The bivalve Pinctada margaritifera exhibits three main transplant phenotypes derived from  the donor (from which a mantle graft tissue, the saibo, is excised), the recipient (into which  the saibo is implanted with a nucleus, leading to the formation of a pearl sac "chimera") and  the cultured pearls themselves. This first phenome study on the species derived from a large  experimental graft. Transplant phenotype was assessed at three scales: 1) macro, pearl size,  colour, grade, 2) micro, pearl surface microstructure, and 3) molecular, biomineralisation  gene expression level in saibo and pearl sac tissues. From donor to pearl, the phenome  revealed fine variations of quality traits dependent on the position on the mantle where the  saibo was cut, whose variation could overlap with inter-individual donor phenotype  differences. A single donor phenotype could therefore produce multiple pearl phenotypes at  the scale of the saibo position, mirroring its original activity at the mantle position level and  the colour and shape of the shell. This phenome study provides essential information on  phenotypic trait architecture enabling us to explore and explain the main biological functions  and pave the way for a phenomic project on P. margaritifera that could benefit the pearl  industry.