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Field collection, preservation and large-scale DNA extraction procedures for cassava (Manihot esculenta Crantz)

Ranjana Bhattacharjee, Morag Ferguson, Melaku Gedil, Dominique Dumet and Ivan Ingelbrecht (2009) AFRICAN JOURNAL OF BIOTECHNOLOGY. 8(15). p.3424-3430
abstract
Some genetic studies using molecular methods such as diversity assessment or marker-assisted selection require collection of a large number of samples from fields located in the vicinity or in remote areas, followed by isolation of good quality DNA in a short time span. In the present study, different tissue preservation methods were compared for subsequent DNA extraction using a modified CTAB method in two 96-well plates, following grinding of leaf tissues with a GenoGrinder 2000. We found that preservation of leaf tissues in NaCl-CTAB-azide buffer (as described in Rogstad, 1992) at 4 degrees C is a better storage procedure than preservation at -20 degrees C to obtain good quality DNA. Comparison of DNA extraction with or without use of phenol revealed that the quality of DNA was not drastically affected when non-phenol extraction protocol was used and did not affect PCR amplification. Thus, the recommended DNA extraction procedure allowed us to process 192 samples per day at a cost of $0.80 per sample, with an average yield of 1.8 mu g, suitable for both PCR and genotyping.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
NaCl-CTAB-azide solution, genogrinder 2000, phenol, Cassava, GENOMIC DNA, GENETIC DIVERSITY, CLONAL ORGANISMS, CIRSIUM-ARVENSE, CANADA THISTLE, AMPLIFICATION, MARKERS, LEAVES
journal title
AFRICAN JOURNAL OF BIOTECHNOLOGY
Afr. J. Biotechnol.
volume
8
issue
15
pages
3424 - 3430
Web of Science type
Article
Web of Science id
000270306200006
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
0.565 (2009)
JCR rank
131/150 (2009)
JCR quartile
4 (2009)
ISSN
1684-5315
language
English
UGent publication?
no
classification
A1
id
1981950
handle
http://hdl.handle.net/1854/LU-1981950
date created
2012-01-10 16:02:16
date last changed
2016-12-19 15:42:22
@article{1981950,
  abstract     = {Some genetic studies using molecular methods such as diversity assessment or marker-assisted selection require collection of a large number of samples from fields located in the vicinity or in remote areas, followed by isolation of good quality DNA in a short time span. In the present study, different tissue preservation methods were compared for subsequent DNA extraction using a modified CTAB method in two 96-well plates, following grinding of leaf tissues with a GenoGrinder 2000. We found that preservation of leaf tissues in NaCl-CTAB-azide buffer (as described in Rogstad, 1992) at 4 degrees C is a better storage procedure than preservation at -20 degrees C to obtain good quality DNA. Comparison of DNA extraction with or without use of phenol revealed that the quality of DNA was not drastically affected when non-phenol extraction protocol was used and did not affect PCR amplification. Thus, the recommended DNA extraction procedure allowed us to process 192 samples per day at a cost of \$0.80 per sample, with an average yield of 1.8 mu g, suitable for both PCR and genotyping.},
  author       = {Bhattacharjee, Ranjana and Ferguson, Morag and Gedil, Melaku and Dumet, Dominique and Ingelbrecht, Ivan},
  issn         = {1684-5315},
  journal      = {AFRICAN JOURNAL OF BIOTECHNOLOGY},
  keyword      = {NaCl-CTAB-azide solution,genogrinder 2000,phenol,Cassava,GENOMIC DNA,GENETIC DIVERSITY,CLONAL ORGANISMS,CIRSIUM-ARVENSE,CANADA THISTLE,AMPLIFICATION,MARKERS,LEAVES},
  language     = {eng},
  number       = {15},
  pages        = {3424--3430},
  title        = {Field collection, preservation and large-scale DNA extraction procedures for cassava (Manihot esculenta Crantz)},
  volume       = {8},
  year         = {2009},
}

Chicago
Bhattacharjee, Ranjana, Morag Ferguson, Melaku Gedil, Dominique Dumet, and Ivan Ingelbrecht. 2009. “Field Collection, Preservation and Large-scale DNA Extraction Procedures for Cassava (Manihot Esculenta Crantz).” African Journal of Biotechnology 8 (15): 3424–3430.
APA
Bhattacharjee, R., Ferguson, M., Gedil, M., Dumet, D., & Ingelbrecht, I. (2009). Field collection, preservation and large-scale DNA extraction procedures for cassava (Manihot esculenta Crantz). AFRICAN JOURNAL OF BIOTECHNOLOGY, 8(15), 3424–3430.
Vancouver
1.
Bhattacharjee R, Ferguson M, Gedil M, Dumet D, Ingelbrecht I. Field collection, preservation and large-scale DNA extraction procedures for cassava (Manihot esculenta Crantz). AFRICAN JOURNAL OF BIOTECHNOLOGY. 2009;8(15):3424–30.
MLA
Bhattacharjee, Ranjana, Morag Ferguson, Melaku Gedil, et al. “Field Collection, Preservation and Large-scale DNA Extraction Procedures for Cassava (Manihot Esculenta Crantz).” AFRICAN JOURNAL OF BIOTECHNOLOGY 8.15 (2009): 3424–3430. Print.