The Evolution of Type II MIKCc MADS-Box Genes in Legumes: An Overview of Their Developmental Functions
TL;DR
A comprehensive phylogenetic and comparative genomic analysis of MIKCc MADS-box genes across Fabaceae, sampling representatives from three of the six subfamilies and spanning major evolutionary lineages suggests that differential retention and loss of duplicated MADS-box genes have played a central role in shaping floral and inflorescence diversity, phenological variation, and ecological adaptation in legumes.
Abstract
Fabaceae (Leguminosae) is one of the most species-rich and ecologically important angiosperm families, encompassing extraordinary diversity in growth form, floral architecture, fruit morphology, and symbiotic nitrogen fixation. Despite the central role of MADS-box transcription factors in controlling key developmental processes underlying these traits, their evolutionary history in legumes remains poorly understood. Here, we present a comprehensive phylogenetic and comparative genomic analysis of MIKCc MADS-box genes across Fabaceae, sampling representatives from three of the six subfamilies and spanning major evolutionary lineages using genomic and transcriptomic data. Our analyses reveal that all type II MIKCc MADS-box gene lineages known from angiosperms are represented in Fabaceae, except for TDR8 homologs. However, several clades, including MAF/FLC , AGL16/17/ANR1 , ABS , and XAL1 , are consistently poorly represented, suggesting lineage-specific constraints or gene loss. While numerous MADS-box genes remain single copy across most legumes, others show duplications prior to the diversification of Fabaceae, including AGL6 , AGL24b , PI , SEP , and SOC1 . Subfamily-specific expansions were detected in key developmental regulators, with duplications of AGL14/19 - like , FUL , TM6 , and SOC1 in Caesalpinioideae, and AG , AGL6 , AGL79 , AP1 , FUL , and SEP lineages in Papilionoideae. These patterns coincide with documented whole-genome duplication events in both subfamilies. In addition, pervasive gene duplication in Glycine reflects a genus-specific polyploidization history. Together, these results suggest that differential retention and loss of duplicated MADS-box genes have played a central role in shaping floral and inflorescence diversity, phenological variation, and ecological adaptation in legumes. By integrating phylogenetic patterns with existing functional data, this study provides an evolutionary framework for understanding how MADS-box gene diversification has contributed to the remarkable developmental and adaptive radiation of Fabaceae.