Data from: Extreme QTL mapping of germination speed in Arabidopsis thaliana

Seed germination is a key life-history transition for annual plants, which largely determines lifetime performance and fitness. Germination speed, the lapsed time for a non-dormant seed to germinate, is a poorly understood trait important for plants’ competitiveness and fitness in fluctuating environments. Germination speed varied by 30% among 18 A. thaliana populations measured, and exhibited weak negative correlation with flowering time and seed weight, with significant genetic effect (p<0.005). To dissect the genetic architecture of germination speed, we developed the Extreme QTL (X-QTL) mapping method in Arabidopsis thaliana. The method has been shown in yeast to increase QTL mapping power by integrating selective screening and bulk-segregant-analysis in an very large mapping population. By pooled genotyping of top 5% of rapid germinants from ~100,000 F3 individuals, three X-QTLs regions were identified on chromosomes 1, 3, and 4. All regions were confirmed as QTL regions by sequencing 192 rapid germinants from an independent F3 selection experiment. Positional overlaps were found between X-QTLs and previously-identified seed, life history, and fitness QTLs, suggesting pleiotropy or tight linkage between life-history trait genes. Our method provides a rapid mapping platform in A. thaliana with potentially greater power. One can also relate identified X-QTLs to the A. thaliana physical map, facilitating candidate gene identification.