Identification of Reference Genes for Quantitative Real-Time PCR in Date Palm (Phoenix dactylifera L.) Subjected to Drought and Salinity.
Date palm is an important crop plant in the arid and semi-arid regions supporting human population in the Middle East and North Africa. These areas have been largely affected by drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is a relatively salt- and drought-tolerant plant and more recently efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Quantitative real-time PCR (qPCR) is a promising technique for the analysis of stress-induced differential gene expression, which involves the use of stable reference genes for normalizing gene expression. In an attempt to find the best reference genes for date palm's drought and salinity research, we evaluated the stability of 12 most commonly used reference genes using the geNorm, NormFinder, BestKeeper statistical algorithms and the comparative ΔCT method. The comprehensive results revealed that HEAT SHOCK PROTEIN (HSP), UBIQUITIN (UBQ) and YTH domain-containing family protein (YT521) were stable in drought-stressed leaves whereas GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDH), ACTIN and TUBULIN were stable in drought-stressed roots. On the other hand, SMALL SUBUNIT RIBOSOMAL RNA (25S), YT521 and 18S ribosomal RNA (18S); and UBQ, ACTIN and ELONGATION FACTOR 1-ALPHA (eEF1a) were stable in leaves and roots, respectively, under salt stress. The stability of these reference genes was verified by using the abiotic stress-responsive CYTOSOLIC Cu/Zn SUPEROXIDE DISMUTASE (Cyt-Cu/Zn SOD), an ABA RECEPTOR, and a PROLINE TRANSPORTER 2 (PRO) genes. A combination of top 2 or 3 stable reference genes were found to be suitable for normalization of the target gene expression and will facilitate gene expression analysis studies aimed at identifying functional genes associated with drought and salinity tolerance in date palm.
Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
Himanshu
H
V Patankar
Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
Dekoum V
DV
M Assaha
Department of Crop Science, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman.
Rashid
R
Al-Yahyai
Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America.
Ramanjulu
R
Sunkar
Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
Mahmoud W
http://orcid.org/0000-0002-5171-3014
MW
Yaish
D000352:Africa, Northern; D055864:Droughts; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D008877:Middle East; D065749:Phoeniceae / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012015:Reference Standards; D054712:Salinity; D012965:Sodium Chloride; D013312:Stress, Physiological / Q000235:genetics*
D012965:Sodium Chloride