Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array

Abstract

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Keywords: genetic diversity; genotyping; high-density map; polyploid wheat; single nucleotide polymorphism; wheat iSelect array.

Figure 1

Assay IWB2818 shows multiple clusters in unrelated hexaploid wheat accessions, which can be tracked within bi-parental mapping populations as biallelic markers. The targeted [T/C] single nucleotide polymorphism (SNP) site is located in the A genome of hexaploid wheat. An SNP is located in the primer binding sequence of the B genome and results in the additional cluster (C3) on the genotyping plot due to failed/reduced hybridization for the assay oligonucleotide probe. Chara × Glenlea DH samples are shown in blue (situation C2/C3, polymorphism in Genome B). Westonia × Kauz DH samples are shown in red (situation C1/C3, polymorphism in Genome A). Diverse germplasm is shown in grey. Theta is the angle of deviation from pure T allele signal, where 0 represents pure T allele signal and 1 represents pure C allele signal; R is the intensity of hybridization signal. The graphical representation of genotypes in clusters C1, C2 and C3 is shown on the right side, where a grey arrow represents the Infinium probe.

Figure 2

Examples of clustering obtained using diploid and polyploid versions of the GenomeStudio software, respectively: (a, b) assay IWB8846; (c, d) assay IWB63414; (e, f) assay IWB36584; (g, h) assay IWB15488; and (i, j) assay IWB54207.

Figure 3

(a) Alignment of chromosome 2 consensus maps with genetic maps from individual bi-parental crosses. BTS/AUS = BT-Schomburgk × AUS33384, Cha/Glen = Chara × Glenlea, Op/Syn = W7984 × Opata M85, Sun/AUS = Sundor × AUS30604, Wes/Kauz = Westonia × Kauz, Yo/AUS = Young × AUS33414. Chromosome 2B from Yo/AUS was excluded from consensus map construction due to the presence of the alien Sr36 introgression in cultivar Young, whose presence restricts recombination and complicates map construction. (b) Comparative analysis of the order of single nucleotide polymorphism (SNP) loci in the wheat genome based on SNPs showing segregation at two (left) and three (right) duplicated loci.

Figure 4

Examples of null alleles in the wheat genome. (a) Assay IWB17050 detecting a null allele; (b) Assay IWB12859 detects a co-dominant single nucleotide polymorphism locus that also shows the evidence of a null allele; (c) Frequency of nulls in the populations of different geographical origin.

Figure 5

Single nucleotide polymorphism (SNP) distribution across populations. (a) Minor allele frequency across populations of different origin. (b) Shared and private SNPs between the analysed tetraploid and hexaploid wheat populations.