Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant

Lila O. Vodkin, Anupama Khanna, Robin Shealy, Steven J. Clough, Delkin Orlando Gonzalez, Reena Philip, Gracia Zabala, Françoise Thibaud-Nissen, Mark Sidarous, Martina V. Strömvik, Elizabeth Shoop, Christina Schmidt, Ernest Retzel, John Erpelding, Randy C. Shoemaker, Alicia M. Rodriguez-Huete, Joseph C. Polacco, Virginia Coryell, Paul S Keim, George Gong & 3 others Lei Liu, Jose Pardinas, Peter Schweitzer

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

Background: Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max) is one of the most economically valuable crop species in the world food supply. In order to accelerate both gene discovery as well as hypothesis-driven research in soybean, global expression resources needed to be developed. The applications of microarray for determining patterns of expression in different tissues or during conditional treatments by dual labeling of the mRNAs are unlimited. In addition, discovery of the molecular basis of traits through examination of naturally occurring variation in hundreds of mutant lines could be enhanced by the construction and use of soybean cDNA microarrays. Results: We report the construction and analysis of a low redundancy 'unigene' set of 27,513 clones that represent a variety of soybean cDNA libraries made from a wide array of source tissue and organ systems, developmental stages, and stress or pathogen-challenged plants. The set was assembled from the 5′ sequence data of the cDNA clones using cluster analysis programs. The selected clones were then physically reracked and sequenced at the 3′ end. In order to increase gene discovery from immature cotyledon libraries that contain abundant mRNAs representing storage protein gene families, we utilized a high density filter normalization approach to preferentially select more weakly expressed cDNAs. All 27,513 cDNA inserts were amplified by polymerase chain reaction. The amplified products, along with some repetitively spotted control or 'choice' clones, were used to produce three 9,728-element microarrays that have been used to examine tissue specific gene expression and global expression in mutant isolines. Conclusions: Global expression studies will be greatly aided by the availability of the sequence-validated and low redundancy cDNA sets described in this report. These cDNAs and ESTs represent a wide array of developmental stages and physiological conditions of the soybean plant. We also demonstrate that the quality of the data from the soybean cDNA microarrays is sufficiently reliable to examine isogenic lines that differ with respect to a mutant phenotype and thereby to define a small list of candidate genes potentially encoding or modulated by the mutant phenotype.

Original languageEnglish (US)
Article number73
JournalBMC Genomics
Volume5
DOIs
StatePublished - Sep 29 2004

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Oligonucleotide Array Sequence Analysis
Soybeans
Complementary DNA
Clone Cells
Genetic Association Studies
Phenotype
Gene Expression
Messenger RNA
Food Supply
Cotyledon
Expressed Sequence Tags
Gene Library
Cluster Analysis
Polymerase Chain Reaction
Research
Genes
Proteins

ASJC Scopus subject areas

  • Medicine(all)
  • Biotechnology
  • Genetics

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Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. / Vodkin, Lila O.; Khanna, Anupama; Shealy, Robin; Clough, Steven J.; Gonzalez, Delkin Orlando; Philip, Reena; Zabala, Gracia; Thibaud-Nissen, Françoise; Sidarous, Mark; Strömvik, Martina V.; Shoop, Elizabeth; Schmidt, Christina; Retzel, Ernest; Erpelding, John; Shoemaker, Randy C.; Rodriguez-Huete, Alicia M.; Polacco, Joseph C.; Coryell, Virginia; Keim, Paul S; Gong, George; Liu, Lei; Pardinas, Jose; Schweitzer, Peter.

In: BMC Genomics, Vol. 5, 73, 29.09.2004.

Research output: Contribution to journalArticle

Vodkin, LO, Khanna, A, Shealy, R, Clough, SJ, Gonzalez, DO, Philip, R, Zabala, G, Thibaud-Nissen, F, Sidarous, M, Strömvik, MV, Shoop, E, Schmidt, C, Retzel, E, Erpelding, J, Shoemaker, RC, Rodriguez-Huete, AM, Polacco, JC, Coryell, V, Keim, PS, Gong, G, Liu, L, Pardinas, J & Schweitzer, P 2004, 'Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant', BMC Genomics, vol. 5, 73. https://doi.org/10.1186/1471-2164-5-73
Vodkin, Lila O. ; Khanna, Anupama ; Shealy, Robin ; Clough, Steven J. ; Gonzalez, Delkin Orlando ; Philip, Reena ; Zabala, Gracia ; Thibaud-Nissen, Françoise ; Sidarous, Mark ; Strömvik, Martina V. ; Shoop, Elizabeth ; Schmidt, Christina ; Retzel, Ernest ; Erpelding, John ; Shoemaker, Randy C. ; Rodriguez-Huete, Alicia M. ; Polacco, Joseph C. ; Coryell, Virginia ; Keim, Paul S ; Gong, George ; Liu, Lei ; Pardinas, Jose ; Schweitzer, Peter. / Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. In: BMC Genomics. 2004 ; Vol. 5.
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AU - Vodkin, Lila O.

AU - Khanna, Anupama

AU - Shealy, Robin

AU - Clough, Steven J.

AU - Gonzalez, Delkin Orlando

AU - Philip, Reena

AU - Zabala, Gracia

AU - Thibaud-Nissen, Françoise

AU - Sidarous, Mark

AU - Strömvik, Martina V.

AU - Shoop, Elizabeth

AU - Schmidt, Christina

AU - Retzel, Ernest

AU - Erpelding, John

AU - Shoemaker, Randy C.

AU - Rodriguez-Huete, Alicia M.

AU - Polacco, Joseph C.

AU - Coryell, Virginia

AU - Keim, Paul S

AU - Gong, George

AU - Liu, Lei

AU - Pardinas, Jose

AU - Schweitzer, Peter

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N2 - Background: Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max) is one of the most economically valuable crop species in the world food supply. In order to accelerate both gene discovery as well as hypothesis-driven research in soybean, global expression resources needed to be developed. The applications of microarray for determining patterns of expression in different tissues or during conditional treatments by dual labeling of the mRNAs are unlimited. In addition, discovery of the molecular basis of traits through examination of naturally occurring variation in hundreds of mutant lines could be enhanced by the construction and use of soybean cDNA microarrays. Results: We report the construction and analysis of a low redundancy 'unigene' set of 27,513 clones that represent a variety of soybean cDNA libraries made from a wide array of source tissue and organ systems, developmental stages, and stress or pathogen-challenged plants. The set was assembled from the 5′ sequence data of the cDNA clones using cluster analysis programs. The selected clones were then physically reracked and sequenced at the 3′ end. In order to increase gene discovery from immature cotyledon libraries that contain abundant mRNAs representing storage protein gene families, we utilized a high density filter normalization approach to preferentially select more weakly expressed cDNAs. All 27,513 cDNA inserts were amplified by polymerase chain reaction. The amplified products, along with some repetitively spotted control or 'choice' clones, were used to produce three 9,728-element microarrays that have been used to examine tissue specific gene expression and global expression in mutant isolines. Conclusions: Global expression studies will be greatly aided by the availability of the sequence-validated and low redundancy cDNA sets described in this report. These cDNAs and ESTs represent a wide array of developmental stages and physiological conditions of the soybean plant. We also demonstrate that the quality of the data from the soybean cDNA microarrays is sufficiently reliable to examine isogenic lines that differ with respect to a mutant phenotype and thereby to define a small list of candidate genes potentially encoding or modulated by the mutant phenotype.

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