Intraspecific Genome Size Variation in <scp> <i>Rorippa indica</i> </scp> Reveals a Tropical Adaptation by Genomic Enlargement

Genome size exhibits substantial variation across organisms, but its causes and ecological consequences remain incompletely understood. While interspecific comparisons have suggested selective pressures against large genomes, intraspecific variation has been less explored. Here, we investigate genome size diversity within the hexaploid yellowcress Rorippa indica by integrating flow cytometry, plastome phylogeography, genomic repeat profiling, and reciprocal common garden experiments. Across 192 accessions from 83 natural populations, genome size ranged from 764 to 892 Mb, a 15.8% difference relative to the mean (812 Mb), representing the widest range yet reported within Rorippa. Plastome haplotype analysis revealed that lineages colonizing tropical habitats tended to retain or enlarge genome size, whereas northern lineages exhibited reductions. Genome size was significantly correlated with tropical environments characterized by higher winter temperatures and reduced seasonality. Variation was largely attributable to repetitive DNA, with 45S rDNA and Ty1-copia retrotransposons (Bianca) explaining up to 15.5% and 26.1% of the differences, respectively. Reciprocal transplantation experiments demonstrated that plants with larger genomes had higher fitness in tropical conditions, producing 32% more fruits. These findings indicate that genome size in R. indica is not a neutral trait but is selectively expressed, with both shrinkage and enlargement representing adaptive strategies under contrasting environments. We propose that genome enlargement, driven primarily by specific repetitive elements, constitutes an adaptive response to stable tropical climates. As global warming progresses, species with larger genomes may exhibit slower growth but increased reproductive output, with broad implications for ecosystem dynamics and agricultural productivity.