Extreme QTL mapping of germination speed in Arabidopsis thaliana

Wei Yuan, Jonathan Flowers, Dustin J. Sahraie, Ian M. Ehrenreich, Michael Purugganan

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)4177-4196
Number of pages20
JournalMolecular Ecology
Volume25
Issue number17
DOIs
StatePublished - Sep 1 2016

Fingerprint

Germination
Arabidopsis
quantitative trait loci
Seeds
germination
Arabidopsis thaliana
seed
fitness
life history
Chromosomes, Human, Pair 4
mapping method
annual plant
Chromosomes, Human, Pair 3
Chromosomes, Human, Pair 1
Genetic Association Studies
competitiveness
Population
flowering
yeast
chromosome

Keywords

  • bulk-segregant analysis
  • life history
  • quantitative genomics
  • seed ecology

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Medicine(all)
  • Genetics

Cite this

Yuan, W., Flowers, J., Sahraie, D. J., Ehrenreich, I. M., & Purugganan, M. (2016). Extreme QTL mapping of germination speed in Arabidopsis thaliana. Molecular Ecology, 25(17), 4177-4196. https://doi.org/10.1111/mec.13768

Extreme QTL mapping of germination speed in Arabidopsis thaliana. / Yuan, Wei; Flowers, Jonathan; Sahraie, Dustin J.; Ehrenreich, Ian M.; Purugganan, Michael.

In: Molecular Ecology, Vol. 25, No. 17, 01.09.2016, p. 4177-4196.

Research output: Contribution to journalArticle

Yuan, W, Flowers, J, Sahraie, DJ, Ehrenreich, IM & Purugganan, M 2016, 'Extreme QTL mapping of germination speed in Arabidopsis thaliana', Molecular Ecology, vol. 25, no. 17, pp. 4177-4196. https://doi.org/10.1111/mec.13768
Yuan, Wei ; Flowers, Jonathan ; Sahraie, Dustin J. ; Ehrenreich, Ian M. ; Purugganan, Michael. / Extreme QTL mapping of germination speed in Arabidopsis thaliana. In: Molecular Ecology. 2016 ; Vol. 25, No. 17. pp. 4177-4196.
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