Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population

To exploit the diversity in Arabidopsis thaliana, eight founder accessions were crossed to produce six recombinant inbred line (RIL) subpopulations, together called an Arabidopsis multiparent RIL (AMPRIL) population. Founders were crossed pairwise to produce four F1 hybrids. These F1s were crossed according to a diallel scheme. The resulting offspring was then selfed for three generations. The F4 generation was genotyped with SNP and microsatellite markers. Data for flowering time and leaf morphology traits were determined in the F5 generation. Quantitative trait locus (QTL) analysis for these traits was performed using especially developed mixed-model methodology, allowing tests for QTL main effects, QTL by background interactions, and QTL by QTL interactions. Because RILs were genotyped in the F4 generation and phenotyped in the F5 generation, residual heterozygosity could be used to confirm and fine-map a number of the QTLs in the selfed progeny of lines containing such heterozygosity. The AMPRIL population is an attractive resource for the study of complex traits.