Comparison of array‐ and sequencing‐based markers for genome‐wide association mapping and genomic prediction in spring wheat

Abstract

Notwithstanding the rapid development of high‐throughput genotyping platforms in recent years, several plant research programs find themselves in a dilemma of which marker system to use while conducting genome‐wide association studies (GWAS) and genomic selection. To gain insight into this, we genotyped an elite spring wheat (Triticum aestivum L.) association mapping initiative (WAMI, 287 lines) panel with various array‐based platforms—(i) Diversity Arrays Technology (DArT), (ii) Illumina Infinium BeadChip wheat 9K iSelect (I9K), and (iii) wheat 90K iSelect (I90K)—and sequencing‐based platform DArTseq. The raw markers refined using a common set of protocols after the bioinformatics analysis were compared by performing a series of genetic analyses: estimates of genetic diversity through nucleotide diversity (π), population structure and familial relatedness, marker‐trait associations (MTAs), and genomic prediction. Results indicated that genetic data from DArTseq consisted of a high proportion of rare allele markers (1% < minor allele frequency < 5%). The nucleotide diversity statistic (π) was higher for the array‐based single nucleotide polymorphisms (SNPs) than sequencing‐based SNPs. The I9K detected population structure caused by the variety ‘Kauz’ and grouped the population into two subgroups, whereas I90K, DArT, and DArTseq detected five subgroups driven by key pedigrees. The I90K with the highest marker density identified a high number of significant MTAs. Genomic prediction accuracy varied among traits; DArTseq and I90K produced similar prediction accuracies. Among the marker platforms compared, I90K was the best genotyping platform for GWAS, and DArTseq—given the low cost per SNP—was the best platform for genomic prediction in spring wheat.

A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Secale cereale L.)

“…We observed low levels of LD extend across the entire genome in elite rye germplasm and in a similar order as most recently estimated for wheat (Liu et al, 2020). A rapid decline of LD fits to the expectation for an outcrossing species with low ancestral LD (Auinger et al, 2016).…”

“…To conclude, the SNP catalog published with this paper can assist scientists to discover and use functional diversity in rye and related Triticeae species that may be essential for meeting the compulsions to act in modern agriculture under the directive of the multiple challenges concerning global food security (Lal, 2016;Liu et al, 2020).…”

Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives

“…DArTseq is a DArT marker platform combined with next generation sequencing (NGS) platforms, which allows reduction in genome complexity mediated by restriction enzymes and sequencing of restriction fragments [82]. Comparative evaluation of various array-based platforms-DArT, Illumina Infinium BeadChip wheat iSelect, and DArTseq-in GS of spring wheat showed that DArTseq-given the low cost per SNP-was the best platform for genomic prediction [83].…”

The 4.(n) wheat breeding era: genomic-based predictions becoming part of the daily routine and beyond

“…The decision on which tool to use will depend on quality, which ultimately, would be reflected in the final prediction accuracy obtained, but also costs must be kept in mind. The comparison of different technologies on spring wheat, has found that DArTseq was the best option for genomic selection, as it allowed for a similar prediction accuracy comparing to the I90K array (Illumina Infinium BeadChip), but at a lower cost (Liu et al, 2020).…”