Pangenome-wide identification of the actin-depolymerizing factor (ADF) gene family across eight Brassica napus genomes and haplotype analysis variation under salt–alkali stress

Actin-depolymerizing factors (ADFs) are important regulators of actin cytoskeleton dynamics and play critical roles in plant development and stress responses. However, the evolutionary patterns and functional diversity of the ADF gene family within the Brassica napus pangenome remain largely unexplored. In this study, we performed a comprehensive pangenome-scale analysis of ADF genes across eight B. napus genomes and identified 263 BnADFs , with gene numbers ranging from 27 to 36 among accessions. Orthology analysis grouped these genes into 21 orthologous clusters, which were classified into nine core, three soft-core, five shell, and four cloud groups, revealing a continuum of conservation across the pangenome. Core genes showed stronger signatures of purifying selection and more conserved gene structures, whereas dispensable genes exhibited greater structural variation and presence–absence polymorphism. Transposable element insertions and structural variants were frequently detected at ADF loci, suggesting that genome structural variation has contributed to the diversification of this gene family. Expression profiling revealed tissue-specific expression patterns and identified several BnADFs that were induced under salt stress, particularly in roots. Four representative genes were independently examined by qRT-PCR in Chuanyou 83 and showed salt-responsive transcription. Using the 2,311-accession population variation resource integrated in BnIR, sequence polymorphism analysis of these four candidate loci identified 144 variants and distinct major haplotypes, several of which were associated with differences in yield performance under salt–alkali conditions. Our results provide new insights into the evolutionary dynamics and functional diversification of BnADFs in the rapeseed pangenome. The favorable haplotypes identified here represent promising targets for the genetic improvement of salt-tolerant rapeseed cultivars.