Genome-wide Association Study of Strawberry Fruit Quality-related Traits Using a MAGIC Population Derived from Crosses Involving Six Strawberry Cultivars

• Published in: Horticulture journal 2020, Vol.89(5), pp.553-566
• Main Authors: Wada, Takuya, Tsubone, Masao, Mori, Miyuki, Hirata, Chiharu, Nagamatsu, Shiro, Oku, Koichiro, Nagano, Soichiro, Isobe, Sachiko, Suzuki, Hideyuki, Shimomura, Katsumi, Baba, Noriko, Hirashima, Keita, Sueyoshi, Takayuki, Obu, Ko-ichi, Ikegami, Hidetoshi, Uchimura, Yosuke, Hayashida, Tatsuya
• Format: Article
• Language: English
• Subjects: Acidity; allelic effect; anthocyanin; Anthocyanins; Chromosomes; Color; Conformation; Correlation coefficient; Correlation coefficients; Cultivars; Cultivation; Expressed sequence tags; Firmness; Food quality; fruit color; Fruit cultivation; fruit firmness; Fruits; Gene mapping; Genomes; Genotyping; Markers; Nucleotide sequence; QTL; Quantitative trait loci; Strawberries
• ISSN: 2189-0102; 2189-0110
• DOI: 10.2503/hortj.UTD-180

Cultivated strawberry is one of the important commercial fruits not only in Japan, but around the world. Even so, analyzing regions responsible for fruit quality traits of cultivated strawberry has been very challenging due to the alloploidy and octoploidy of genome conformation. In order to solve this problem, we previously developed a strawberry multi-parent advanced generation inter-cross (MAGIC) population derived from crosses involving six cultivars. Here, we performed genotyping of the MAGIC population with simple sequence repeat (SSR) markers, which were generated from an expressed sequence tag site, and conducted a genome-wide association study of 13 strawberry fruit quality-related traits to reveal associated quantitative trait loci (QTLs). Correlation coefficients among fruit color-related traits, such as fruit surface color (FSC), fruit surface anthocyanin content (FSA), and fruit flesh anthocyanin content (FFA) were relatively higher, but FSC, FSA, and FFA did not show any higher correlation with other traits. Fruit weight (FW), FSC, and fruit firmness, including whole fruit firmness (WFF), fruit surface firmness (FSF), and fruit flesh firmness (FFF), indicated higher year to year correlation coefficients than other fruit quality-related traits. Among FW, FSC, and WFF, there were only two QTLs for FW, five for FSC, and 38 for WFF (the most) and they were detected on all chromosomes. QTLs for some traits shared common flanking simple sequence repeat markers, and allelic differences of one marker affected the variation of other traits. QTLs for fruit firmness were most frequently detected, followed by those for SSC and titratable acidity (TA). Allelic differences in these QTLs negatively affected FSC, the fruit surface anthocyanin content (FSA), and fruit flesh anthocyanin content (FFA), implying that alleles which increase fruit firmness, SSC, and TA lighten fruit color. Similarly, QTLs for FSC, FSA, and FFA mostly negatively affected FSF, FFF, SSC, and TA and did not affect WFF. This indicated that simultaneous improvement in fruit firmness, SSC, and TA is possible with many markers, but improving fruit firmness and deepening fruit color are highly challenging.