An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation

Abstract

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/.

Keywords: MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); Multiparental populations; QTL mapping; genome-wide association scan; high-density genotyping; quantitative genetics; recombinant inbred line (RIL); single nucleotide polymorphism.

Figure 1

Analysis of LD in the MAGIC population. (A) Heatmap of LD decay of ordered SNPs over 21 chromosomes, ordered 1A, 1B…7D, D′ above the diagonal and r² below. (B) Heatmap of SNPs scaled by the genetic map. Each chromosome has been extended to a nominal 250 cM. Examples of individual chromosomes, LD heatmaps, and plots of LD decay are illustrated for (C) chromosome 2B and (D) chromosome 2D. (C and D) Upper left: ordered SNPs; lower left: scaled by genetic map; upper right: D′ plotted against genetic distance; lower right: r² plotted against genetic distance.

Figure 2

Diagnostic awn presence/absence KASP marker, BobWhite_c8266_227_TG_5AL, genotyped in the AM panel.