Pan-Family Analysis of HAK/KUP/KT Potassium Transporters in Brassica napus Prioritizes a Candidate Locus Associated with Salt-Related Variation

The HAK/KUP/KT family represents a major group of plant potassium transporters involved in K+ uptake, ion homeostasis and stress responses. However, the accession-level diversity of HAK/KUP/KT genes in Brassica napus remains insufficiently characterized. In this study, we performed a pan-family analysis of HAK/KUP/KT genes across eight B. napus accessions. A total of 269 annotated HAK/KUP/KT family members were identified and classified into core, soft-core, dispensable and private orthogroups based on their representation across the analyzed genome annotations. Phylogenetic analysis grouped these proteins into four major clades together with reference HAK/KUP/KT members from Arabidopsis thaliana and rice. Ka/Ks analysis indicated that HAK/KUP/KT orthogroups were predominantly under purifying selection, while accession-variable orthogroups showed greater variation in sequence conservation. Gene structure, conserved domain, motif and predicted promoter cis-element analyses revealed conserved transporter-related protein features together with orthogroup-level structural and sequence variation. Expression profiling using the ZS11 BnIR dataset further revealed tissue-, hormone- and stress-responsive expression patterns among ZS11 HAK/KUP/KT genes. By integrating expression features, predicted promoter information, evolutionary characteristics, published salt GWAS context and BnVIR haplotype–phenotype information, BnaA08T0085800ZS was prioritized as a candidate locus located near salt-associated variation. This study provides a pan-genome perspective on HAK/KUP/KT family diversity in B. napus and establishes a framework for prioritizing candidate genes for future functional investigation.