Identification of Quantitative Trait Loci and Development of Molecular Markers Associated With Yield‐Related Traits in Pyropia haitanensis Through Genome‐Wide Association Studies

ABSTRACT

Pyropia/Porphyra algae are an important mariculture species, yet genome‐wide association studies (GWAS) on agronomic traits remain scarce. To bridge this gap, we conducted a comprehensive genetic analysis of 280 double‐haploid offspring strains derived from a previously constructed population. Eleven phenotypic traits—including thallus length, width, fresh weight, and maturity days—were systematically recorded, with heritability ranging from 0.08 to 0.39, except for thickness (0.57). Whole‐genome sequencing and GWAS identified 454 candidate genes (37 annotated), with major loci predominantly clustered on chromosome 4, collectively explaining 7.00%–58.02% of phenotypic variation. Sequence site validation revealed that RPN5 (encoding 26S proteasome regulatory subunit N5) might control thallus length, a C/G mutation at Chr4:4,319,644 (G for long, C for short); DWF1 (encoding Delta24‐sterol reductase) might regulate thallus maturation, a T/G mutation at Chr4:4,485,590 (T for early, G for late). Additionally, physiological phenotypic analysis combined with real‐time quantitative PCR suggested that PhmIDH might regulate thallus thickness by controlling the synthesis of cell wall components. These findings provide functional markers and mechanistic insights to advance marker‐assisted breeding and genetic improvement in Pyropia haitanensis .