Candidate gene identification for soybean dwarf mutant df1

Genetic mutations can be induced by external physical and chemical factors. This chromosomal genomic change not only creates new genetic variation materials for genetic improvement and molecular breeding of plants, but also serves as an important technical tool for studying gene function. In this study, a dwarf mutant, df1, was identified in the mutant library generated by gamma radiation of the widely cultivated cultivar Heihe 43 in Northeast China. Genetic analysis indicated that the df1 mutation is controlled by a single recessive gene. By analyzing the resequencing data of df1 and wild-type bulked pools sampled from a segregating line using the BVF-IGV pipeline, a large fragment deletion containing 69 genes on chromosome 1 is identified as the causal genetic factor for the df1 mutation. Association analysis using molecular markers derived from the large fragment deletion and transcriptome analysis of RNA-seq data of bulked df1 and wild-type supports the above conclusion. Twenty-six candidate genes including Glyma.01G066600 are finally determined by combined analysis of gene expression profiles and over 5000 cultivars from the public database. The results of this study could facilitate the cloning of the functional gene for df1 mutation through fine-mapping and understanding of its molecular mechanism in regulating plant growth and development.