title: Extreme QTL mapping of germination speed in Arabidopsis thaliana.
abstract: 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.
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Yuan
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA.|Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Flowers
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA.
authors.forename: Dustin J
authors.initials: DJ
authors.lastname: Sahraie
authors.affiliation: Molecular and Computational Biology Section, University of Southern California, Ray R. Irani Hall 201, Los Angeles, CA, 90089-2910, USA.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Ehrenreich
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Purugganan
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D002874:Chromosome Mapping / Q000379:methods*; D005838:Genotype; D018525:Germination / Q000235:genetics*; D010641:Phenotype; D040641:Quantitative Trait Loci
keywords: bulk-segregant analysis; life history; quantitative genomics; seed ecology