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Coffea arabica L.

Basic Information

Coffea arabica L.
Accession: ICG00032
Latin Name: Coffea arabica L.
Common Name: Coffee
Taxonomy ID: 13443
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.

Gene Summary

mRNA

ICG00032-3
GAPHD Cycl UBQ10 Ap47 EF-1A ACT Apt
ICG00032-2
MDH ACT S15
ICG00032-1
EF1 EF1a GAPDH MDH UBQ10

Studies (3)

ICG00032-1

Abiotic Stresses
Temperature Conditions
Nutrient Conditions

Internal Control Genes

Gene Symbol Gene Model Application Scenario Accession Number Primers(5' - 3')
(Forward/Reverse)		 Size (bp) Annealing Temperature Detection
EF1 Elongation Factor
Nitrogen Starvation
Salinity Stress
High Temperature Condition
 GW484749.1
F: CTGTCCTTGATTGCCACACTTCT
R: CTTGGGCTCCTTCTCAAGCTC
 - 60 SYBR
EF1a Elongation Factor
Nitrogen Starvation
Salinity Stress
High Temperature Condition
 GT708303.1
F: AAGGGAGCTTCCAGCTTTACCT
R: TGTGAGAGGTGTGGCAGTCAA
 - 60 SYBR
GAPDH Glyceraldehyde-3-Phosphate Dehydrogenase
Nitrogen Starvation
Salinity Stress
High Temperature Condition
 GW488886.1
F: AGGCTGTTGGGAAAGTTCTTC
R: ACTGTTGGAACTCGGAATGC
 - 60 SYBR
MDH Malate Dehydrogenase
Nitrogen Starvation
Salinity Stress
High Temperature Condition
 GW464198.1
F: CCTGATGTCAACCACGCAACT
R: GTGGTTATGAACTCTCCATTCAACC
 - 60 SYBR
UBQ10 Ubiquitin
Nitrogen Starvation
Salinity Stress
High Temperature Condition
 GT697658.1
F: CAGACCAGCAGAGGCTGATT
R: AGAACCAAGTGAAGGGTGGA
 - 60 SYBR

Molecular Types:

mRNA

Evaluation Methods

geNorm
NormFinder
BestKeeper

Contact

Name: Kenia de Carvalho
Email: keniadecarvalho@gmail.com
Institution: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, PR, Brazil

Reference

Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization.
de Carvalho K, Bespalhok Filho JC, dos Santos TB, de Souza SG, Vieira LG, Pereira LF, Domingues DS.
Molecular biotechnology. 2013-03-01

ICG00032-2

Temperature Conditions
Abiotic Stresses

Internal Control Genes

Gene Symbol Gene Model Application Scenario Accession Number Primers(5' - 3')
(Forward/Reverse)		 Size (bp) Annealing Temperature Detection
MDH Malate Dehydrogenase
Universal Reference Gene
 GW464198.1
F: CCTGATGTCAACCACGCAACT
R: GTGGTTATGAACTCTCCATTCAACC
 100 60 SYBR
ACT Actin
Universal Reference Gene
 GT000704
F: AAGCTTGCCTATGTGGCTCTTG
R: TCACTTGTCCATCTGGCAATTC
 100 60 SYBR
S15 15S Ribosomal RNA
Universal Reference Gene
 GR987196
F: CAATAGGGGCTTGAAGAGG
R: TACGCTGCCAATCATCTCAG
 146 60 SYBR

Molecular Types:

mRNA

Evaluation Methods

geNorm
NormFinder
BestKeeper

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

Reference

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.
Martins MQ, Fortunato AS, Rodrigues WP, Partelli FL, Campostrini E, Lidon FC, DaMatta FM, Ramalho JC, Ribeiro-Barros AI.
Frontiers in plant science. 2017-03-07

ICG00032-3

Temperature Conditions
Abiotic Stresses

Internal Control Genes

Gene Symbol Gene Model Application Scenario Accession Number Primers(5' - 3')
(Forward/Reverse)		 Size (bp) Annealing Temperature Detection
GAPHD Glyceraldehyde-3-Phosphate Dehydrogenase
Universal Reference Gene
 DV692958
F: AGGCTGTTGGGAAAGTTCTTC
R: ACTGTTGGAACTCGGAATGC
 - 60 SYBR
Cycl Cytochrome
Universal Reference Gene
 GT007167
F: AGCTCTACGCAGACACGACTCC
R: GGTCGATCCTTTGAAGTGCAAG
 - 60 SYBR
UBQ10 Ubiquitin
Universal Reference Gene
 DV686961
F: CAGACCAGCAGAGGCTGATT
R: AGAACCAAGTGAAGGGTGGA
 - 60 SYBR
Ap47 Adaptor Related Protein Complex
Genotype Effect
 DV690764
F: CCAGATTGGAGGATGCTCTT
R: AAATGCACAAGCAACATTGG
 - 60 SYBR
EF-1A Elongation Factor
Genotype Effect
Low Temperature Condition
Drought Stress
 GR996930
F: CATTGTGGTCATTGGTCATGTC
R: ACACGCTTGTCAATTCCTCCA
 - 60 SYBR
ACT Actin
Low Temperature Condition
Drought Stress
 GT000704
F: AAGCTTGCCTATGTGGCTCTTG
R: TCACTTGTCCATCTGGCAATTC
 - 60 SYBR
Apt Adenine Phosphoribosyltransferase
Drought Stress
 GR996015
F: ACTCTCCGGGGCTAAAACTGTC
R: AGGTCGTGCTGGTTGAGTTAGG
 - 60 SYBR

Molecular Types:

mRNA

Evaluation Methods

geNorm
NormFinder
BestKeeper

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

Reference

Selection of Reference Genes for Normalizing Quantitative Real-Time PCR Gene Expression Data with Multiple Variables in Coffea spp.
Luis F. Goulao,Ana S. Fortunato,José C. Ramalho
Plant Molecular Biology Reporter. 2011-12-22