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Title: Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist

Abstract

In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive geneticmore » tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.« less

Authors:
 [1];  [2];  [1];  [3];  [1];  [3];  [1]
  1. ORNL
  2. Oak Ridge National Laboratory (ORNL)
  3. Nanjing Forestry University, China
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
948538
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Genome Research
Additional Journal Information:
Journal Volume: 181
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AMPLIFICATION; CHROMOSOMES; GENETICS

Citation Formats

Yin, Tongming, ZHANG, Dr. XINYE, Gunter, Lee E, Li, Shuxian, Wullschleger, Stan D, Huang, Prof. Minren, and Tuskan, Gerald A. Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist. United States: N. p., 2009. Web.
Yin, Tongming, ZHANG, Dr. XINYE, Gunter, Lee E, Li, Shuxian, Wullschleger, Stan D, Huang, Prof. Minren, & Tuskan, Gerald A. Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist. United States.
Yin, Tongming, ZHANG, Dr. XINYE, Gunter, Lee E, Li, Shuxian, Wullschleger, Stan D, Huang, Prof. Minren, and Tuskan, Gerald A. Thu . "Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist". United States.
@article{osti_948538,
title = {Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist},
author = {Yin, Tongming and ZHANG, Dr. XINYE and Gunter, Lee E and Li, Shuxian and Wullschleger, Stan D and Huang, Prof. Minren and Tuskan, Gerald A},
abstractNote = {In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.},
doi = {},
url = {https://www.osti.gov/biblio/948538}, journal = {Genome Research},
number = ,
volume = 181,
place = {United States},
year = {2009},
month = {1}
}