A Theoretical Framework for Understanding Polyploidy Evolution and Its Implications for Crop Improvement in African Yam Germplasm

African yams (Dioscorea spp.) are among the most genetically complex crop species, with polyploidy, hybridisation, and apomixis creating remarkable genome complexity that presents both challenges and opportunities for plant breeding, and developing an original theoretical framework for understanding polyploidy evolution in Nigerian Dioscorea germplasm constitutes an important contribution to crop evolution and breeding science. This study developed an original theoretical framework for polyploidy evolution and its breeding implications in African yam germplasm collected from South East and South South Nigeria. A combined evolutionary genomics and plant breeding theory methodology was employed. Flow cytometry was used to estimate genome size and ploidy levels of 80 accessions collected from Benue, Anambra, Imo, and Cross River States. Phylogenomic analysis using whole plastome sequences and transcriptome-derived nuclear gene datasets characterised evolutionary relationships and polyploidisation events. Meiotic chromosome behaviour was characterised in high-polyploid accessions to assess fertility and recombination potential. The flow cytometry results confirmed ploidy levels from diploid (2x=20) to dodecaploid (12x), with tetra- and hexaploids most frequent in D. rotundata accessions. Phylogenomic analysis provided original evidence for at least two independent polyploidisation events within the D. cayenensis-rotundata complex, with one Benue-origin hexaploid cluster showing evidence of allopolyploid origin combining parental genomes from D. abyssinica and D. praehensilis. The original Yam Polyploidy Breeding Implications Framework proposes strategies for exploiting polyploid heterosis while managing fertility costs. Expert review confirmed the study's original contribution to crop evolution science.

Keywords: yam polyploidy, Dioscorea evolution, crop improvement, genome complexity, African yam genetics