Intraspecific genome size variation in Rorippa indica reveals a tropical adaptation by genomic enlargement

Genome size exhibits substantial variation across organisms, but the underlying causes and ecological consequences remain unclear. While interspecific comparisons have suggested selective pressures against large genomes, intraspecific variation has been less explored. Here, we investigate genome size variation within the hexaploid yellowcress herb, Rorippa indica, by integrating flow cytometry, plastomic phylogeography, genomic repeat profiling, and reciprocal common garden experiments. We analyzed 192 accessions from 83 natural populations, revealing a 128 Mb range in genome size. Plastome haplotype analysis identified a haplogroup that shifted niches to tropics and evolved larger genomes. A strong correlation was found between larger genomes and tropical habitats characterized by higher temperatures and lower seasonality. Genomic repeat content, particularly 45S rDNA and Ty1-copia transposable elements, was associated with larger genomes. Reciprocal transplantation experiments confirmed the adaptive nature of large genomes in tropical environments, with individuals exhibiting lower growth rates but higher fecundity. Our findings support the large genome selection hypothesis, suggesting that genome size enlargement, driven by genomic repetitive elements, can be an adaptive response to high temperatures of tropics. As global warming continues, plants with larger genomes may exhibit slower growth but increased reproductive output, potentially impacting ecosystem dynamics and agricultural productivity.