Strawberry fruit shape: quantification by image analysis and QTL detection by genome-wide association analysis

• Published in: Breeding Science Vol. 71; no. 2; pp. 167 - 175
• Main Authors: Nagamatsu, Shiro, Tsubone, Masao, Wada, Takuya, Oku, Koichiro, Mori, Miyuki, Hirata, Chiharu, Hayashi, Atsushi, Tanabata, Takanari, Isobe, Sachiko, Takata, Kinuko, Shimomura, Katsumi
• Format: Journal Article
• Language: English
• Published: Tokyo Japanese Society of Breeding 01.01.2021; Japan Science and Technology Agency
• Subjects: Association analysis; Breeding; Coefficient of variation; Cultivation; elliptic Fourier descriptor; Fragaria ananassa; Fruit cultivation; fruit morphology; Fruits; Gene mapping; Genome-wide association studies; genome-wide association study; Genomes; Image analysis; Image processing; Marker-assisted selection; Morphology; Phenotypes; Population studies; principal-components analysis; Quantitative analysis; Quantitative trait loci; Research Paper; Strawberries; strawberry; Target detection
• ISSN: 1344-7610; 1347-3735
• DOI: 10.1270/jsbbs.19106

Fruit shape of cultivated strawberry (Fragaria × ananassa Duch.) is an important breeding target. To detect genomic regions associated with this trait, its quantitative evaluation is needed. Previously we created a multi-parent advanced-generation inter-cross (MAGIC) strawberry population derived from six founder parents. In this study, we used this population to quantify fruit shape. Elliptic Fourier descriptors (EFDs) were generated from 2 969 two-dimensional binarized fruit images, and principal component (PC) scores were calculated on the basis of the EFD coefficients. PC1–PC3 explained 96% of variation in shape and thus adequately quantified it. In genome-wide association study, the PC scores were used as phenotypes. Genome wide association study using mixed linear models revealed 2 quantitative trait loci (QTLs) for fruit shape. Our results provide a novel and effective method to analyze strawberry fruit morphology; the detected QTLs and presented method can support marker-assisted selection in practical breeding programs to improve fruit shape.