Zinc Finger Proteins ( ZFP ) represent a crucial class of transcription factors in plants. In this study, we developed the Pan-Gene Family Analysis Toolkit (PGFAT) and utilized it to perform a genome-wide identification of ZFP across 19 representative plant genomes, including Brassica napus , and identified a total of 7667 ZFP genes. Comparative genomic analysis revealed a continuous expansion in the C3HC4 subfamily, whereas the C2HC5 subfamily exhibited high conservation. Notably, B. napus harbored the largest ZFP gene family among the species examined. As an important oilseed crop, B. napus serves as a major source of high-quality edible oil rich in unsaturated fatty acids, as well as a raw material for biodiesel production. PGFAT was further applied to integrate 11 B. napus genomes to construct a pan-genome map, which recovered 11,779 ZFP members. Pan-genomic analysis elucidated distinct evolutionary features and functional divergence between core and non-core genes. A novel univariate association analysis strategy based on copy number variation (CNV) and presence/absence variation (PAV) was used to identify a key orthologous group significantly correlated with seed weight, OG0000169 (homologous to Arabidopsis CDF1 ). Subsequent in-depth analysis revealed a distinct pattern in which gene copy number expansion and adaptive amino acid substitutions synergistically influence seed development. This study provides new insights into the evolutionary plasticity of the ZFP superfamily and offers a robust computational framework for the efficient mining of trait-associated genes in the genomic-assisted breeding of B. napus . • Development of the Pan-Gene Family Analysis Toolkit (PGFAT) for evolutionary surveys and pan-genomic analyses. • Comparative and duplication analyses were conducted to provide insights into the evolution of the ZFP Superfamily. • Core and non-core ZFP genes in B. napus showed evolutionary and functional divergence. • CNV- and PAV-based association analyses identified candidate genes for key agronomic traits.
Qin et al. (Fri,) studied this question.