the authors did some genetic and phenotypic analysis on ~600 attempted japanese plum - apricot hybrid seedlings and had some findings that line up with some guesses I’ve seen on grower forums:
the big takeaways for me
all successful crosses had japanese plum seed parents
existing claimed crosses (zaiger etc.) have a strong possibility of being simply japanese plums (only 5% of the study’s attempts verified as true crosses)
all true crosses they observed had pubescent skin (and likely apricot-like leaves, flower types, and bloom time). I think we’ve all seen/eaten some plumcots that have pubescent skin which is pretty undeniable since that trait doesn’t exist in japanese plums. plus the leaf type differences can be seen in many hybrids
they hope to obtain self fertility, and the apricot gene for that seems to transfer over, but all plumcots in their study [page 7] and most in other studies [page 10]) have been found to have androsterility (infertile pollen or similar) - important for home growers to understand
paper summary/ excerpts
600 new crosses made. seeds germinated using embryo rescue (page 2)
only about 30 were strongly indicated to be true japanese plum x apricot. the remainder were likely plain old japanese plum:
“The interspecific nature of plumcot hybrids has been successfully verified using molecular markers, as demonstrated in previous studies (Byrne and Littleton, 1989; Ahmad et al., 2004; Jun et al., 2009; Szymajda et al., 2022). However, most of the genotypes considered interspecific, because they came from seeds of fruits resulting from controlled crosses, were shown not to be interspecific based on validation using SSR markers (33 interspecific plumcots from 612 genotypes verified). This could be due to escapes from uncontrolled pollination, as well as possible cleistogamy in the case of crosses with a self-compatible female apricot parent. To date, there have been very few studies that have confirmed the interspecific nature of plumcot hybrids by SSR. As a result, many hybrids considered as plumcots may actually be Japanese plum-type hybrids” (page 9)
“most hybrids have segregated the Sc allele from apricot, which confers apricot self-compatibility (Vilanova et al., 2006; Halasz ´ et al., 2007), so they should a priori be self-compatible. However, pollen viability studies have shown androsterility in all the plumcots that flourished. This is consistent with the results obtained in various studies in which the majority of plumcots do not produce pollen or their pollen is not viable (Okie, 2005; Jun et al., 2009, 2011; Nam et al., 2016), suggesting that interspecific hybridization causes androsterility in the offspring, which could explain why most plumcots were not very productive” (page 10)
“The phenotypic characterization of the plumcot hybrids also revealed their interspecific nature. They showed characteristics acquired from apricot such as leaf morphology and pistil and fruit pubescence (present in apricot, absent in plum). The presence of pubescence on the ovaries and fruits of plumcot hybrids has been reported in numerous studies (Ledbetter et al., 1994; Okie, 2005; Jun et al., 2009; Zhivondov and Uzundzhalieva, 2012; Nam et al., 2016). Considered a dominant trait in interspecific crosses between Japanese plums and apricots (Jun et al., 2009), this could serve as a physical characteristic to distinguish a true plumcot from other types of hybrids. Hakoda et al. (1998) also obtained all of their offspring from interspecific hybrids between Japanese apricot (P. mume) and Japanese plum with fruit that had pubescence. Our results confirm that the presence of pubescence on ovaries and fruit skin is an unequivocal characteristic for verifying the “real” plumcots.” (page 10)
this chart on page 8 where they sort some characteristics from apricot to plum:
“Hybridization was only successful in this study when Japanese plum was used as the female parent. These findings are consistent with those reported in previous works (Yoshida et al., 1975; Singh et al., 1997; Claverie et al., 2004; Jun and Chung, 2007; Szymajda et al., 2015). These studies have noted that hybridization success rates are influenced by the direction of the cross and that crosses involving P. salicina as the maternal parent generally prove more fruitful than those involving P. armeniaca” (page 9)
the paper is worth a skim, there’s more in there I didn’t quote
It’s great to see some confirmation that a high percentage of the Zeiger “hybrids” were actually not the hybrid status claimed. I don’t think they intended to mislead anyone, but I just can’t understand why they’d want to claim something is a hybrid if it didn’t inherit any noticeable traits from the species they were attempting to cross in.
I wouldn’t go that far, they only tested their own F1 hybrids not zaiger’s, but it’s interesting that they only got 5%, and all of them showed pubescence. it could be that F2 etc. hybrids can get back to non-pubescence and still be true crosses and if you look at zaiger’s patents they usually have pretty deep pedigree charts
but yeah, it seems easy to fool yourself when you’re just dealing with one japanse plum seed vs. another - never any apricot seeds - and there’s been little to no actual DNA evidence before this paper and one or two others
Could someone that is well versed in the paper’s topic help clarify something? If I understood correctly the authors performed controlled crosses and then used genetic markers to verify the hybrid nature of the offspring. Now if prunus salicina is generally self sterile, shouldn’t proper controlled crossing procedures mean that all offspring is implicitly hybrid nature?
Basically what I am asking, if one selects some genetic markers from apricot and then tests the hybrid offspring, how do you ensure that these markers provide full coverage of all possible hybrids?
As was said by z0r, many (most?) of the commercial pluots are more complex hybrids/backcrosses (F2 and onwards) with jap. plum, which would likely decrease the probability of finding certain genetic markers from apricot.
I’d apply Occam’s razor here. If most commercial pluot varieties don’t have these markers then maybe the markers aren’t able to identify all (complex) hybrids rather than all of them simply being pure jap. plum.
they didn’t test zaiger’s fruit, they could well be legitimate crosses. see the quote below and the bolded part
as for occam’s razor, it could as well be used to say that when you plant a seed from a japanese plum and you think you pollinated it by hand, the simplest explanation for what grows could be that your control failed, japanese plum pollen got there first, and it’s just a japanese plum, because pollen is small and “life, uh, finds a way”
“The interspecific nature of plumcot hybrids has been successfully verified using molecular markers, as demonstrated in previous studies (Byrne and Littleton, 1989; Ahmad et al., 2004; Jun et al., 2009; Szymajda et al., 2022). However, most of the genotypes considered interspecific, because they came from seeds of fruits resulting from controlled crosses, were shown not to be interspecific based on validation using SSR markers (33 interspecific plumcots from 612 genotypes verified). This could be due to escapes from uncontrolled pollination, as well as possible cleistogamy in the case of crosses with a self-compatible female apricot parent. To date, there have been very few studies that have confirmed the interspecific nature of plumcot hybrids by SSR. As a result, many hybrids considered as plumcots may actually be Japanese plum-type hybrids” (page 9)
The first issue is that molecular markers do not function in the way that horticultural geneticists believe. To date, they have only estimated the length of PCR products produced by the markers, believing that length is correlated with content. Lately it has been shown this is not true.
The second issue is that the data analysis methods they (or their software) have used to compare the lengths are mathematically flawed. Consequently, all horticultural studies of plant relations by molecular markers should be reconsidered.
I’m trying to understand the study setup and what the results show. If these markers strictly have to be present in every hybrid that can exist, then the logic would make sense. However if these markers just indicate hybrid nature, i.e. if they are present then it must be a hybrid, then basically you can not conclude from a lack of these markers that it is not a hybrid. This is would be a logic flaw and the claim they make that a large part of the tested material wasn’t interspecific doesn’t hold. ( All they can say is the characteristic markers weren’t there. Thats it)
If only around 5% of their tested material is actually an interspecific hybrid according to their test, it does raise the question whether plumcot breeding is mostly just handwaving. Hence my Occam’s razor comment that maybe their setup or conclusions are flawed.
This is next to the apparent structural issues with molecular markers that Richard pointed out.
In any case, regardless if interspecific or not, many pluots are fantastic fruit and if you count them as a jap. plum surely among the best tasting out there.
The term is understandably often misunderstood. Molecular markers come in pairs, labeled F, R for “forward”, “reverse”. With the exception of SNPs, each marker pair is designed to delimit a feature. In all cases they are designed to respond to a biochemical reaction with the DNA (or RNA) of an organism. This reaction (PCR) results in a “product”.
An F marker PCR reaction produces zero or more a short DNA sequences from the organism leading up to and including the R sequence(s) in the organism. In this manner, the F product is a record of what precedes the R marker(s) (and includes them). Likewise, an R marker PCR reaction is a record of F marker occurrences.
A major limitation with PCR is that you do not know where in the DNA the reactions occurred. So, your F reaction might have been in a different chromosome than your R reaction. If true, then you might have missed the feature of interest. If you don’t examine the contents (tedious) you have no way of knowing. This is one of the many pitfalls of using PCR product lengths instead of examining the contents.
SSR markers for an organism are discovered by searching more or less random short sequences for F, R pairs. Any F, R “enclosures” found in these sequences are examine for repeating motifs. When found, the F, R pair is retained for further study. A vetting process is then performed to judge the merits of the markers.
An issue with SSRs is that they statistically do not occur in portions of DNA corresponding to functional biology. Instead, they exist in “filler” material. Thus, SSRs only inform you about a few minute structural detail, not DNA function.
On the scale of the complete DNA of plants, we know very little details of how the characteristics of an individual plant specimen are expressed in DNA / RNA. Investigators who engage in extrapolation only add to our misunderstandings and waste resources in the process.
these are statistical tools, it isn’t sequencing, and there are problems with polyploidy, the test methods, and so on. I don’t think they’re making a claim that their methods and statistics lead to 100% accuracy. if a cross doesn’t have the eight markers they picked out, or some other hiccup happens, it won’t be caught. but, these are cross-species markers which makes them potentially more powerful than just a few markers within a single species
you might be interested in this study “Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry” Liu et al. 2022
the study authors worked backwards from full sequences and picked out an ideal set of markers. they found with their best 5 markers they got ~95% accuracy in F1 hybrid identification when they used pcr-ssr and those 5
the plumcot study certainly picked out worse markers, without so much statistical power, but they used 8 of them. who knows
I have Richard on ignore and I haven’t been reading his replies, sorry. pcr-ssr is an industry standard tool which helps real breeders make decisions and like any tool it has capabilities and limitations and pointing out its limitations - I dunno - I think these working breeders and scientists understand those just fine. someday it’ll go away - is already going away - when sequencing is cheaper
I find pluots to be bigger, sweeter, even more prolific than plums. I love the various flavors. Most plums are so boring to me. I don’t know what the difference between plums and pluots exactly is. But no doubt a difference is obvious.
I agree and some I really like. Pluots are definitely different though. I have had more than one person say best fruit ever. I would not go that far. Nectarines are better
I’m not sure you can apply the findings of the paper to pluots and plumcots in general. It just means they’re hard to cross. From what I understand Floyd Zaiger spent years and lots of trials to get his crosses
Also for spring satin plumcot at least the leaves do not look like plum leaves and look somewhere in between plum and apricot
I think the difference between pluots and plums is that Zaiger bred some outstanding stone fruit and the pluots we love come from their breeding. Whether they are just plums, or are interspecific, many of them are outstanding.
Thank you for the link. I revisited the original paper and I think I have a clearer picture now. You need to be very careful with forming conclusions such as the one above.
The authors were quite careful not to underline too much why they were only able to identify around 5.4% hybrids in their crosses. Here is the acknowledgement though:
This finding highlights the need to improve the hybridization protocol.
Basically, the hybridization procedures they used must have allowed for pollen contamination…
What the paper in effect found was that their own hybridization program/process was likely a bit too sloppy, allowing for a large portion of “false hybrids” which was confirmed by their molecular markers.
In light of this finding it maybe is a bit amusing that the authors conclude " As a result, many hybrids considered as plumcots may actually be Japanese plum-type hybrids "
I can’t really comment on the molecular markers and whether the choice or accuracy they offer provides a good test for interspecific hybrids (especially if these were to be used on F2 or further crosses, which most pluots or apriums are)
I think the interesting take-aways from the study are that you should use a japanese plum as the female parent if you want to hybridize prunus salicina and prunus armeniaca and that you should be meticulous with your hybridization protocol to avoid cross-contamination.
In the paper by Liu et al., they wisely chose to survey a genome library instead of manually searching for SSRs by restriction endonuclease. Their less than 100% identification of known F1s is likely due to their scoring method. Afterwards, they used their vetted markers to discern hybrids among accessions of unknown ancestry. This is a blatent exercise in extrapolation. It has no statistical merit.
