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

Seed germination is a key life history transition for annual plants and partly determines lifetime performance and fitness. Germination speed, the elapsed time for a nondormant seed to germinate, is a poorly understood trait important for plants’ competitiveness and fitness in fluctuating environments. Germination speed varied by 30% among 18 Arabidopsis thaliana populations measured, and exhibited weak negative correlation with flowering time and seed weight, with significant genotype effect (P < 0.005). To dissect the genetic architecture of germination speed, we developed the extreme QTL (X-QTL) mapping method in A. thaliana. The method has been shown in yeast to increase QTL mapping power by integrating selective screening and bulk-segregant analysis in a very large mapping population. By pooled genotyping of top 5% of rapid germinants from ~100 000 F3 individuals, three X-QTL 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. 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.种子萌发是一年生植物关键的生活史转变环节，在一定程度上决定了植株的终身生长表现与适合度（fitness）。萌发速度，即非休眠种子完成萌发所需的耗时，是一个尚未得到充分解析的性状，但其对植物在波动环境中的竞争力与适合度至关重要。在所检测的18个拟南芥（Arabidopsis thaliana）种群中，萌发速度的变异幅度达30%；该性状与开花时间、种子重量呈微弱负相关，且存在显著的基因型效应（P < 0.005）。为解析萌发速度的遗传架构，我们在拟南芥中开发了极端QTL（extreme QTL, X-QTL）定位方法。该方法已在酵母体系中得到验证：通过在超大规模定位群体中整合选择性筛选与集群分离分析（bulk-segregant analysis），可提升QTL定位效力。通过对约10万个F3代个体中萌发速度最快的5%单株进行混样基因分型，我们在第1、3、4号染色体上共定位到3个X-QTL区域。通过对独立F3代筛选实验中获得的192株快速萌发单株进行测序，所有上述区域均被验证为QTL区域。研究还发现，这些X-QTL与此前已报道的种子相关、生活史相关以及适合度相关QTL存在位置重叠。本方法为拟南芥提供了一套快速定位平台，具备更高的定位潜力；同时，可将定位得到的X-QTL与拟南芥物理图谱进行关联，从而助力候选基因的筛选与鉴定。