Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple

Abstract

The apple dwarfing rootstock 'Malling9' ('M9') has been used worldwide both to reduce scion vigour and as a genetic source for breeding new rootstocks. Progeny of 'M9' segregate for rootstock-induced dwarfing of the scion, indicating that this trait is controlled by one or more genetic factors. A quantitative trait locus (QTL) analysis of a rootstock population derived from the cross between 'M9' × 'Robusta5' (non-dwarfing) and grafted with 'Braeburn' scions identified a major QTL (Dw1) on linkage group (LG) 5, which exhibits a significant influence on dwarfing of the scion. A smaller-effect QTL affecting dwarfing (Dw2) was identified on LG11, and four minor-effect QTLs were found on LG6, LG9, LG10 and LG12. Phenotypic analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing, and that Dw1 has a stronger effect than Dw2. Genetic markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion growth. The majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and Dw2. This suggests that most apple dwarfing rootstocks have been derived from the same genetic source.

Figure 1

Three-year-old compound trees with ‘Braeburn’ scions grafted to sibling rootstocks from a segregating population of ‘M9’ × ‘R5’. The tree on the left is grafted to a rootstock with Dw1 and Dw2, the one on the right has a rootstock with neither. Red arrowheads indicate graft junction, 2-m measure for scale.

Figure 2

Representation of rootstock QTLs influencing dwarfing and flowering traits on the LGs of ‘M9’ and ‘R5’. The solid part of the bars indicates the most likely position of the QTL and the lines represent the confidence interval. Traits phenotyped are listed in Table 1. The QTLs identified from ‘M9’ are in blue and located on the left side of the LGs, and the QTLs identified from ‘R5’ are in orange and located on the right side of the LGs. The markers flanking Dw1 and Dw2 are underlined and Pyrus SSR markers are indicated in red. Scale bar indicates genetic distance in cM. Details on the markers used to construct the ‘M9’ and ‘R5’ genetic maps are given in Celton et al. cM, centiMorgans.

Figure 3

Number of trees in each flowering class and composition of classes by Dw1 and Dw2 genotype. Flowering was assessed by estimating the total number of flower clusters on each tree in the spring of year 2, and placing them into quartiles relative to the most highly floral trees, i.e., 1%–25%, 26%–50%, 51%–75% and 76%–100%. Trees with no flowers were also recorded. Data are from 109 trees from the first population, replicate 1.

Figure 4

Average year 7 TCA of trees in each genotypic class. The number of individuals in each class is given in parentheses; error bars indicate standard error. Average TCAs were compared to the group with neither Dw1 nor Dw2 by ANOVA; asterisks indicate the means are significantly different with a P value of <0.001. Data are from 303 trees from the second population.

Figure 5

Composition of each phenotypic class by Dw1 and Dw2 genotype. Trees from both populations (449 trees in total) were visually assessed after 7 years of growth and placed into one of five phenotypic classes, D=dwarf, SD=semi-dwarf, I=intermediate, V=vigorous and VV=very vigorous.

Figure 6

Summary of Dw1 and Dw2 genotyping of rootstock accessions. A green square indicates the presence of a single allele of Dw1; yellow represents Dw2. Details on the markers employed to genotype Dw1 and Dw2 and the sizes of products amplified by each accession are specified in Supplementary Tables S1 and S3, respectively.