Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR

Abstract

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTMtechnology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTMSNP array to maximize genome coverage and polymorphism rates. When sample depth was summarized by marker, the power lawμ∼σ0.8was consistently observed between the mean (μ) and standard deviation (σ). The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Our hypothesis that linkage analysis would be highly accurate for imputing tetraploid marker data was confirmed: the RMSE was 0.15 compared to 0.95 by the Random Forest method in a half-diallel population. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.Core IdeasA mid-density, targeted genotyping-by-sequencing (GBS) assay was developed for potato.The GBS assay includes markers for resistance to potato virus Y, golden cyst nematode, and potato wart.The GBS assay includes multi-allelic markers for potato maturity and tuber shape.The polyBreedR software has functions for manipulating and imputing polyploid marker data in Variant Call Format.Linkage Analysis was more accurate than the Random Forest method when imputing from 2K to 10K markers.

Genomic Prediction for Inbred and Hybrid Polysomic Tetraploid Potato Offspring

“…Targeting genotyping using a genotype-by-sequencing approach [36] was used for characterizing the S 0 , S 1 and F 1 with 2340 single-nucleotide polymorphisms (SNPs), which were previously used in genomic prediction of breeding values for cultivars released in western Europe along with Svensk potatisförädling clones [25]. We removed markers whose minor allele frequency was smaller than 0.05; after that, 2194 SNPs were available for further analyses.…”

“…We assume that the random terms are independently distributed. We fitted model ( 1) using all available records for the three environments (Umeå 2021, Umeå 2022, Helgegården 2022) using the Bayesian generalized linear regression (BGLR) package [36] within the Bayesian framework and using default priors and hyperparameters provided by the software. Inferences were based on 15,000 MCMC iterations and obtained after discarding 15,000 iterations.…”

Breeding for potato cyst nematode resistance in Solanum tuberosum

“…The cost of marker assays has diminished to the point where most public sector breeding programs can afford to implement MAS for resistance genes or large-effect quantitative trait loci (QTLs) during field year 3 or 4 (Figure 3) using tightly linked markers that have already been developed (Table 1). Simplifying the process even further, several companies now offer DNA extraction and marker analyses as a service; all the breeding program needs to do is send in leaf samples (e.g., Endelman et al, 2024;Excellence in Breeding, 2022). By excluding clones lacking desired markers from the program, resources can be channeled toward candidate clones of greatest interest.…”