Difference between revisions of "Coffea arabica L."
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=='''Description'''== | =='''Description'''== | ||
− | ==''''' | + | [[File:Coffea arabica.png|right|200px|link=Coffea arabica L.]] |
− | === | + | *'''''Coffea arabica''''' is a species of Coffea originally indigenous to the forests of the southwestern highlands of Ethiopia. It is an important crop and is crucial to the economy of many developing countries as international exchange commodities in agricultural trade, generating around US$70 billion per year. Its cultivation, processing, transportation and marketing provide employment for millions of people worldwide. |
+ | * <font color=blue>'''Common Name:'''</font> '''Coffee''' | ||
+ | * [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=13443 <font color=blue>'''NCBI Taxonomy'''</font>] | ||
+ | |||
+ | =='''''Abiotic Stress'''''== | ||
+ | ===Internal Control Genes=== | ||
{|class="wikitable sortable" style="font-size:10pt; width:100%" | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
|- | |- | ||
Line 8: | Line 13: | ||
! style="width=25% font-size:9pt "|Application Scope | ! style="width=25% font-size:9pt "|Application Scope | ||
! Accession Number | ! Accession Number | ||
− | ! | + | ! Primers (5'-3')<br>[Forward/Reverse] |
! Size [bp] | ! Size [bp] | ||
! Tm [℃] | ! Tm [℃] | ||
Line 16: | Line 21: | ||
|align="center"| Elongation factor 1 | |align="center"| Elongation factor 1 | ||
| | | | ||
− | * | + | *Nitrogen starvation |
− | * | + | *Salinity treatment |
− | * | + | *Heat treatment |
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW484749.1 '''GW484749.1'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW484749.1 '''GW484749.1'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 30: | Line 35: | ||
|align="center"| Elongation factor 1-alpha | |align="center"| Elongation factor 1-alpha | ||
| | | | ||
− | * | + | *Nitrogen starvation |
− | * | + | *Salinity treatment |
− | * | + | *Heat treatment |
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GT708303.1 '''GT708303.1'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GT708303.1 '''GT708303.1'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 42: | Line 47: | ||
|- | |- | ||
|align="center"| GAPDH<ref name="ref1"/> | |align="center"| GAPDH<ref name="ref1"/> | ||
− | |align="center"| | + | |align="center"| Glyceraldehyde-3-phosphate-dehydrogenase |
| | | | ||
− | * | + | *Nitrogen starvation |
− | * | + | *Salinity treatment |
− | * | + | *Heat treatment |
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW488886.1 '''GW488886.1'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW488886.1 '''GW488886.1'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 58: | Line 63: | ||
|align="center"| Malate dehydrogenase | |align="center"| Malate dehydrogenase | ||
| | | | ||
− | * | + | *Nitrogen starvation |
− | * | + | *Salinity treatment |
− | * | + | *Heat treatment |
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW464198.1 '''GW464198.1'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW464198.1 '''GW464198.1'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 72: | Line 77: | ||
|align="center"| Polyubiquitin 10 | |align="center"| Polyubiquitin 10 | ||
| | | | ||
− | * | + | *Nitrogen starvation |
− | * | + | *Salinity treatment |
− | * | + | *Heat treatment |
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GT697658.1 '''GT697658.1'''] | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GT697658.1 '''GT697658.1'''] | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
Line 84: | Line 89: | ||
|} | |} | ||
− | === | + | ===Molecular Types=== |
* mRNA | * mRNA | ||
Line 95: | Line 100: | ||
*'''Name''': Kenia de Carvalho | *'''Name''': Kenia de Carvalho | ||
*'''Email''': : keniadecarvalho@gmail.com | *'''Email''': : keniadecarvalho@gmail.com | ||
− | *''' | + | *'''Institution''': Programa de Po´s-Graduac ¸a ˜o em Agronomia (Produc ¸a ˜o Vegetal),Departamento de Fitotecnia e Fitossanitarismo, Universidade Federal do Parana ´, Curitiba, PR CEP 80035-050, Brazil |
+ | |||
===Citation Statistics=== | ===Citation Statistics=== | ||
− | Cited by ''' | + | Cited by [https://scholar.google.com/scholar?cites=3592759687893290730&as_sdt=2005&sciodt=0,5&hl=en '''23'''] (Based on Google Scholar [2017-09-01]) |
=='''''Different Air CO2 Supply & Temperature'''''== | =='''''Different Air CO2 Supply & Temperature'''''== | ||
− | === | + | ===Internal Control Genes=== |
{|class="wikitable sortable" style="font-size:10pt; width:100%" | {|class="wikitable sortable" style="font-size:10pt; width:100%" | ||
|- | |- | ||
Line 107: | Line 113: | ||
! style="width=25% font-size:9pt "|Application Scope | ! style="width=25% font-size:9pt "|Application Scope | ||
! Accession Number | ! Accession Number | ||
− | ! | + | ! Primers (5'-3')<br>[Forward/Reverse] |
! Size [bp] | ! Size [bp] | ||
! Tm [℃] | ! Tm [℃] | ||
Line 119: | Line 125: | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
* F:CCTGATGTCAACCACGCAACT | * F:CCTGATGTCAACCACGCAACT | ||
− | * R: | + | * R:GTGGTTATGAACTCTCCATTCAACC |
|align="center"| 100 | |align="center"| 100 | ||
|align="center"| 60 | |align="center"| 60 | ||
Line 131: | Line 137: | ||
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
* F:AAGCTTGCCTATGTGGCTCTTG | * F:AAGCTTGCCTATGTGGCTCTTG | ||
− | * R: | + | * R:TCACTTGTCCATCTGGCAATTC |
|align="center"| 100 | |align="center"| 100 | ||
|align="center"| 60 | |align="center"| 60 | ||
Line 140: | Line 146: | ||
| | | | ||
* Univeral reference gene | * Univeral reference gene | ||
− | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GR987196 ''GR987196''] | + | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GR987196 '''GR987196'''] |
|nowrap style="font-size:9pt"| | |nowrap style="font-size:9pt"| | ||
* F:CAATAGGGGCTTGAAGAGG | * F:CAATAGGGGCTTGAAGAGG | ||
− | * R: | + | * R:TACGCTGCCAATCATCTCAG |
|align="center"| 146 | |align="center"| 146 | ||
|align="center"| 60 | |align="center"| 60 | ||
Line 149: | Line 155: | ||
|} | |} | ||
− | === | + | ===Molecular Types=== |
*mRNA | *mRNA | ||
+ | |||
===Evaluation Methods=== | ===Evaluation Methods=== | ||
* [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'''] | ||
Line 161: | Line 168: | ||
*'''Email''': cochichor@isa.ulisboa.pt | *'''Email''': cochichor@isa.ulisboa.pt | ||
*'''Institution''': Plant-Environment Interactions and Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food, Departmento de Recursos Naturais, Ambiente e Território, Instituto Superior de Agronomia, Universidade de Lisboa (ULisboa), Oeiras, Portugal | *'''Institution''': Plant-Environment Interactions and Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food, Departmento de Recursos Naturais, Ambiente e Território, Instituto Superior de Agronomia, Universidade de Lisboa (ULisboa), Oeiras, Portugal | ||
+ | ===Citation Statistics=== | ||
+ | Cited by [https://scholar.google.com/scholar?cites=1587087814594235308&as_sdt=2005&sciodt=0,5&hl=en '''2'''] (Based on Google Scholar [2017-09-01]) | ||
+ | |||
+ | =='''''Different Genotypes & Abiotic 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"| GAPHD<ref name="ref3"/> | ||
+ | |align="center"| Glyceraldehyde 3-phosphate dehydrogenase | ||
+ | | | ||
+ | * Total assay | ||
+ | *Genotypes | ||
+ | *Cold stress | ||
+ | *Drought stress | ||
+ | |||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/DV692958 '''DV692958'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F:AGGCTGTTGGGAAAGTTCTTC | ||
+ | * R:ACTGTTGGAACTCGGAATGC | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| Cycl<ref name="ref3"/> | ||
+ | |align="center"| Cyclophilin | ||
+ | | | ||
+ | * Total assay | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GT007167 '''GT007167'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F:AGCTCTACGCAGACACGACTCC | ||
+ | * R:GGTCGATCCTTTGAAGTGCAAG | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| UBQ10<ref name="ref3"/> | ||
+ | |align="center"| Ubiquitin | ||
+ | | | ||
+ | * Total assay | ||
+ | *Genotype | ||
+ | *Cold stress | ||
+ | |||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/DV686961 '''DV686961'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F:CAGACCAGCAGAGGCTGATT | ||
+ | * R:AGAACCAAGTGAAGGGTGGA | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| Ap47<ref name="ref3"/> | ||
+ | |align="center"| Clathrin adaptor complexes subunit | ||
+ | | | ||
+ | *Genotype | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/DV690764 '''DV690764'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F: CCAGATTGGAGGATGCTCTT | ||
+ | * R: AAATGCACAAGCAACATTGG | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| EF-1A<ref name="ref3"/> | ||
+ | |align="center"| Elongation factor 1-alpha | ||
+ | | | ||
+ | *Genotype | ||
+ | *Cold stress | ||
+ | *Drought stress | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GR996930 '''GR996930'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F: CATTGTGGTCATTGGTCATGTC | ||
+ | * R: ACACGCTTGTCAATTCCTCCA | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| ACT<ref name="ref3"/> | ||
+ | |align="center"| Actin | ||
+ | | | ||
+ | *Cold stress | ||
+ | *Drought stress | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GT000704 '''GT000704'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F:AAGCTTGCCTATGTGGCTCTTG | ||
+ | * R:TCACTTGTCCATCTGGCAATTC | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |- | ||
+ | |align="center"| Apt<ref name="ref3"/> | ||
+ | |align="center"| Adenine phosphoribosyltransferase | ||
+ | | | ||
+ | *Drought stress | ||
+ | |align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GR996015 '''GR996015'''] | ||
+ | |nowrap style="font-size:9pt"| | ||
+ | * F: ACTCTCCGGGGCTAAAACTGTC | ||
+ | * R:AGGTCGTGCTGGTTGAGTTAGG | ||
+ | |align="center"| NA | ||
+ | |align="center"| 60 | ||
+ | |align="center"| SYBR | ||
+ | |} | ||
+ | |||
+ | ===Molecular Types=== | ||
+ | * mRNA | ||
+ | |||
+ | ===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'''] | ||
+ | * [http://www.gene-quantification.com/bestkeeper.html '''BestKeeper method'''] && [https://www.ncbi.nlm.nih.gov/pubmed/15127793 '''Related Reference'''] | ||
+ | ===Contact=== | ||
+ | *'''Name''': José C. Ramalho | ||
+ | *'''Email''': goulao@iict.pt | ||
+ | *'''Institution''': Centro de Ecofisiologia, Bioquímica e Biotecnologia Vegetal, Instituto de Investigação Científica Tropical I.P. (IICT, IP), Av. da República, Quinta do Marquês, 2784-505 Oeiras, Portugal | ||
+ | ===Citation Statistics=== | ||
+ | Cited by [https://scholar.google.com/scholar?cites=17147318173485000408&as_sdt=2005&sciodt=0,5&hl=en '''37'''] (Based on Google Scholar [2017-09-01]) | ||
=='''References'''== | =='''References'''== | ||
Line 166: | Line 297: | ||
<ref name="ref1"> | <ref name="ref1"> | ||
de Carvalho K, Bespalhok Filho J C, Dos Santos T B, et al. Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization[J]. Molecular biotechnology, 2013, 53(3): 315-325. | de Carvalho K, Bespalhok Filho J C, Dos Santos T B, et al. Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization[J]. Molecular biotechnology, 2013, 53(3): 315-325. | ||
+ | </ref> | ||
+ | <ref name="ref2"> | ||
+ | Martins M Q, Fortunato A S, Rodrigues W P, et al. Selection and validation of reference genes for accurate RT-qPCR data normalization in Coffea spp. under a climate changes context of interacting elevated [CO2] and temperature[J]. Frontiers in plant science, 2017, 8. | ||
+ | </ref> | ||
+ | <ref name="ref3"> | ||
+ | Goulao L F, Fortunato A S, Ramalho J C. Selection of Reference Genes for Normalizing Quantitative Real-Time PCR Gene Expression Data with Multiple Variables in Coffea spp[J]. Plant Molecular Biology Reporter, 2012, 30(3): 741-759. | ||
</ref> | </ref> | ||
</references> | </references> | ||
+ | =='''Categories'''== | ||
+ | [[Category:Plants]] | ||
+ | [[Category:mRNA]][[Category:SYBR]] | ||
+ | [[Category:ACT]] [[Category:ACT]] [[Category:AP]] [[Category:APT]] [[Category:Cyclophilin]] [[Category:EF1α]] [[Category:EF1α]] [[Category:EF1α]] [[Category:GAPDH]] [[Category:GAPDH]] [[Category:MDH]] [[Category:MDH]] [[Category:RPS]] [[Category:Ubiquitin]] [[Category:Ubiquitin]] | ||
+ | [[Category:Nitrogen Treatment]] [[Category:Salinity Treatment]] [[Category:Abiotic Stress]] [[Category:Heat Treatment]] [[Category:Drought Treatment]] [[Category:Different Air CO2]] [[Category:Air Temperature]] [[Category:Different Genotypes]] [[Category:Cold Treatment]] | ||
+ | |||
+ | [[Category:geNorm]] | ||
+ | [[Category:NormFinder]] | ||
+ | [[Category:BestKeeper]] | ||
+ | [[Category:RefFinder]] |
Latest revision as of 09:36, 1 September 2017
Contents
Description
- Coffea arabica is a species of Coffea originally indigenous to the forests of the southwestern highlands of Ethiopia. It is an important crop and is crucial to the economy of many developing countries as international exchange commodities in agricultural trade, generating around US$70 billion per year. Its cultivation, processing, transportation and marketing provide employment for millions of people worldwide.
- Common Name: Coffee
- NCBI Taxonomy
Abiotic Stress
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
EF1[1] | Elongation factor 1 |
|
GW484749.1 |
|
NA | 60 | SYBR |
EF1a[1] | Elongation factor 1-alpha |
|
GT708303.1 |
|
NA | 60 | SYBR |
GAPDH[1] | Glyceraldehyde-3-phosphate-dehydrogenase |
|
GW488886.1 |
|
NA | 60 | SYBR |
MDH[1] | Malate dehydrogenase |
|
GW464198.1 |
|
NA | 60 | SYBR |
UBQ10[1] | Polyubiquitin 10 |
|
GT697658.1 |
|
NA | 60 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
- geNorm method && Related Reference
- NormFinder method && Related Reference
- BestKeeper method && Related Reference
Contact
- Name: Kenia de Carvalho
- Email: : keniadecarvalho@gmail.com
- Institution: Programa de Po´s-Graduac ¸a ˜o em Agronomia (Produc ¸a ˜o Vegetal),Departamento de Fitotecnia e Fitossanitarismo, Universidade Federal do Parana ´, Curitiba, PR CEP 80035-050, Brazil
Citation Statistics
Cited by 23 (Based on Google Scholar [2017-09-01])
Different Air CO2 Supply & Temperature
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
MDH[2] | Malate Dehydrogenase |
|
GW464198.1 |
|
100 | 60 | SYBR |
ACT [2] | Actin |
|
GT000704 |
|
100 | 60 | SYBR |
S15[2] | 40S ribosomal protein S15 |
|
GR987196 |
|
146 | 60 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
- geNorm method && Related Reference
- NormFinder method && Related Reference
- BestKeeper method && Related Reference
- Ref-Finder method && Related Reference
Contact
- Name: José C. Ramalho
- Email: cochichor@isa.ulisboa.pt
- Institution: Plant-Environment Interactions and Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food, Departmento de Recursos Naturais, Ambiente e Território, Instituto Superior de Agronomia, Universidade de Lisboa (ULisboa), Oeiras, Portugal
Citation Statistics
Cited by 2 (Based on Google Scholar [2017-09-01])
Different Genotypes & Abiotic Stress
Internal Control Genes
Gene Symbol | Gene Name | Application Scope | Accession Number | Primers (5'-3') [Forward/Reverse] |
Size [bp] | Tm [℃] | Detection |
---|---|---|---|---|---|---|---|
GAPHD[3] | Glyceraldehyde 3-phosphate dehydrogenase |
|
DV692958 |
|
NA | 60 | SYBR |
Cycl[3] | Cyclophilin |
|
GT007167 |
|
NA | 60 | SYBR |
UBQ10[3] | Ubiquitin |
|
DV686961 |
|
NA | 60 | SYBR |
Ap47[3] | Clathrin adaptor complexes subunit |
|
DV690764 |
|
NA | 60 | SYBR |
EF-1A[3] | Elongation factor 1-alpha |
|
GR996930 |
|
NA | 60 | SYBR |
ACT[3] | Actin |
|
GT000704 |
|
NA | 60 | SYBR |
Apt[3] | Adenine phosphoribosyltransferase |
|
GR996015 |
|
NA | 60 | SYBR |
Molecular Types
- mRNA
Evaluation Methods
- geNorm method && Related Reference
- NormFinder method && Related Reference
- BestKeeper method && Related Reference
Contact
- Name: José C. Ramalho
- Email: goulao@iict.pt
- Institution: Centro de Ecofisiologia, Bioquímica e Biotecnologia Vegetal, Instituto de Investigação Científica Tropical I.P. (IICT, IP), Av. da República, Quinta do Marquês, 2784-505 Oeiras, Portugal
Citation Statistics
Cited by 37 (Based on Google Scholar [2017-09-01])
References
- ↑ 1.0 1.1 1.2 1.3 1.4 de Carvalho K, Bespalhok Filho J C, Dos Santos T B, et al. Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization[J]. Molecular biotechnology, 2013, 53(3): 315-325.
- ↑ 2.0 2.1 2.2 Martins M Q, Fortunato A S, Rodrigues W P, et al. Selection and validation of reference genes for accurate RT-qPCR data normalization in Coffea spp. under a climate changes context of interacting elevated [CO2] and temperature[J]. Frontiers in plant science, 2017, 8.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Goulao L F, Fortunato A S, Ramalho J C. Selection of Reference Genes for Normalizing Quantitative Real-Time PCR Gene Expression Data with Multiple Variables in Coffea spp[J]. Plant Molecular Biology Reporter, 2012, 30(3): 741-759.