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Cross-compatibility of apple cultivars and pollinizers

Written by  Sheick, R., Serra, S. and Musacchi, S. October 2019. Reviewed Feb 13, 2024.

Many members of the family Rosaceae, including cultivated apples (Malus ×domestica) and their relatives (Malus spp.), exhibit gametophytic self-incompatibility. In these species, cross-pollination is necessary to achieve sexual reproduction. The successful fertilization of floral egg cells by compatible pollen (sourced from a different parent tree) gives rise to seeds, and it is the fertilization event that stimulates the onset of fruit growth. Thus, the importance of cross-compatible pollen in the orchard cannot be overstated.

Although environmental factors may influence the success of pollination, fertilization, and fruit growth, the self-incompatibility trait in apple is largely controlled by genetic factors. At the DNA level, the S locus contains multiallelic genes expressed in the (male) pollen (S-locus F-box Brothers; SFBB) and the (female) pistil (S-RNase) that function in concert to either enable or reject pollen tube growth in the floral style on the basis of the allelic combination of the parent cultivars.

Most apple varieties are diploid and carry two copies of S-locus genes (S-haplotypes); however, some are polyploid and carry more than two sets of genes. The full composition of a variety’s S-haplotypes is known as its S-genotype, and the S-genotype can be determined by DNA testing.  Although there are multiple genes involved with the self-incompatibility mechanism, the pistil-specific gene, S-RNase, is most commonly used as a target for DNA tests. There are over 50 known variants (alleles) of the S-RNase gene in Malus.

Because the S-locus is inherently heterozygous, pollination combinations fall into one of three scenarios: full incompatibility, in which the pollen (male) parent S-alleles are identical to those of the seed (female) parent; semi-compatibility, in which the pollen parent shares one S-allele with the seed parent, but carries one S-allele differing from the seed parent; and full compatibility, in which none of the pollen parent S-alleles are identical to those of the seed parent (Figure 1). Due to low pollen viability, triploid cultivars should not be used as pollinizers.

When alleles are different the pollenizer is compatable.
Figure 1. Example of incompatible (S1S2 × S1S2), semi-compatible (S1S2 × S1S3), and fully compatible (S1S2 × S3S4), crosses. Pollen tube growth is halted in the style if the pollen S-haplotype matches any of the seed parent S-haplotypes. For maximum pollen effectiveness, fully compatible pollinizers should be provided to pollinate commercial cultivars of interest.

To achieve cross-pollination, orchards can be designed as mixed blocks with rows of alternating cultivars or, more commonly, pollinizers (often crabapples) are interplanted with otherwise solid blocks of a single cultivar. Thus, the need to characterize the S-genotypes of new and popular cultivars as well as crabapples used as pollinizers is evident. The S-genotypes of many apple cultivars have been published over the past several decades, but crabapples have thus far been relatively understudied. The S-genotypes of some popular crabapple and apple cultivars grown in Washington State are summarized below.

Table 1

S-genotypes of crabapple cultivars that may be considered as pollinizers. Note that Adirondack is triploid, and therefore unsuitable as a pollinizer due to low pollen viability. The S39b, S45b, and S50b alleles were characterized by DNA sequencing and determined to be close, but not exact, matches of S39, S45, and S50 sequences, respectively. Further experimental evidence is needed to confirm whether the “b” -variants are compatible with their counterparts.

Crabapple cultivar S genotype Reference
Adirondack S30 S45b S46 1
Evereste™ S20 S26 1
Frettingham S24 S25 1
Indian Summer S26 S50b 1
Manchurian S5 S39b 1
Mt. Blanc™ S3 S58 1
Snowdrift S25 S45b 1


Table 2

S-genotypes of some of the most important apple cultivars grown in Washington State.

Apple cultivar S genotype Reference
Braeburn S9 S24 2
Cameo S2 S28 3
Cosmic Crisp™ (cv. WA 38) S5 S24 10
Cripps Pink S2 S23 4
Fuji S1 S9 5
Gala S2 S5 6
Golden Delicious S2 S3 5
Granny Smith S3 S23 4
Honeycrisp S2 S24 3
Kanzi® (cv. Nicoter) S5 S24 7
Red Delicious S9 S28 8
Rome S20 S24 9



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