Gene flow enhances genetic diversity and local adaptation in Pyropia yezoensis populations

Pyropia yezoensis , a vital intertidal seaweed, plays a crucial role in the preservation of marine biodiversity. In recent years, the rapid expansion of its cultivation has raised concerns regarding the sustainability of seaweed aquaculture practices. However, research on gene exchange among P. yezoensis populations remains limited. In this study, we conducted a comprehensive analysis of gene flow using 228 whole-genome resequencing samples from key wild and cultivated P. yezoensis populations in China, as well as populations from Japan. We identified seven potential gene flow events, with gene flow regions encompassing 0.3%–25.43% of the genome. Genetic analysis revealed that these genomic regions were characterized by high genetic diversity, low genetic differentiation, and increased coding DNA sequence (CDS) density and guanine-cytosine (GC) content. Moreover, 53% of these regions contain at least one signal of selection, with genes involved in RNA and protein processing, transport, cellular homeostasis, and stress response functions associated with thallus growth, development, and stress resistance suggesting a role in environmental adaptability and artificial selection. Notably, we found that the genetic load in cultivated populations was significantly higher than in wild populations; fortunately, gene flow was not the primary factor driving this phenomenon. On the contrary, we found that gene flow events in two trios significantly reduced the genetic load caused by loss-of-function mutations. These findings enhance our understanding of intraspecific gene flow in seaweeds and provide valuable insights for the sustainable cultivation of seaweed aquaculture. • Seven instances of gene flow were identified between cultivated and wild populations of Pyropia yezoensis. • Gene flow introduced new variation into populations without significantly increasing their genetic load. • Studying gene flow enhances desired traits while safeguarding local gene pools and ecological balance.