Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa
- 16 March 2006
- journal article
- Published by Wiley in Molecular Ecology
- Vol. 15 (5), 1367-1378
- https://doi.org/10.1111/j.1365-294x.2006.02885.x
Abstract
Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa , and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula , based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucle- otide diversity, measured as π Total , was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r 2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.Keywords
This publication has 34 references indexed in Scilit:
- TILLING without a plough: a new method with applications for reverse geneticsCurrent Opinion in Plant Biology, 2005
- Poplar genomics comes of ageNew Phytologist, 2004
- The genetic control of lignin deposition during plant growth and developmentNew Phytologist, 2004
- Overlapping and non-redundant functions of theArabidopsisauxin response factorsMONOPTEROSandNONPHOTOTROPIC HYPOCOTYL 4Development, 2004
- DnaSP, DNA polymorphism analyses by the coalescent and other methodsBioinformatics, 2003
- A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype DataAmerican Journal of Human Genetics, 2003
- Analysis of the Molecular Basis of Flowering Time Variation in Arabidopsis AccessionsPlant Physiology, 2003
- Large-Scale Discovery of Induced Point Mutations With High-Throughput TILLINGGenome Research, 2003
- Large-Scale Identification of Single-Feature Polymorphisms in Complex GenomesGenome Research, 2003
- Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired ResistanceCell, 2000