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QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.)


Sweet cherry (Prunus avium L.) skin and fruit colors vary widely due to differences in red and yellow pigment profiles. The two major market classes of sweet cherry represent the two color extremes, i.e., yellow skin with red blush and yellow flesh and dark mahogany skin with mahogany flesh. Yet, within these extremes, there is a continuum of skin and flesh color types. The genetic control of skin and flesh color in sweet cherry was investigated using a quantitative trait locus (QTL) approach with progeny derived from a cross between cherry parents representing the two color extremes. Skin and flesh colors were measured using a qualitative color-card rating over three consecutive years and also evaluated quantitatively for darkness/lightness (L*), red/green (a*), and yellow/blue (b*). Segregations for the color measurements (card, L*, a*, and b*) did not fit normal distributions; instead, the distributions were skewed towards the color of the dark-fruited parent. A major QTL for skin and flesh color was identified on linkage group (LG) 3. Two QTLs for skin and flesh color were also identified on LG 6 and LG 8, respectively, indicating segregation for minor genes. The significance and magnitude of the QTL identified on LG 3 suggests the presence of a major regulatory gene within this QTL interval. A candidate gene PavMYB10, homologous to apple MdMYB10 and Arabidopsis AtPAP1, is within the interval of the major QTL on LG 3, suggesting that PavMYB10 could be the major determinant of fruit skin and flesh coloration in sweet cherry.

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This project was supported in part by the National Research Initiative Competitive Grant 2005-35300-15454 of USDA's National Institute of Food and Agriculture, a post-Doctoral Fellowship to A. Khan from the Higher Education Commission, Pakistan, and a PhD Excellence Award to J. Bushakra from Plant and Food Research, NZ. We thank an anonymous reviewer for constructive comments.

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Corresponding author

Correspondence to Amy F. Iezzoni.

Additional information

Communicated by: E. Dirlewanger

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Below is the link to the electronic supplementary material.

Supplemental Figure 1

Skin color 1 (SC1), skin color 2 (SC2), and flesh color (FC) for EF and NY (DOC 40 kb)

Supplemental Figure 2

Locations of QTLs on LG3 for color-card data of 2006, 2007, and 2008 for SC1 (darkest location of the fruit skin), SC2 (lightest location of the fruit skin) and FC (flesh color) using the multiple QTL mapping method. 1-LOD and 2-LOD support intervals of each QTL are marked by thick and thin bars, respectively. The percentage variability explained by the QTL (R2) and the level of QTL significance in number of asterisks (***LOD value significant at P < 0.05 genome-wide based on 1,000 permutation tests) are shown with the QTLs (DOC 44.5 kb)

Supplemental Table 1

Description of color-card categories for sweet cherry fruit skin color used for QTL analysis. (DOC 34.5 kb)

Supplemental Table 2

Description of color-card ratings for sweet cherry fruit flesh color used for QTL analysis. (DOC 32.5 kb)

Supplemental Table 3

Mean, standard deviations (in parentheses) and minimum and maximum values for skin color 1 (SC1), skin color 2 (SC2), and flesh color (FC) values for ‘Emperor Francis’ (EF) and ‘New York 54’ (NY) in 2008. (DOC 37.5 kb)

Supplemental Table 4

The progression of fruit skin and flesh color over four harvest dates in 2008 for “Emperor Francis” (EF) and “New York 54” parents. (DOC 59 kb)

Supplemental Table 5

The progression of fruit skin and flesh color over four harvest dates in 2008 for NY × EF progeny sorted into blush and mahogany color classes (DOC 50 kb)

Supplemental Table 6

Mean L* and b* values for skin color 1 (SC1) for NY×EF progeny in the different haplotype classes for the QTL region on linkage group 6. Numbers in parenthesis are the number of progeny individuals (DOC 33.5 kb)

Supplemental Table 7

Mean a* of flesh color (FC) of different haplotype classes for the QTL region on linkage group 8. Numbers in parenthesis are the number of progeny individuals (DOC 32 kb)

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Sooriyapathirana, S.S., Khan, A., Sebolt, A.M. et al. QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.). Tree Genetics & Genomes 6, 821–832 (2010).

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  • Rosaceae
  • Anthocyanin
  • L*
  • a*
  • b* color measurements