Most of the mapping populations designed to map drought tolerance QTL, derived from indica x japonica crosses, usually detect favorable alleles for drought-resistance traits contributed by japonica lines [ 20].
Much of the potential for fine-mapping in crops has remained largely unrealized, because progress in mapping population design has failed to match rapid advances in genotyping technologies.
In addition, recent developments in genetic mapping population design widen the opportunities for genetic analyses in crops.
Advanced intercross lines (AILs) are an experimental population designed to increase the actual recombination proportion across the genome, providing higher mapping resolution.
In contrast, much higher rates of polymorphic SNPs can be achieved by transcriptome resequencing of parental genotypes in the target mapping population, allowing the design of customized OPAs containing SNPs that are segregating in the mapping pedigree.
SAP produced the mapping population, generated the phenotypic data, designed the genotyping assay, and generated the genotypic data.
To establish the mapping population, we used a North Carolina Design 3 (NCD3), in which individual F2 males were backcrossed to females from both parental lines.
For a mapping population with the particular breeding design, the realized junction densities and IBD probabilities are saved for all individuals in each generation in each simulation replicate, and they are averaged over in total 2 × 10 4 replicates.
We evaluated polymorphisms in the mapping population (the "B" map) using SSR primer pairs designed from data from the RNA-seq analysis, the genomic SSR library, and Sanger-sequencing expressed sequence tag (EST) analysis [ 15].
Fully connected designs, for example, a diallel (Rebaï and Goffinet 1993; Blanc et al. 2006) would have required a strongly increased size of the mapping population and consequently the partially connected design was chosen.
