Analysis of Allelic Diversity of Drought Responsive ERF Genes in Sri Lankan Rice Germplasm
No Thumbnail Available
Date
2021
Journal Title
Journal ISSN
Volume Title
Publisher
Uva Wellassa University of Sri Lanka
Abstract
Ethylene response factor (ERF), is a prominent transcription factor gene family that governs
numerous abiotic stress-related physiological activities in plants. Drought is the foremost yield-
limiting factor of the second-largest staple crop of the globe. Bioinformatics tools provide a robust
platform to investigate the genetic characteristics towards rice plant drought responses. The present
study aimed to analyze the allelic variations of OsEBP89, OsERF101, OsERF71, OsERF48,
OsERF12 and OsLG3; drought-responsive ERF genes in silico within the Sri Lankan rice pool.
Genes were selected from the Rice Annotation Project (RAP) database concerning Oryza sativa sp.
japonica cv. „Nipponbare‟ as the reference genome. Selected gene sequences of 47 Sri Lankan rice
varieties were retrieved from the Rice SNP-Seek database and allelic variation was assessed
concerning the corresponding gene sequences of Nipponbare using MEGA 7- Clustal W method.
Present Results revealed several InDels and SNPs: 6 SNPs in OsEBP89 (A/G at 15nt, G/T at 380nt,
C/T at 381nt, T/A at 555nt, C/T at 709nt and G/T at 951nt), 1 InDel and 3 SNPs in OsERF101 (C/A
at 87nt, A/G at 687nt and C/T at 725nt), 8 SNPs in OsERF71 (C/A at 118nt, G/A at 360nt, C/T at
623nt, G/A at 742nt, G/T at 849nt, C/T at 867nt, T/C at 939nt and G/A at 981nt), 1 InDel and 5 SNPs
in OsERF48 (C/G at 655nt, G/Tat 768nt, C/G at 812nt, C/T at 1112nt and G/C at 1162nt), 1 InDel
and 5 SNPs in OsERF12 (G/T at 41nt, C/T at 150nt, G/A at 336nt, C/G at 365nt and C/T at 957nt)
and 3 SNPs in OsLG3 (C/T at 293nt, C/T at 487nt and A/G at 810nt).The MEGA 7 assisted
phylogenetic analysis unveil apparent allelic variation within the Sri Lankan rice germplasm. The
encoded proteins of OsERF101, OsERF48 and OsERF12 genes were subjected to secondary structure
prediction and physicochemical analysis. The Physicochemical properties varied among structures of
corresponding proteins. However, major differences in folding patterns were not observed.
Functional characterization and phenotypic validations are essential to investigate the potential of
these genes in drought-tolerant rice improvement programs.
Keywords: Allelic variation; Drought stress; Ethylene Response Factor; Rice
Description
Keywords
Agriculture, Crop Production, Crop Production Technology, Rice