Assessment of genetic diversity among Sri Lankan rice varieties by AFLP markers

Abstract

Salinity is a major abiotic stress that affects rice cultivation. Osmotic stress caused by salinity activates tolerance mechanisms in rice. The Abscisic Acid Responsive Element Binding Protein (ABRE-BP), transcribes for a bZIP family transcription factor that binds to the cis-regulatory element Abscisic Acid Responsive Element (ABRE) at the promoter of downstream salinity responsive genes and regulates their expression. Hence, the study was focused on analyzing the nucleotide diversity of a region in ABRE-BP promoter. Analysis of the ABRE-BP sequences of 47 Sri Lankan rice varieties and two reference varieties retrieved from a public database revealed many insertions and deletions (INDELs) and single nucleotide polymorphisms (SNPs) in the promoter. Eleven, abiotic stress related cis-elements were identified, but none of the INDELs spanned over them. However, SNPs either deleted existing cis-elements or created new cis-elements. The salinity stress responsive elements, MYBCORE and GT1GMSCAM4 were detected in few varieties, and were not associated with salinity tolerance based on current available salinity ratings. The presence of SNPs in cis-elements clustered them to nine groups at 68% similarity. The DNA polymorphisms on stress responsive cis-acting elements did not show a strong association with the known salinity ratings of many varieties. Nevertheless, the presence of INDELs affects the relative distance between elements, and thus may alter the expression of the ABRE-BP that regulates downstream stress responsive genes.

Agromorphological characterization of Sesamum radiatum (Schum. and Thonn.), a neglected and underutilized species of traditional leafy vegetable of great importance in Benin)

“…accessions, the use of molecular markers such as AFLPs (Andru et al, 2011) will be necessary as it was the case for many crops such as fonio (Adoukonou et al, 2007), wheat (Altintas et al, 2008), yam (Sonibare et al, 2010) and rice (Rajkumar et al, 2011).…”

Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance

“…1 . This grouping is not reflected in the two large clusters of Sri Lankan accessions identified by Rajkumar et al ( 2011 ); 14 of the accessions have common names revealing that their “cluster 2” contains 10 landrace used here from indica 1 , 3 , 4 , tropical japonica and admix while their “cluster 3” has four landraces used here from indica 1 and 2 , aus and admix. The splitting of indica s into distinct subpopulations is not common in rice diversity studies but has been reported in China (Huang et al 2010 ) where evidence showed latitude played a role in differentiating three indica subpopulations.…”

“…Of the 47 accessions of the 3 K rice genomes project only four are the same as used here (8944 ALAGUSAMBA, 8901 MATHOLUWAA, 15485 MODDAI KARUPPAN and 11938 PODIWEE) while three have the same name but different accession numbers to this study (HEENDIKWEE, HONDARAWALA and KURULUWEE). A study using AFLPs to examine specifically Sri Lankan rice assessed 74 accessions plus six wild rices (Rajkumar et al 2011 ), applying 772 molecular markers to characterise local diversity but since the marker system does not transfer to other studies, placing those results into the wider context of global diversity is difficult. In the study reported here, by using SNP markers that have been characterised on the OryzaSNP set (McNally et al 2009 ) and most of which have been tested on the RDP1, the global context is more easily evaluated.…”

The scope of Rp EPIC markers in population genetic studies: a preliminary study with dengue vectors

“…low genomic frequency, null alleles, band stuttering and low polymorphisms (Fagerberg et al, 2001;Janderson et al, 2002;Goubert et al, 2016;Wei et al, 2019). Besides these pros and cons, these markers have been used in population genetic studies covering a large spectrum of fauna and fl ora in Sri Lanka (Gunawickrama, 2007;Dammannagoda et al, 2008;De Croos & Pálsson, 2010;Rajkumar et al, 2011;Abeysinghe et al, 2014;Dangalle et al, 2015;Sandamal et al, 2018;Weeraratne et al, 2018). The Ribosomal protein Exon Primed Intron Crossing (Rp EPIC) markers, which have been used to infer genetic variability since 1990's, fl ank the exon regions and detect the polymorphisms across the conserved intron region (Lessa, 1992;Slade et al, 1993).…”