Developing genetic tests for pome fruit

As a result of the apple project, growers and researchers now have cost-effective options for genetic identification of apple rootstocks. The project also established a database of verified rootstock controls, so that people submitting samples for testing do not have to provide their own controls.

“The next step was to do this research on pears,” says Dorfling. “In an ideal world, we would like to make this tool available for as many crop types as possible.” Similar to the apple project, the pear project will require the researchers to apply a panel of genetic markers to differentiate between rootstock cultivars. Markers are bits of DNA that vary between individuals (for more details, refer to “Making sense of markers” on page 62).

However, fingerprinting pear rootstocks poses additional obstacles, especially as many pear rootstocks are, in fact, quince cultivars. “Apples are a model crop, planted worldwide, and a lot of research is done on them,” says Dorfling. “There’s a little less on pears, and not much on quinces.”

From pears to quinces

The first phase of the project focuses on pears. CenGen will test a panel of 45 SNP (single-nucleotide polymorphism) pear markers obtained from the Dutch pome-fruit breeder Dr Marijn Rymenants of Better3Fruit.

Geneticist Dr Renée Prins, founder and director of CenGen, emphasises that this panel, which represents a massive investment by Better3Fruit, was developed by analysing the DNA of a genetically diverse pear population. The same research hasn’t been done for quinces, so the second phase of the project, which focuses on quinces, will be challenging.

The first hurdle is the lack of known quince SNP markers. Locating SNP markers requires sequencing and comparing the DNA of genetically diverse individuals. This sounds simple, but genomes consist of millions of base pairs, and SNPs are differences in single bases.

For context, the quince genome is estimated to contain 686 million base pairs, more than 100 times the number of letters in all seven Harry Potter novels combined. Sifting through all those base pairs in search of SNPs is an expensive, time-consuming process, even with specialised software.

“The other problem is that some quince rootstocks are derived mutations, so they are genetically very close to one another,” says plant breeder Dr Iwan Labuschagne, founder of Provar. “They were discovered as chance seedlings or mutations, not bred, so quince rootstocks may differ by only a few genes, which may not be detectable.”

Despite these complexities, the team hopes that the project will generate a useful tool for the South African industry. “We want to enable growers to make sure of what they’re buying,” says Dorfling.

The project is expected to be completed in 2028.

Which apples are compatible?

Many flowering plants, including most apples, pears, and plums, are self-incompatible, which means they require a cross-pollinator of a different cultivar to set fruit. Self-incompatibility is due to genes that code for proteins in pollen and styles. If a pollen grain lands on a flower with the same self-incompatibility gene variants, the pollen tube will be destroyed by the flower before it can reach the ovule (Figure 1).

Alleles are variants of a gene. The gene variants that determine compatibility are called S-alleles (the S is short for self-incompatibility). Apple trees have two S-alleles because they inherit one gene copy from each parent.

There are more than 50 S-alleles in apples and crab apples. However, many apple cultivars are closely related, so some S-alleles are very common. For example, a study of 150 apple cultivars found that there are three S-alleles that each occurs in about a third of cultivars. Hence, many modern apple cultivars are, at best, partially compatible.

Many modern apple cultivars are, at best, partially compatible.

Consider Granny Smith, a widely planted cross-pollinator. It shares its one S-allele with Cripps Pink, and the other with Golden Delicious. Therefore, only half the pollen produced by a Granny would be able to pollinate either of these cultivars.

International research indicates that partial incompatibility can be overcome by planting a higher proportion of cross-pollinators and bringing in extra hives, but this takes second place to planting fully compatible cross-pollinators.

Characterising S-alleles of apples

In 2020, Provar and CenGen joined forces to determine the S-alleles of commonly planted Japanese plum cultivars. They generated a table showing which cultivars are genetically compatible or incompatible (available in Fresh Quarterly issue 10).

They will now expand this work to establish an S-allele genotyping database for South African apples. One part of the project involves optimising genetic markers for known S-alleles.

The other aspect of the project is applying the markers to 12 commercially-planted apple cultivars, including Afri-Blush, Afri-Glow, Cripps Red, Early Red One, Fuji, Gala, Golden Delicious, Granny Smith, Lady in Red, Nicoter, SQ159 and WA 38. This will tell us which of these cultivars are compatible and allow them to be used as controls in future S-allele testing.

“With many new cultivars that are imported, we don’t know what cross-pollinators to plant,” says Labuschagne. “In many cases, the breeder doesn’t know either. This project will give us a bank of information, so we can offer S-allele testing as a service and then tell the growers which of the genotypes in the bank are potential cross-pollinators.” The project is expected to be completed in 2027.

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More on compatibility

Figure 1 originally appeared in the June 2024 issue of Fresh Quarterly, the Hortgro Science technical magazine for growers. For a fuller explanation of compatibility, read the article on the Fresh Quarterly website.

The tables of plum compatibility are available in the September 2020 issue of Fresh Quarterly, which also discusses fundamentals of fruit set and effective pollination period.