Glucose chains in starch are phosphorylated and contribute to structural stabilization. Phosphate groups contained in starch also play a role in retaining moisture. α-Glucan water dikinase 1 (GWD1) is involved in the phosphorylation of glucose chains in starch. In this study, we generated potato mutants of the
GWD1
gene using the CRISPR/dMac3-Cas9 system. Observation of the phenotypes of the
GWD1
-deficient mutants revealed their physiological roles in tuber starch formation. The 4-allele mutants showed growth retardation and a delay in tuber formation. A significant decrease in phosphorus content was detected in the tuber starch of the
gwd1
mutant. This mutant starch showed a higher amylose content than the wild-type starch, whereas its gelatinization temperature was slightly lower than that of the WT starch. The peak viscosity of the mutant starch was lower than that of the WT starch. These observations revealed that the starch of the
gwd1
mutants had peculiar and unique properties compared to those of WT,
sbe3
and
gbss1
mutant starches. The amount of tissue-released water due to freeze–thawing treatment was determined on tubers of the
gwd1
mutant and compared with those of WT and the other mutants. Significantly less water loss was found in the
gwd1
,
sbe3
and
gbss1
mutant tubers than in the WT tubers. Our results indicate that the
GWD1
gene is not only important for potato growth, but also largely effective for the traits of tuber starch.