Propagation Fidelity and Kinship of Tomato Varieties ‘UC 82’ and ‘M82’ Revealed by Analysis of Sequence Variation

Abstract

Plant varieties are named and released based on distinct, unique and stable characteristics but may be maintained separately by genebanks or stock centers under separate accession identification numbers. Genetic heterogeneity of the original variety, genetic drift, failure to exclude cross pollination, and propagation error may erode the integrity of genetic resources. The availability of resequencing and genotyping data for duplicate samples enables an analysis to clarify the relationship between specific varieties or independently curated accessions of the same variety while also assessing the fidelity of germplasm maintenance. We accessed both Single Nucleotide Polymorphism (SNP) array genotypes and resequencing data for two important tomato varieties ‘UC 82’and ‘M82’ that have been maintained as separate accessions in collections as important resources for the research and breeding communities. Our analysis of these data suggests that polymorphism rates from resequencing of cultivated tomato are overestimated in the literature due to heterozygous calls caused by either sequence error or coalignment of repetitive sequences. We defined a set of 32,352 robust SNPs from a file containing data for all samples and we compared the distribution of data with SNPs called from a genotyping array. For both analyses, intravariety variation was found in haplotype blocks, with the same haplotypes identified using SNPs detected from array and sequence data. The distribution pattern of variation across the entire genome sequence was similar for both ‘UC 82’and ‘M82’. Overall, the differences between distinct 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 selection from partially inbred progeny. The data also suggest that these tomato genetic resources have been propagated with high fidelity.