An in-silico analysis of the genetic diversity of ABRE-BP among Sri Lankan rice varieties: could a polymorphism in ABRE-BP be diagnostic of salinity tolerance?
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Date
2016-11
Authors
Senavirathne, W.M.A.
Jayatilake, D.V.
Herath, V.
Wickramasinghe, H.A.M.
Journal Title
Journal ISSN
Volume Title
Publisher
University of Peradeniya, Sri Lanka
Abstract
The ABRE-BP (Abscisic Acid Responsive Element binding protein) is a key gene in the abscisic acid (ABA)-dependent plant salinity stress-responsive regulon. The gene transcribes for a transcriptional factor and binds with the ABREcis-acting element in salinity stress responsive genes, regulating its expression. A greater diversity in salinity tolerance has been reported in Sri Lankan rice germplasm while Pokkalic has been consistently identified as a tolerant variety. In the current in-silico study, we assessed the nucleotide diversity of the ABRE-BP genic region of 47Sri Lankan rice varieties to identify putative diagnostic sites associated with salinity responses. The ABRE-BP sequences were retrieved from the Rice SNP-Seek data base and the exon/intron regions and protein domains were annotated. DNA polymorphisms leading to non-synonymous mutations were identified compared to Pokkali. A cluster analysis was carried out considering the non-synonymous mutations and the nucleotide diversity index (Pi) were calculated. The entire ABRE-BPgenic region consists, 208 single nucleotide polymorphisms (SNPs) including 13 singletons and 195 parsimony variables. The ABRE-BP coding sequence (CDS; Pi:0.00617) was generally conserved comparing to the genic region (Pi:0.00817). The intron region of ABRE consisted of 179 SNPs. In the CDS, the exon one has the highest polymorphism with 23SNPs followed by exon five (3), exon two (2), and exon three (1). The exon four was conserved across all varieties. The ABRE-BP polypeptide chain consisted of 12 non-synonymous mutations where, 11 in exon one and one in exon three, that clustered the selected varieties in to four groups. The exon three contains the bZIP domain which produces the ABRE transcription factor. The bZIP domain was annotated to be longer in six varieties compared to the rest, enclosing the non-synonymous mutation at exon 3 (lysine to asparagine). The cluster of 26 varieties contained, tolerant varieties Pokkali, Kuruluthudu and Kotteyaran with known intolerant varieties Pachchaperumal and Hondarawalu. The ABRE-BP sequence of Pokkali differed from the rest, by a single non-synonymous mutation (Tyrosin to Aspartate) on exon 1, however, could not be associated with salinity tolerance. Thus, the tolerance of Pokkali and other tolerant varieties could not be diagnostically associated to the polymorphisms detected in the ABRE-BP genic region.
Description
Keywords
ABRE-BP , Rice
Citation
Proceedings of the Peradeniya University International Research Sessions (iPURSE) – 2016, University of Peradeniya, P 393