Triploid Varieties
DNA SSR fingerprinting is being used for varietal identification, and increasingly to parentage assessment, based upon matching with a reference collection. The analysis given here of triploid variety relationships is an interpretation on best endeavours; the only certainty is that there will be errors and omissions. The report is available here.
Assuming that all those varieties that have more than 25 alleles are triploids rather than some being aneuploids, two routes have been followed for finding possible relationships.
a) Following Ordidge et al (2018), I sought diploids whose SSR fingerprint was entirely contained within a triploid. From Considine et al. (2012) these (maternal is considered more likely than paternal) diploids may be contributing their entire complement of 34 chromosomes to progeny as a result of first division meiosis failing. Paternal parent contributes a normal haploid gamete and may then be found with Explorer-P2P. In some cases there are multiple triploids with the same maternal parent and these are (half or full siblings). In total I feel some confidence in nearly 70 of these.
b) It may happen that the maternal parent is no longer extant, or hasn’t yet been fingerprinted. Triploids were compared against each other to find families that had at least 24 alleles in common with at least two per marker-pair. Where there is no maternal diploid gamete found they are possible orphaned siblings. There were another 40 orphaned triploids.
In total that is about 20% of the triploids investigated. Having found candidates, wherever possible the DNA SSR fingerprints were compared with the DArT scores, the provenances and NFC (etc.) photographs for assessing the reasonableness of these relationships. Many examples are presented.
Yet that it has been possible to create such methodologies suggests that further work with SNP datasets could be productive.
Explorer-P2P was designed to find parents contributing haploid gametes, it has to be used carefully for finding triploid parents.
Aneuploidly is another complication in understanding triploid parentage, where, following Considine et al., one (maternal) parent contributes a haploid gamete and the other an aneuploidy gamete (18-33 chromosomes). Without ploidy from flow cytometry no simple procedure for interpreting this situation seems feasible.
