Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat

Abstract

Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel of 378 winter wheat genotypes including 190 elite lines and 188 plant genetic resources (PGR), which were phenotyped in multi-environmental trials for grain yield and plant height. We observed an ascertainment bias for the array-based SNP markers, which led to an underestimation of the molecular diversity within the population of PGR. In contrast, the marker system played only a minor role for the overall picture of the population structure and precision of genome-wide predictions. Interestingly, we found that rare markers contributed substantially to the prediction ability. This combined with the expectation that valuable novel diversity is most likely rare suggests that markers with minor allele frequency deserve careful consideration in the design of a prebreeding program.

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

“…This result is comparable with previous DArTseq and GBS wheat studies. For example, Riaz and coworkers(21) identified 34,311 DArTseq markers in 295 samples, and Chu et al(22) obtained a similar result using GBS in 378 samples. Finally, Vikram and collaborators(23) obtained 20,526 SNPs in 8,416 samples.…”

Haploid maize seeds prediction using deep learning and using mock reference genomes for genomic prediction of hybrids

“…Darrier et al (2019) studied the influence of the genotyping platform (array versus GBS) on the assessment of genetic diversity and observed only 496 common SNP, indicating that these genotyping platforms capture different regions of polymorphism in wheat. Besides, we noticed that GBS-B73 and GBS-Mock-All identified a higher rare variant frequency (MAF < 0.05), which is more interesting for diversity studies, where these rare alleles can be a new source of variation (Darrier et al, 2019;Chu et al, 2020).…”

“…Both approaches have their advantages and disadvantages, affecting costs, procedures, and further genetic analyzes. Recent studies have been carried to verify the influence of SNP platforms in genetic diversity, GWAS, and genomic prediction, but restricted mainly to inbred lines (Elbasyoni et al, 2018;Darrier et al, 2019;Negro et al, 2019;Chu et al, 2020). In our study, a wide range of analysis was performed to study the influence of the genotyping method on the assessment of parental lines diversity and prediction of hybrids.…”

“…The decision of the best genotyping platform will depend on the target germplasm, the genetic study to be carried out, and the budget available for the acquisition of the genomic information. Recent studies have compared these SNP platforms on estimates of genetic diversity, GWAS, and genomic prediction in wheat (Elbasyoni et al, 2018;Chu et al, 2020), barley (Darrier et al, 2019), and inbred maize lines (Negro et al, 2019).…”

“…Moreover, the population structure knowledge permits the plant breeder to describe heterotic groups (Wu et al, 2016) and select more interesting combinations between inbred lines. Recent studies aimed at verifying how the array and GBS scored markers affect genetic diversity (Darrier et al, 2019;Chu et al, 2020). However, our focus is to investigate how the use of a mock reference during the SNP calling affects the discovered markers and how they assess the populational structure.…”