RODRIGUEZ Gustavo Ruben
Propagation Fidelity and Kinship of Tomato Varieties ‘UC 82’ and ‘M82’ Revealed by Analysis of Sequence Variation
CAMBIASO, VLADIMIR; RODRÍGUEZ, GUSTAVO RUBÉN; FRANCIS, DAVID MERRILL
Año: 2020 vol. 10
Plantvarieties are named and released based on distinct, unique and stablecharacteristicsbutmaybemaintainedseparatelybygenebanksorstockcentersunderseparateaccessionidentiﬁcationnumbers. Genetic heterogeneity of the original variety, genetic drift, failure toexclude cross pollination, and propagation error may erode the integrity ofgenetic resources. The availability of resequencing and genotyping data forduplicate samples enables an analysis to clarify the relationship betweenspeciﬁc varieties or independently curated accessions of the same variety whilealso assessing the ﬁdelity of germplasm maintenance. We accessed both SingleNucleotide Polymorphism (SNP) array genotypes and resequencing data for two importanttomato varieties ?UC82? and ?M82? that have been maintained as separateaccessions in collections as important resources for the research and breedingcommunities. Our analysis of these data suggests that polymorphism rates fromresequencing of cultivated tomato are overestimated in the literature due toheterozygous calls caused by either sequence error or coalignment of repetitivesequences. We deﬁned a set of 32,352 robust SNPs from a ﬁle containing data forall samples and we compared the distribution of data with SNPs called from agenotyping array. For both analyses, intravariety variation was found inhaplotype blocks, with the same haplotypes identiﬁed using SNPs detected fromarray and sequence data. The distribution pattern of variation across the entiregenome sequence was similar for both ?UC82? and ?M82?. Overall, the diﬀerences betweendistinct accessions of a variety were nearly as great as the diﬀerences between?UC 82?and ?M82?. The similarities between ?UC82? and ?M82? range from 99.33%to 99.74% and are highly consistent with a common pedigree and shared selectionfrom partially inbred progeny. The data also suggest that these tomato geneticresources have been propagated with high ﬁdelity.