Difference between revisions of "Glycine max"
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=='''''Heavy Metals & Heat Treatments'''''== | =='''''Heavy Metals & Heat Treatments'''''== | ||
− | === | + | ===Internal Control Genes=== |
{|class="wikitable sortable" style="font-size:10pt; width:100%" | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
|- | |- | ||
Line 22: | Line 22: | ||
|align="center"| Tubulin alpha-4 | |align="center"| Tubulin alpha-4 | ||
| | | | ||
− | *Al stress | + | * Roots under Al stress |
− | * | + | * Roots and leaves under heat stress |
|align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/XM_003555953.3 '''LOC100781185'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/XM_003555953.3 '''LOC100781185'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 33: | Line 33: | ||
|- | |- | ||
|align="center"| Fbox<ref name="ref1"/> | |align="center"| Fbox<ref name="ref1"/> | ||
− | |align="center"| | + | |align="center"| F-box protein SKIP16-like |
| | | | ||
− | *Cd stress | + | * Roots and leaves under Cd stress |
|align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/NM_001254106.2 '''LOC100809876'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/NM_001254106.2 '''LOC100809876'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 47: | Line 47: | ||
|align="center"| Hypothetical protein | |align="center"| Hypothetical protein | ||
| | | | ||
− | * Cd stress | + | * Roots and leaves under Cd stress |
− | * | + | * Roots and leaves under heat stress |
|align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/XM_003528209.3 '''LOC100789577'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/XM_003528209.3 '''LOC100789577'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 60: | Line 60: | ||
|align="center"| 60S ribosome protein | |align="center"| 60S ribosome protein | ||
| | | | ||
− | * Cd stress | + | * Roots and leaves under Cd stress |
|align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/XM_003551021.3 '''LOC100778077'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/XM_003551021.3 '''LOC100778077'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 76: | Line 76: | ||
* [https://genorm.cmgg.be/ '''geNorm method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/12184808 '''Related Reference'''] | * [https://genorm.cmgg.be/ '''geNorm method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/12184808 '''Related Reference'''] | ||
* [https://moma.dk/normfinder-software '''NormFinder method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15289330 '''Related Reference'''] | * [https://moma.dk/normfinder-software '''NormFinder method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15289330 '''Related Reference'''] | ||
+ | * [http://www.gene-quantification.com/bestkeeper.html '''BestKeeper method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15127793 '''Related Reference'''] | ||
* '''Comparative ΔCt method''' && [https://www.ncbi.nlm.nih.gov/pubmed/17026756 '''Related Reference'''] | * '''Comparative ΔCt method''' && [https://www.ncbi.nlm.nih.gov/pubmed/17026756 '''Related Reference'''] | ||
− | |||
* '''Ref-Finder method''' && [https://www.ncbi.nlm.nih.gov/pubmed/22290409 '''Related Reference'''] | * '''Ref-Finder method''' && [https://www.ncbi.nlm.nih.gov/pubmed/22290409 '''Related Reference'''] | ||
+ | |||
===Contact=== | ===Contact=== | ||
*'''Name''': Yan Li | *'''Name''': Yan Li | ||
Line 84: | Line 85: | ||
*'''Institution''': National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China | *'''Institution''': National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China | ||
===Citation Statistics=== | ===Citation Statistics=== | ||
− | Cited by '''1''' (Based on Google Scholar [2017- | + | Cited by [https://scholar.google.com/scholar?cites=11707883890029736734&as_sdt=2005&sciodt=0,5&hl=en '''1'''] (Based on Google Scholar [2017-09-01]) |
=='''''Biotic Stresses'''''== | =='''''Biotic Stresses'''''== | ||
− | === | + | ===Internal Control Genes=== |
{|class="wikitable sortable" style="font-size:10pt; width:100%" | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
|- | |- | ||
Line 168: | Line 169: | ||
* [https://moma.dk/normfinder-software '''NormFinder method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15289330 '''Related Reference'''] | * [https://moma.dk/normfinder-software '''NormFinder method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15289330 '''Related Reference'''] | ||
* [http://www.gene-quantification.com/bestkeeper.html '''BestKeeper method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15127793 '''Related Reference'''] | * [http://www.gene-quantification.com/bestkeeper.html '''BestKeeper method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15127793 '''Related Reference'''] | ||
+ | |||
===Contact=== | ===Contact=== | ||
*'''Name''': Raman Bansal | *'''Name''': Raman Bansal | ||
Line 173: | Line 175: | ||
*'''Institution''': Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, 44691, United States of America | *'''Institution''': Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, 44691, United States of America | ||
===Citation Statistics=== | ===Citation Statistics=== | ||
− | Cited by ''' | + | Cited by [https://scholar.google.com/scholar?cites=11290884871876745927&as_sdt=2005&sciodt=0,5&hl=en '''10'''] (Based on Google Scholar [2017-09-01]) |
=='''''Different Tissues & Abiotic Stress'''''== | =='''''Different Tissues & Abiotic Stress'''''== | ||
− | === | + | ===Internal Control Genes=== |
{|class="wikitable sortable" style="font-size:10pt; width:100%" | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
|- | |- | ||
Line 275: | Line 277: | ||
*'''Institution''': National Center for Soybean Biotechnology and Division of Plant Sciences,University of Missouri, Columbia, Missouri, United States of America | *'''Institution''': National Center for Soybean Biotechnology and Division of Plant Sciences,University of Missouri, Columbia, Missouri, United States of America | ||
===Citation Statistics=== | ===Citation Statistics=== | ||
− | Cited by ''' | + | Cited by [https://scholar.google.com/scholar?cites=7394442497640494154&as_sdt=2005&sciodt=0,5&hl=en '''83'''] (Based on Google Scholar [2017-09-01]) |
=='''''Hypoxic Condition'''''== | =='''''Hypoxic Condition'''''== | ||
− | === | + | ===Internal Control Genes=== |
{|class="wikitable sortable" style="font-size:10pt; width:100%" | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
|- | |- | ||
Line 326: | Line 328: | ||
*'''Institution''': Laboratório de Biotecnologia Vegetal, Embrapa Soja, Londrina, PR, Brasil | *'''Institution''': Laboratório de Biotecnologia Vegetal, Embrapa Soja, Londrina, PR, Brasil | ||
===Citation Statistics=== | ===Citation Statistics=== | ||
− | Cited by '''10''' (Based on Google Scholar [2017- | + | Cited by [https://scholar.google.com/scholar?cites=9946429395020319479&as_sdt=2005&sciodt=0,5&hl=en '''10'''] (Based on Google Scholar [2017-09-01]) |
+ | |||
+ | ==''''' Abiotic or Biotic Stress'''''== | ||
+ | ===Internal Control Genes=== | ||
+ | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
+ | |- | ||
+ | ! Gene Symbol | ||
+ | ! Gene Name | ||
+ | ! style="width=25% font-size:9pt "|Application Scope | ||
+ | ! Accession Number | ||
+ | ! Primers (5'-3')<br>[Forward/Reverse] | ||
+ | ! Size [bp] | ||
+ | ! Tm [℃] | ||
+ | ! Detection | ||
+ | |- | ||
+ | |align="center"| miR1520d<ref name="ref5"/> | ||
+ | |align="center"| miR1520d | ||
+ | | | ||
+ | * Different soybean tissues and genotypes | ||
+ | * Abiotic or biotic stress treatments | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/NR_048594.1 '''NR_048594'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F:ATCAGAACATGACACGTGACAA-3 | ||
+ | * R:GTGCAGGGTCCGAGGT-3 | ||
+ | |align="center"| 70 | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| miR156b<ref name="ref5"/> | ||
+ | |align="center"| miR156b | ||
+ | | | ||
+ | * Different soybean tissues and genotypes | ||
+ | * Abiotic or biotic stress treatments | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nuccore/NR_126594.1 '''NR_126594'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F:TGACAGAAGAGAGAGAGCACA-3 | ||
+ | * R:GTGCAGGGTCCGAGGT-3 | ||
+ | |align="center"| 72 | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |} | ||
+ | |||
+ | ===Molecular Types=== | ||
+ | * miRNA | ||
+ | |||
+ | ===Evaluation Methods=== | ||
+ | * [https://genorm.cmgg.be/ '''geNorm method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/12184808 '''Related Reference'''] | ||
+ | * [https://moma.dk/normfinder-software '''NormFinder method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15289330 '''Related Reference'''] | ||
+ | ===Contact=== | ||
+ | *'''Name''': Rogério Margis | ||
+ | *'''Email''': rogerio.margis@ufrgs.br | ||
+ | *'''Institution''': Centre of Biotechnology, Laboratory of Genomes and Plant Population, Building 43431, Federal University of Rio Grande do Sul–UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil | ||
+ | ===Citation Statistics=== | ||
+ | Cited by [https://scholar.google.com/scholar?cites=14367671962286600074&as_sdt=2005&sciodt=0,5&hl=en '''83'''] (Based on Google Scholar [2017-09-01]) | ||
=='''References'''== | =='''References'''== | ||
Line 344: | Line 399: | ||
<ref name="ref4"> | <ref name="ref4"> | ||
Nakayama T J, Rodrigues F A, Neumaier N, et al. Reference genes for quantitative real-time polymerase chain reaction studies in soybean plants under hypoxic conditions[J]. Genet Mol Res, 2014, 13: 860-871. | Nakayama T J, Rodrigues F A, Neumaier N, et al. Reference genes for quantitative real-time polymerase chain reaction studies in soybean plants under hypoxic conditions[J]. Genet Mol Res, 2014, 13: 860-871. | ||
+ | </ref> | ||
+ | <ref name="ref5"> | ||
+ | Kulcheski, Franceli Rodrigues, et al. The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Analytical biochemistry 406.2 (2010): 185-192. | ||
</ref> | </ref> | ||
</references> | </references> | ||
+ | |||
+ | =='''Categories'''== | ||
[[Category:Plants]] | [[Category:Plants]] | ||
− | [[Category:mRNA]] | + | [[Category:mRNA]][[Category:Non-coding RNA]] |
[[Category:SYBR]] | [[Category:SYBR]] | ||
− | [[Category:60SRP]] [[Category: | + | [[Category:60SRP]] [[Category:RPL]] [[Category:ABCT]] [[Category:ABCT]] [[Category:ACT]] [[Category:Cyclophilin]] [[Category:EF1α]] [[Category:F-box]] [[Category:F-box]] [[Category:F-box]] [[Category:IDE]] [[Category:Tubulin]] [[Category:Tubulin]] [[Category:Tubulin]] |
[[Category:Salinity Treatment]] [[Category:Different Tissues]] [[Category:Abiotic Stress]] [[Category:Heat Treatment]] [[Category:Dehydration Treatment]] [[Category:Biotic Stress]] [[Category:Hormone Treatment]] [[Category:Hypoxic Treatment]] [[Category:Cold Treatment]] [[Category:Heavy Metals Treatments]] | [[Category:Salinity Treatment]] [[Category:Different Tissues]] [[Category:Abiotic Stress]] [[Category:Heat Treatment]] [[Category:Dehydration Treatment]] [[Category:Biotic Stress]] [[Category:Hormone Treatment]] [[Category:Hypoxic Treatment]] [[Category:Cold Treatment]] [[Category:Heavy Metals Treatments]] | ||
+ | [[Category:geNorm]] | ||
+ | [[Category:NormFinder]] | ||
+ | [[Category:BestKeeper]] | ||
+ | [[Category:Delta Ct]] | ||
+ | [[Category:RefFinder]] | ||
+ | [[Category:SKIP]] |
Latest revision as of 07:17, 1 September 2017
Contents
Description
- Glycine max is a species of legume native to East Asia. It is the world's major economically important agricultural crop widely grown for its edible bean. It also provides important source of vegetable oil and proteins and has numerous uses such as biofuel, feedstock, industrial products, and cosmetics. The main countries growing soybeans are the United States, Brazil and Argentina[1][2].
- Common Name: Soybean
- NCBI Taxonomy
Heavy Metals & Heat Treatments
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
TUA4[1] | Tubulin alpha-4 |
|
LOC100781185 |
|
159 | 60 | SYBR |
Fbox[1] | F-box protein SKIP16-like |
|
LOC100809876 |
|
93 | 60 | SYBR |
UKN2[1] | Hypothetical protein |
|
LOC100789577 |
|
156 | 60 | SYBR |
60SRP[1] | 60S ribosome protein |
|
LOC100778077 |
|
125 | 60 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
- geNorm method && Related Reference
- NormFinder method && Related Reference
- BestKeeper method && Related Reference
- Comparative ΔCt method && Related Reference
- Ref-Finder method && Related Reference
Contact
- Name: Yan Li
- Email: yanli1@njau.edu.cn
- Institution: National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
Citation Statistics
Cited by 1 (Based on Google Scholar [2017-09-01])
Biotic Stresses
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
ABCT[2] | ATP-binding cassette transporter |
|
Glyma.12g020500 |
|
166 | 79.5 | SYBR |
FBOX[2] | F-box only protein |
|
Glyma.12g051100 |
|
99 | 80 | SYBR |
TUA4[2] | Tubulin alpha-4 |
|
Glyma.20g136000 |
|
150 | 79.5 | SYBR |
CYP[2] | Cyclophilin |
|
Glyma.12g024700 |
|
158 | 85 | SYBR |
TUB4[2] | Tubulin beta-4 |
|
Glyma.19g127700 |
|
117 | 83 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
- geNorm method && Related Reference
- NormFinder method && Related Reference
- BestKeeper method && Related Reference
Contact
- Name: Raman Bansal
- Email: bansal.67@osu.edu
- Institution: Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, 44691, United States of America
Citation Statistics
Cited by 10 (Based on Google Scholar [2017-09-01])
Different Tissues & Abiotic Stress
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
Fbox[3] | F-box protein family |
|
Glyma12g05510 |
|
118 | 60 | SYBR |
ABCT[3] | ATP-binding cassette transporter |
|
Glyma12g02310 |
|
106 | 60 | SYBR |
60SRP[3] | 60s Ribosomal protein L30 |
|
Glyma17g05270 |
|
125 | 60 | SYBR |
ELF1b[3] | Eukaryotic elongation factor 1 beta |
|
Glyma02g44460 |
|
118 | 60 | SYBR |
IDE[3] | Insulin-degrading enzyme |
|
AW310136 |
|
131 | 60 | SYBR |
Act27[3] | Actin |
|
Glyma19g32990 |
|
119 | 60 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
- geNorm method && Related Reference
- Comparative ΔCt method && Related Reference
Contact
- Name: Henry T. Nguyen
- Email: nguyenhenry@missouri.edu
- Institution: National Center for Soybean Biotechnology and Division of Plant Sciences,University of Missouri, Columbia, Missouri, United States of America
Citation Statistics
Cited by 83 (Based on Google Scholar [2017-09-01])
Hypoxic Condition
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
ELF1B[4] | Elongation factor 1-beta |
|
Glyma02g44460 |
|
118 | 60 | SYBR |
ACTB[4] | Actin-11 |
|
Glyma15g05570 |
|
118 | 60 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
Contact
- Name: A.L. Nepomuceno
- Email: alexandre.nepomuceno@embrapa.br
- Institution: Laboratório de Biotecnologia Vegetal, Embrapa Soja, Londrina, PR, Brasil
Citation Statistics
Cited by 10 (Based on Google Scholar [2017-09-01])
Abiotic or Biotic Stress
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
miR1520d[5] | miR1520d |
|
NR_048594 |
|
70 | 60 | SYBR |
miR156b[5] | miR156b |
|
NR_126594 |
|
72 | 60 | SYBR |
Molecular Types
- miRNA
Evaluation Methods
Contact
- Name: Rogério Margis
- Email: rogerio.margis@ufrgs.br
- Institution: Centre of Biotechnology, Laboratory of Genomes and Plant Population, Building 43431, Federal University of Rio Grande do Sul–UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
Citation Statistics
Cited by 83 (Based on Google Scholar [2017-09-01])
References
- ↑ 1.0 1.1 1.2 1.3 1.4 Gao M, Liu Y, Ma X, et al. Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean[J]. PloS one, 2017, 12(1): e0168965.
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Bansal R, Mittapelly P, Cassone B J, et al. Recommended reference genes for quantitative PCR analysis in soybean have variable stabilities during diverse biotic stresses[J]. PloS one, 2015, 10(8): e0134890.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Le D T, Aldrich D L, Valliyodan B, et al. Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions[J]. PLoS One, 2012, 7(9): e46487.
- ↑ 4.0 4.1 Nakayama T J, Rodrigues F A, Neumaier N, et al. Reference genes for quantitative real-time polymerase chain reaction studies in soybean plants under hypoxic conditions[J]. Genet Mol Res, 2014, 13: 860-871.
- ↑ 5.0 5.1 Kulcheski, Franceli Rodrigues, et al. The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Analytical biochemistry 406.2 (2010): 185-192.