Exciting new genetic tool for Pears

General Fruit Growing
#1

The Axiom 70K pear microarray is a new, cheap, accurate way to genotype many pears. It is a “DNA chip” (same technology that www.23andme.com uses), but Pears don’t get the same love as Apple (Axiom Apple 480K micoarray) or corn (Axiom Maize 600K microarray).

The pear array only has 70,000 SNP markers vs the much bigger apple (480k) and corn (600k) arrays.

It was developed by whole genome sequencing 55 pears (of different species) and finding SNPs (single nucleotide polymorphisms - single base pair differences between them) which were then identified and put onto a glass chip as a single strand (so 70k single stranded stretches of DNA on a chip); since DNA is complimentary, the single strand on the array will pair with another single strand from the sample being tested and will light up when they match. It is cheap and accurate.

The USDA used this chip on the Germ Plasm at Corvallis (their 2,300 accessions)

pear1
pear1724×131 7.02 KB

They found very interesting lineages:

Seckel is Rousselet de Reims x White Doyenne
Comice is Duchess d’Angouleme x Glou Morceau
Anjou is White Doyenne x Sucre Verte
Fondante de Moulins Lille is Napoleon x Easter Beurre
Dana Hovey is Messire Jean x Seckel
Docteur Desportes is Glou Morceau x Duchess d"Angouleme
El Dorado = Winkleman and is Winter Nelis x Bartlett
Doyenne Gris is Bartlett x Winter Nelis (and is a sister to Packham’s Triumph)
Orcas is Bartlett x Comice (and Orcas is sister to California, Paragon, Highland, Canal, Cascade)
Comice and Beurre Superfin are sisters
Beierschmitt is Beurre Clairgeau x Bartlett
Winter Nelis is an offspring of Besi de La Motte
Ewart is Farmingdale x Lemon (Farmingdale is Anjou x Duchess d’Angouleme)
Devoe is Dorset (daughter of Anjou) x Clapp Favorite
Sheldon is Anjou x Bartlett
Ayers is Vermont Beauty (daughter of Seckel) x Garber
Abbe Fetel is an offspring of Beurre Clairgeau (which is an offspring of Duchess d’Angouleme)
Old Home x Farmingdale is erroneously named; Bartlett is the pollen parent of OHxF rootstocks (should they be called OHxB now?)

Bosc is still a mystery, however (as is Conference)

There are too many lineages to list here

In addition, in another paper this axiom microarray was also used to find the location of FB resistance on pears

pear2
pear2791×261 30.3 KB

After finding these resistance genes (they seem to all be in 1 location on Chromosome 2), they can clone them and put them in existing pears or select new FB pears much more quickly

@clarkinks if you wanted to discover small yellow pear’s lineage, this is the cheapest and most efficient way to do this; my guess is this array is under $100 and many labs will have a GeneTitan reader to get the data from it.

The future looks bright

16 Likes
#2

The University of Minnesota used the Axiom apple 480k array to correct their lineages

apple
apple787×685 253 KB

Quite a few of the older crosses have been corrected and even some newer ones (e.g., Frostbite)

It would be great if Geneva NY did this for their Germ Plasm (like Corvallis did)

4 Likes
#3

Looks like all apples and no pears to me.

So, Triumph is same as First Kiss?

1 Like
#4

I believe Rave and First Kiss are the same; called Rave in WA and First Kiss in MN but yes the chart looks funky

yes the apple array used to determine lineages of apples only;

1 Like
#5

This type of SNP analysis is superior to previous work because the SNP markers were verified to be in actual chromosome DNA of species cultivars. It is the current state of the art in plant ID.

The vast majority of prior studies using genetic markers did not do this, primarily because the DNA libraries did not exist. Instead, it was believed that PCR assay of markers would only produce a positive response when a marker was in the sample. It turns out this is grossly inaccurate.

The current end-to-end cost of a DNA library for a single specimen is about $5,000 including all the bells and whistles. The waiting period to have a specimen sequenced is about 3 months, plus another 2 months for some collateral assays. The data sets then need to be “assembled” into a “library” which contains the sequences for each chromosome plus ancillary information. The assembly process can take 6 months to 2.5 years depending on whether previous assemblies of the species already exist. The sequences are not error free, but the newer sequencing hardware is very good compared to pre-2018 methodologies.

5 Likes
#6

That should say “different cultivars”.

2 Likes
#7

Yes different cultivars were sequenced (among P communis: Bartlett, Anjou, Bosc, Seckel, Harrow sweet, Coscia, Old Home, Gin, Harrow Delight) but they also looked at P. pyrifolia, P. pseudopashia, P. pashia, P. betulaefolia, etc

It is a genotyping chip for the Genus Pyrus so many species

1 Like
#8

@rubus_chief
Yes, although P. communis is a landrace hybrid. I believe they included selections from those ancestral species to provide a broad base for their assay of pear cultivars in U.S. production.

1 Like
#9

In the 2020 paper on pears, the authors state

while SSRs are still the markers of choice for routine fingerprinting analyses

This was a bit of protectionism on the part of N. Bassil who has numerous SSR publications. However, I believe her opinion will change given recent results demonstrating the SSR marker set (the primer pairs) she developed for Rubus are not wholly present in the Rubus ‘Hillquist’ genome.

1 Like
#10

The Axiom arrays can be very good for genetic ID, provided the signature for a true specimen has already been acquired.

The analysis methods employed by these researchers for lineages are questionable and contain mathematical fallacies. They have also resisted requests to share their data for re-analysis. They are due for a reckoning.

2 Likes
#11

Thanks for posting this, it is amusing to see this list as it “all makes sense” in retrospect having grown many of these pears. Docteur Desportes is something like Comice, no surprise as they have the same parents. Seckel indeed has something of both Rousselet and White Doyenne in it. etc etc. It is interesting that of these classic pears the same parents show up many times … similar to modern apples where only a few parents dominate.

5 Likes
#12

So yes, Parker = Flemish Beauty. I wasn’t going crazy after all. Wait, maybe that’s unrelated :slight_smile:

2 Likes