Insights into the genetic structure and domestication patterns in cultivated populations of Neopyropia yezoensis

Abstract

Neopyropia yezoensis is a commercially important seaweed that has been subjected to industrial cultivation for more than six decades, making it a longstanding and economically valuable marine resource. However, there is a paucity of genomic information on its genetic structure and underlying domestication patterns. We examined 124 N. yezoensis samples collected from China and Japan, and identified 1,004,593 high-quality single-nucleotide polymorphisms (SNPs). Our results indicated that the genetic background of the cultivated population in China is complex, with evidence of germplasm mixing within the same cultivation area. We identified the genomic signatures and SNP hotspots of domestication related to growth, reproductive regulation, and improved stress resistance, thereby highlighting potential target genes for future nori breeding programs. Finally, two SNP loci, which are significantly associated with length, were identified through a genome-wide association study and were located within the region of selective sweeps in cultivated populations. Functional analysis indicated that one of the SNP loci might be involved in the regulation of flavin metabolism and transport. Our results will help elucidate the genetic diversity and evolutionary history of nori, and guide future breeding and conservation strategies.