The introduction of the article is interesting! I cannot paste plain text of the entire article as it is excessive but here is an intro " The apple (Malus×domestica ) cultivar Honeycrisp has become important economically and as a breeding parent. An earlier study with SSR markers indicated the original recorded pedigree of ‘Honeycrisp’ was incorrect and ‘Keepsake’ was identified as one putative parent, the other being unknown. The objective of this study was to verify ‘Keepsake’ as a parent and identify and genetically describe the unknown parent and its grandparents. A multi-family based dense and high-quality integrated SNP map was created using the apple 8 K Illumina Infinium SNP array. This map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNP haplotypes and to identify pedigree relationships. ‘Keepsake’ was verified as one parent of ‘Honeycrisp’ and ‘Duchess of Oldenburg’ and ‘Golden Delicious’ were identified as grandparents through the unknown parent. Following this finding, siblings of ‘Honeycrisp’ were identified using the SNP data. Breeding records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection, MN1627. This selection is no longer available, but now is genetically described through imputed SNP haplotypes. We also present the mosaic grandparental composition of ‘Honeycrisp’ for each of its 17 chromosome pairs. This new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect ‘Honeycrisp’ with other cultivars used widely in apple breeding programs. The created SNP linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNP arrays."
Both SSR markers and SNP linkage are based on an old technology using PCR marker counts. I have a paper under review demonstrating that these counts are hardware anomalies. All publications utilizing PCR type markers should be treated with great suspicion.
Longer answer: PCR technology attempts to produce inflorescences when markers are present in cell chromosomes. It cannot provide location information. I acquired high-precision whole chromosome sequences and used mathematical correlation algorithms to search for previously documented markers. The results were terrible. Two things need to occur in horticultural science before reliable genetic assays can be produced by most researchers:
They need to get rid of their current analysis software.
They need to adopt long-read digital sequencing.
The testing may be a solid building block but at the end of the day of very limited use for breeding varieties.
There is no shortage of great material out there and while it is time consuming to mix them the old fashioned way, there is very little incentive to GMO apples for new varieties. At best we can hope them to GMO commercial varieties to make them resistant to certain diseases.
Heck the modern apple game is largely a marketing game. If you take any named variety that you like and cross pollinate it with any other great variety that you like, your chances of ending up with a very special snowflake will be pretty darn good. It won’t amount to much unless you get somebody like Stark Bros (pumpers of new varieties since the 1800’s) to try and generate some hoopla about it.
I know. And what I’m saying is that in reality there is little economic incentive to do that. As I say I see a lot more potential to introduce genetic material that will make existing breeds resistant to diseases.
There are over 7,500 varieties of apples in the world. The only thing between a great apple and name recognition is not quality but marketing. On the breeding side I just don’t see apples having the same economic curve as the monocrop staple foods where the Monsanto’s of the world can make a killing by introducing crops that are resistant to pesticides and such.
Maybe off topic, I had a " prove you’re not a robot" question to join a forum. It was “What color are apples ?”
When I responded many, red, yellow, green, brown, almost white, lots of blends I was declined!
DNA tests have already impacted many areas of breeding. I had DNA tests run on 12 roosters a couple of years ago to find out which were homozygous for the oocyanin (blue egg) gene. Three were homozygous so I culled the rest of the roosters. I have hens just starting to lay that are producing sky blue eggs as a result. I need 2 more generations of DNA testing to stabilize a pure breeding line for the trait. This can also be done with standard test breeding methods but would take several more years. DNA tests cut directly to the point.
Funny enough Honey Crisp broke the hegemony of quality over beauty. Since them lots of well deserving apples that are not perfectly colored have entered the market.
I found both amusing and promising that “miniature” apples are being marketed, I have to keep explaining to people that there are not just edible crab apples but superior crab apples. Then again I tried one and it was pretty meh; a chestnut crab runs circles around it. But going back to the whole marketing bit; the company has a patent on Rockit (babylove) so they market not what is better but what they can profit the best from.
Absolutely true , we are all here for good tasting fruit and how we get to that level. As an example imagine if even 1 in 1000 apples was tested for nutrient content. Lots of growers would change their methods very fast!
You can still be honest about it. Just yesterday I tried yet again to talk somebody away from buying a Jostaberry. They are horrible producers that prefer to grow tons of foliage instead of fruit which is probably a good thing, considering what a huge magnet they are to sawfly larvae. But they are ‘different’, and people (myself included) like to try things that are different.
They are one of the easiest things to propagate, only slightly harder than green mold on bread. Every year I do 10 or so of them, try to talk people away from them, but they keep taking one with the other stuff they buy.