Haplotype-based genotyping-by-sequencing in oat genome research

Abstract

In a de novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high-resolution genome analysis and genomic selection in oats. A combined genome-wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component-based genome-wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS-derived markers facilitate genome analysis and genomic selection in oat.

Keywords: Avena sativa; genomics-assisted breeding; genotyping-by-sequencing; haplotype.

Figure 1

Manhattan plots for TL haplotype (left)‐ and GBS‐SNP (right)‐based genome‐wide association scans. The 21 chromosome representations from the oat consensus map are shown on the horizontal axis, and −log10(P) values of association tests at each marker are shown on the vertical axis. The horizontal orange lines show the Bonferroni threshold (P = 0.05) for each respective marker system. The upper plots show the GWAS result using each of the two marker systems alone (a, b), followed by GWAS using only the CL haplotypes (c, d), and the lower plots show GWAS results using the union of CL haplotype and original markers (e, f), excluding the markers that are components of the respective CL haplotypes.

Figure 2

PCA‐based genome‐wide scan for selection. The Manhattan plot shows −log10(P) on the vertical axis. Significant P‐values below a threshold false discovery rate of (∞ = 0.05) are indicated by stars.

Figure 3

Cross‐validation accuracy of the CORE diversity panel (n = 635) using TL haplotype (a) and GBS‐SNP markers (b). Heading date data from 16 location‐by‐year combinations and the line BLUP values are represented by different colours and line patterns. The x‐axis shows the calibration set sizes, and the y‐axis represents mean correlations of predicted phenotypic values to observed heading date.

Figure 4

Prediction accuracy of the heading date BLUP using six levels of maximum percentage missing values (PMV) before imputation. Predictions using TL haplotype markers are shown on the left (a, c), while predictions with SNP markers are shown on the right (b, d). The bar graphs at the bottom (c, d) show the total number of markers used for the genomic selection model. The top boxplots (a, b) show the results of 500 iteration cross‐validation accuracies. The values on top of the median line show mean cross‐validation accuracies.