Molecular delineation, development and validation of functional markers for brachytic2 (br2) gene governing dwarfing...

Globally, dwarfing genes have significantly enhanced cereal yield by several fold. Recessive brachytic2 (br2) in maize possesses enormous potential to prevent lodging and ensure high plant density, thereby increasing productivity. However, commercial use of dwarfing br2 gene remains unexplored due to lack of breeding priorities combined with need for higher biomass present in tall hybrids. The ATP-binding cassette (ABC) transporter encoded by Br2 allele regulates the polar auxin transport, the disruption of which will result in dwarfism. Here, we report two novel br2 dwarf mutants (br2-mutant1 and br2-mutant2) validated through sequencing the entire 7745 bp of Br2 gene across diverse inbreds, identifying a set of 131 SNPs and 85 InDels within the gene. Of these, a 17 bp deletion in exon-3 at position 2231 bp, and a 4763 bp insertion in exon-5, characterised as Ty1-copia LTR retrotransposon differentiated br2-mutant1 and br2-mutant2, respectively, from the wild-types. Moreover, the mutant proteins showed distorted nucleotide binding domains. We developed and validated two breeder-friendly PCR-based functional markers, MGU-br2M1 and MGU-br2M2, among 48 diverse inbreds and four F₂ populations, revealing a segregation ratio of 1 (Br2Br2): 2 (Br2br2): 1 (br2br2) in F₂ populations. Furthermore, 46 haplotypes of Br2 among 48 diverse inbreds were elucidated using 15 gene-based InDel markers. The study also identified 25 paralogues of Br2 gene. This is the first report on the development and validation of co-dominant functional molecular markers of br2 gene that hold significance in genomics-assisted breeding for developing dwarf maize hybrids.

The online version contains supplementary material available at 10.1007/s12298-025-01685-0.