Identification of candidate thin blade-related SNPs and genes in Pyropia haitanensis

Pyropia haitanensis , an economically important species of red algae, is widely cultivated in China. Agronomic traits of P. haitanensis , particularly blade thickness, influence product quality and processing methods. This study aimed to identify growth-related single nucleotide polymorphisms (SNPs) and candidate genes for thin blades using genome-wide association studies (GWAS) and transcriptome analysis. A total of 100 samples were sequenced, yielding 224,494 high-quality SNPs. GWAS identified 99 significant loci related to blade length, width, weight, and thickness. Transcriptome analysis revealed eleven annotated genes associated with thickness, including the triose-phosphate isomerase gene ( PhTPI ) that demonstrated significant upregulation in thicker strains. Integrative KEGG and GO pathway analyses highlighted enrichment in carbon metabolism, glycolysis/gluconeogenesis, and photosynthesis-related pathways, indicating their potential roles in regulating these traits. The TPI gene was validated by qRT-PCR, confirming its association with the variation in blade thickness. These findings provide a foundation for the molecular breeding of P. haitanensis with thin blades, thereby enabling enhanced precision in genetic improvement for better economic and processing outcomes. • The study presents the first GWAS analysis of economically important traits of Pyropia haitanensis . • In total, 99 loci and 34 genes related to blade thickness were identified. • The association of PhTPI with variation in blade thickness was verified. • The roles of carbon metabolism and agar synthesis in blade thickness are highlighted. • The results provide precise targets for molecular breeding of P. haitanensis .