Mutation of the VAR2 gene plays a role as one of the causes of leaf variegation in the moth orchid Phalaenopsis ‘Sogo Vivien’

Phalaenopsis ‘Sogo Vivien’ is a hybrid orchid that can produce a mutant with foliar variegation. Variegation can be divided into structural-type and pigment-type variegation. Foliar variegation was mostly caused by mutations in plastid genes. Even though there are various studies on foliar variegation in other plants, studies on foliar variegation in orchids are quite limited. This study aimed to determine the variegated leaf phenotype characteristics and their cause in P. ‘Sogo Vivien’. This study observed the anatomy of variegated leaves by comparing the green and white parts of the leaf, measured the concentration of chlorophyll pigments, and detected leaf starch content between both parts. In addition, polymorphism analysis was also performed on the VAR2 gene partial sequences. Based on leaf anatomy structure, the difference between variegated zones is only in the number of chloroplasts, the diameter of parenchyma cells, and chloroplasts. The chloroplast diameter within the white part is smaller than the green part. The chloroplasts’ diameters in the green part are two times larger than the white part, with four times more in amount. The two parts were formed due to differences in the distribution pattern of functional chloroplasts in the leaves. The concentration of chlorophyll in the green part is higher than in the white part, a characteristic of the chlorophyll-type variegation. The green parts have more starch grains than the white parts. Stomata distance between variegated zones on the abaxial side is different, and it was suggested as a distinctive character between variegated zones. A thymine insertion in exon 1 contributed to nonsense and missense mutations on the VAR2 gene isolated from the white part. This mutation caused the amino acid motif to change from KAKFQ to KA—Q. This mutation is suggested to cause the variegated leaf phenomenon in P. ‘Sogo Vivien’.