In silico genotyping of the maize nested association mapping population

Baohong Guo 0 1 William D. Beavis 0 1 0 Present Address: B. Guo Syngenta Seeds, Inc, Slater, IA 50244, USA 1 B. Guo W. D. Beavis (&) Department of Agronomy, Iowa State University , 1208 Agronomy Hall, Ames, IA 50011, USA Nested Association Mapping (NAM) has been proposed as a means to combine the power of linkage mapping with the resolution of association mapping. It is enabled through sequencing or array genotyping of parental inbred lines while using lowcost, low-density genotyping technologies for their segregating progenies. For purposes of data analyses of NAM populations, parental genotypes at a large number of Single Nucleotide Polymorphic (SNP) loci need to be projected to their segregating progeny. Herein we demonstrate how approximately 0.5 million SNPs that have been genotyped in 26 parental lines of the publicly available maize NAM population can be projected onto their segregating progeny using only 1,106 SNP loci that have been genotyped in both the parents and their 5,000 progeny. The challenge is to estimate both the genotype and genetic location of the parental SNP genotypes in segregating progeny. Both challenges were met by estimating their expected genotypic values conditional on observed flanking markers through the use of both physical and linkage maps. About 90%, of 500,000 genotyped SNPs from the maize HapMap project, were assigned linkage map positions using linear interpolation between the maize Accessioned Gold Path (AGP) and NAM linkage maps. Of these, almost 70% provided high probability estimates of genotypes in almost 5,000 recombinant inbred lines. - Forward genetic approaches for relating genomic variability with phenotypic variability can be grouped as either linkage or association mapping. Because it is easy to create and maximize linkage disequilibrium in plant species the former set of methods were initially referred to as Quantitative Trait Locus (QTL) mapping, although it is now clear that association mapping also can be applied to quantitative traits. Linkage mapping is powerful but of low resolution, resulting in identifying genomic regions consisting of about 10 cM, which often consists of tens of millions of bases for most plant species. With the advent of high-throughput technologies for resequencing and genotyping, association mapping has emerged for species where it is not easy to create linkage disequilibrium. This approach exploits historical linkage and recombination accumulated over a large number of generations (Andersson and Georges 2004). Thus, it can provide high resolution information that can be used to identify the causative nucleotides underlying phenotypic variability. Depending upon the amount of linkage disequilibrium (LD) across the genome in the breeding population, association mapping can require genotyping with very high densities of molecular markers (Yu et al. 2008) and extremely large samples to achieve reasonable power (Hirschhorn and Daly 2005; Kingsmore et al. 2008). A third approach is to combine the power of linkage mapping with the resolution of association mapping. This third approach can be thought of as an extension of the multiple family QTL approach (Jansen et al. 2003; Blanc et al. 2006), but is distinctive in that parental inbred lines are resequenced or array genotyped and this information is coupled with low-cost genotyping of their segregating progenies. The approach is conceptually equivalent to the human quantitative transmission disequilibrium test (QTDT) (Abecasis et al. 2000) combined with imputation of genotypes of relatives (Burdick et al. 2006). For the special case where the mapping population consists of multiple families of segregating progeny, usually Recombinant Inbred Lines (RILs), derived from inbred lines crossed to a single reference inbred line, the method has been called Nested Association Mapping (NAM) (Yu et al. 2008; Nordborg and Weigel 2008). For purposes of mapping functional markers in NAM populations, parental genotypes at a large number of SNP loci need to be projected to their segregating progeny. For example, approximately 0.5 million SNPs have been genotyped in the 26 parental lines of the publicly available maize NAM population whereas only 1,106 SNP loci have been genotyped in both the parents and their 5,000 progeny. The challenge is to estimate both the genotype and genetic location of the parental genotypes in the segregating progeny. Three approaches might be considered (Yi and Shriner 2007): (1) estimate all missing genotypes by their expected values conditional on observed flanking markers (Haley and Knott 1992), (2) consider genotypes as unknowns to be predicted using an MCMC update procedure, and (3) multiple sampling of genotypes from a conditional probability distribution for each unknown locus (Sen and Churchill 2001). Given the large number of SNP loci and large number of families and progeny in NAM populations, the latter two approaches could be computationally challenging, depending upon the quality of the physical map. The first approach, however, may be accurate while computationally feasible. Herein, we report on: (1) development of a method for imputing genotypes using an expectation approach, and (2) illustrate its use by applying it to the maize NAM population. In human family based association mapping (Burdick et al. 2006) parental SNPs are projected onto progeny in intervals with no recombinants. Herein, the method is extended to intervals with known recombination events. Data and methods The following data sets were obtained from public information resources: (1) genotypes of 5,000 RILs representing 25 segregating families of the maize NAM mapping population (McMullen et al. 2009). These data are represented as NAM_SNP_genos_ raw_20080703 at http://www.panzea.org/. (2) A composite linkage map created by McMullen et al. (2009) using the maize NAM genotypic data (http:// www.panzea.org/). (3) The maize Accessioned Gold Path (AGP v1) (Wei et al. 2009), consisting of 10 chromosome pseudo-assemblies guided by the physical map, was obtained from the Arizona Genomics Institute (http://www2.genome.arizona.edu/genomes/ maize). (4) the maize HapMap for the 26 founder lines of the maize NAM population. These data comprise nearly half a million SNP genotypes, and can be obtained from http://www.maizegenetics.net/ maize-hap-map. Note that the maize HapMap data are continuing to be updated with new releases, so the version utilized herein will likely be outdated before publication of this manuscript. Estimation of linkage map positions In order to detect the associations between genotypes and complex quantitative traits, it is necessary to know the linkage map positions of the polymorphic loci and to trace inheritance of these using flanking markers. The linkage map positions are unknown for the majority of the 0.5 million SNPs which are genotyped in the parental lines maize NAM families. Their linkage map positions were assigned throug (...truncated)