:italic>Kon Joha<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The mutant was unique, and a single recessive gene conditions the induced photoperiod insensitivity. Mutant gene tagging involved 402 SSR and InDel markers, and later polymorphic markers were used for bulk segregant analysis (BSA) in the F2 population of \u2018mutant\u00a0\u00d7\u00a0<jats:italic>Kalijeera<\/jats:italic>\u00a0(distant parent)\u2019. BSA revealed an association between the SSR marker RM527 and this mutant trait. This marker is present on chromosome 6 of the rice genome. Using chromosome 6-specific SSR markers in polymorphic screening and BSA revealed another associated marker, RM19725, for the mutant trait. The genomic interval between RM527 and RM19725 harbors a photoperiod-insensitive gene,\u00a0Hd1, on chromosome 6. Cloning and sequencing of\u00a0Hd1\u00a0genomic fragments from the parents and mutants revealed a single-base deletion in exon 2, leading to a frameshift mutation in the Hd1 protein. This mutation in exon 2 leads to severe structural abnormalities in the CCT domain of the Hd1 protein that is critical for the interaction of the repressing complex with conserved response elements in the florigen gene under long-day conditions, thereby causing photoperiod insensitivity.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The mutant's pleasant aroma and other quality characteristics, comparable to those of the parent cultivar, hold significant promise. They expand its potential use in a structured breeding programme aimed at developing high-value aromatic\u00a0<jats:italic>Joha<\/jats:italic>\u00a0rice. This rice, resilient to winter- and summer-growing environments and with broad seasonal adaptability, could revolutionize the rice market. The practical value of our research is underscored by this exciting possibility.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s40659-024-00553-7","type":"journal-article","created":{"date-parts":[[2024,11,30]],"date-time":"2024-11-30T01:24:50Z","timestamp":1732929890000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A single-base deletion in exon 2 of\u00a0Hd1\u00a0delineates monogenic recessive photoperiod insensitivity in aromatic\u00a0Joha rice: a novel allele for seasonal adaptability"],"prefix":"10.1186","volume":"57","author":[{"given":"Bodeddula Jayasankar","family":"Reddy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shreekant M.","family":"Baradkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamma V. S. 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