Arabidopsis Doubled Haploids: Rapid Homozygous Lines for Quantitative Trait Locus Mapping

Quantitative trait locus (QTL) mapping is a powerful tool for investigating the genetic basis of natural variation. QTLs can be mapped using a number of different population designs, but recombinant inbred lines (RILs) are amongst the most effective. Unfortunately, homozygous RIL populations are time consuming to construct, typically requiring at least six generations of selfing starting from a heterozygous F1. Haploid plants produced from an F1 combine the two parental genomes and have only one allele at every locus, but are sterile. Converting these haploids into fertile diploids (termed "doubled haploids") produces immortal homozygous lines in only two steps. Here we describe a new technique for the rapid development of recombinant doubled haploid populations: the use of centromere-mediated genome elimination. Our population was genotyped using reduced representation Illumina sequencing and found to have a genetic map distance and parental allele frequency similar to those found in existing RIL sets. We phenotyped for traits related to flowering time and for petiole length, and successfully mapped QTL controlling each of these traits. This demonstrates that doubled haploid populations offer a rapid, easy alternative to RILs for Arabidopsis genetic analysis. Now, using genome elimination, it is possible to expedite construction of recombinant populations.