Localization of a Dwarfing Mutation in Upland Cotton Using InDel Markers Based on Genome Re-Sequencing Data

Objective] InDel markers that were developed by comparing whole genome re-sequencing data were used to map the AS98 gene of a dwarf mutant of upland cotton (Gossypium hirsutum L.). Method] An F2 segregation population was constructed from an upland-cotton dwarf mutant (AS98) and its wild type (LHF10), and InDel markers were developed based on genome re-sequencing data from the two parents. The InDel markers and the F2 generation were then used to map the AS98 gene of the dwarf mutant. Result] A total of 114 InDel markers located in a previous mapping region were screened and used to genotype 223 F2 individuals. Ultimately, phenotypic data and 20 polymorphic primer pairs were used to construct a genetic linkage map. Molecular marker analysis mapped AS98 within a 6.9 cM distance of the marker InDel-50 on chromosome D12. Conclusion] This study has demonstrated the feasibility of using InDel markers developed from re-sequencing data for gene localization in isolated populations derived from upland cotton dwarf materials. The resulting gene map provides a basis for future fine mapping and molecular-assisted selection breeding.