Genetic architecture of fruit quality traits in Malus x domestica (Borkh.) compared between own-rooted seedlings and vegetative propagules on ??M. 9?? rootstock

The comparative performance of vegetative propagules (VP) grafted on ‘M. 9’ rootstock and own-rooted (OR) seedlings of the same genotypes was investigated for apple Malus x domestica (Borkh.)] fruit quality traits using offspring from 22 control-pollinated families. Fifteen fruit quality traits including fruit size and shape, skin colour, russet and sensory eating characteristics were evaluated for individual seedlings. Estimates of genetic variance–covariance matrices (G) were obtained and compared between the two treatments (OR versus VP) using Mantel’s test and regression approaches. Empirical estimates of correlations, at the individual-tree and family-mean levels, between the two treatments were compared with those obtained from deterministic simulations. Estimates of narrow-sense heritability (h ²) were higher in the VP population than in the OR population for 11 of the 15 traits. The estimated G matrices were significantly different between the two treatments. Simulation study showed that with an increase in the total genetic variance, the correspondence between the two treatments at the family-mean level improved dramatically for different family sizes. As the ratio of dominance/additive variance increased from 0 to 1, the family-mean correlations between the two treatments decreased for all family sizes. The average estimated correlations between the two treatments at the family-mean level were higher than at the individual-tree level (0.78 and 0.42, respectively). These observed correlations were very similar to our theoretical expectations. In the light of these results, caution is required when comparing apple seedlings tested on their own roots with those tested on ‘M. 9’ rootstock, as potential cultivar breeding parents.