Comparative Application of Terminal Restriction Fragment Analysis Tools to Large-Scale Genomic Assays.

Abstract

The analysis of telomere length is an important component of many studies aiming to characterize the role of telomere maintenance mechanisms in cellular lifespan, disease, or in general chromosome protection and DNA replication pathways. Several powerful methods to accurately measure the telomere length from Southern blots have been developed, but their utility for large-scale genomic studies has not been previously evaluated. Here, we performed a comparative analysis of two recently developed programs, TeloTool and WALTER, for the extraction of mean telomere length values from Southern blots. Using both software packages, we measured the telomere length in two extensive experimental datasets for the model plant Arabidopsis thaliana , consisting of 537 natural accessions and 65 T-DNA (transfer DNA for insertion mutagenesis) mutant lines in the reference Columbia (Col-0) genotype background. We report that TeloTool substantially overestimates the telomere length in comparison to WALTER, especially for values over 4500 bp. Importantly, the TeloTool- and WALTER-calculated telomere length values correlate the most in the 2100-3500 bp range, suggesting that telomeres in this size interval can be estimated by both programs equally well. We further show that genome-wide association studies using datasets from both telomere length analysis tools can detect the most significant SNP candidates equally well. However, GWAS analysis with the WALTER dataset consistently detects fewer significant SNPs than analysis with the TeloTool dataset, regardless of the GWAS method used. These results imply that the telomere length data generated by WALTER may represent a more stringent approach to GWAS and SNP selection for the downstream molecular screening of candidate genes. Overall, our work reveals the unanticipated impact of the telomere length analysis method on the outcomes of large-scale genomic screens.

Plant phenotyping relevance

植物のテロメア長という形質をSouthern blotから抽出する2つの解析ツールを大規模データで比較・評価しており、測定法の技術的妥当性が研究の中心である。

Code and data availability

The paper's plant-phenotyping measurements (TeloTool- and WALTER-derived telomere length datasets for 537 Arabidopsis accessions and 65 T-DNA mutant lines, used for GWAS) are stated to be contained in Supplemental Data S1 and S2, publicly downloadable from the MDPI supplement URL listed in the allowed URLs. No author-c