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/.

Multiple Quantitative Trait Analysis Using Bayesian Networks

“…The latter pair of scenarios is motivated by the fact that taller plants are less susceptible to Fusarium than shorter plants. The LD analysis in Mackay et al (2014) suggests that this SNP is located in chromosome 4D in this population and that it may be tagging RhtD1b, a dwarfing gene that is also closely associated with resistance to Fusarium (Srinivasachary et al 2009). In addition, G266 (BobWhite_c30043_150) appears to be located in chromosome 2D and to be tagging Ppd-D1, which controls photoperiod response.…”

“…On the one hand, the particular pattern of crosses used to produce a MAGIC population results in a very low population structure. This reduces the confounding effect of relatedness on the estimation of SNP effects (Astle and Balding 2009) and on mapping approaches based on LD (Mackay et al 2014). On the other hand, the size of of the population is large enough to detect weak associations and associations with rare variants.…”

“…The population was created using a multiparent advanced generation inter-cross (MAGIC) scheme. Such a scheme is designed to produce a mapping population from several generations of intercrossing among eight founders and has the potential to improve quantitative trait loci (QTL) mapping precision (for more details and to access the data see Mackay et al 2014). The use of multiple founder varieties results in a population that is segregating for more QTL and traits than a biparental population, and the balanced crossing used in each generation reduces LD and family structure by ensuring that each founder has an equal opportunity to contribute to each genotype.…”

“…The labels are those used in Figure 1, while the SNP names are from Mackay et al (2014) and Wang et al (2014).…”

A Random-Model Approach to QTL Mapping in Multiparent Advanced Generation Intercross (MAGIC) Populations

“…The population will be described later. Subsequently, MAGIC populations have been developed in wheat (Huang et al 2012;Mackay et al 2014), rice (Bandillo et al 2013), and other crop species (Gaur et al 2012;Pascual et al 2015;Sannemann et al 2015). One key difference between MAGIC populations and other multiparent populations is that all MAGIC lines have experienced multiple generations of inbreeding and thus all are inbred lines.…”