SLIIT Conference and Symposium Proceedings

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Open Access
In Silico Identification of Abiotic Stress-Responsive Candidate Genes in Rice and Their Allelic Differences Between At 354 and Bg 352
(Faculty of Humanities and Sciences, SLIIT, 2023-11-01) Rathnayake, S; Kottearachchi, N; Lankika, S. P. C.
Rice (Oryza sativa L) feeds more than half of the world’s population. One of the main elements that harm yield globally is abiotic stress. Therefore, it is important to develop abiotic stress tolerant rice varieties in order to increase rice productivity and to extend the cultivation. The lack of knowledge of the genetic mechanisms underlying abiotic stress tolerance is the primary issue with the traditional breeding technique. Hence, studying genes responsible for abiotic stress mechanisms is important to accelerate breeding by molecular marker - based detection techniques. Aiming at finding the candidate genes for abiotic stress tolerance ,two rice genome sequences of At 354 and Bg 352 varieties given by National Research Council, Sri Lanka -16 -16 project were analyzed. At 354 has some abiotic stress tolerance (salt) traits and Bg 352 has some susceptible traits. Next-generation sequencing-derived genome sequences were used to identify SNPs and Indels in the At 354 and Bg 352 varieties with reference to Oryza sativa japonica group cultivar Nipponbare. The STRING Database was used to extract the most correlated genes with abiotic stress. The allelic differences among Nipponbare, At 354 and Bg 352 sequences were detected from Multiple Sequence Alignment by using the Rice Annotation Project database, UGENE software and MEGA 11 software. The mutations of the genes were validated if they were present in another germplasm in the NCBI database. Altogether 100 genes were used to examine, and 166 mutations were observed including 163 SNPs and 3 Indels while 09 genes were validated due to their presence in other rice accessions. The amino acid sequences of the validated sequences were determined by Expasy Translate tool. The Swiss model database and ProtParam tool were used to predict the protein structures and their parameters, which showed some structural differences among tested alleles. These mutant alleles further need to be assessed against abiotic stress and varietal turnover in order to use them in rice improving breeding programs to be used in abiotic stress-prone ecosystems.
Open Access
Nitrogen, Phosphorus and Potassium Concentrations in the Grains of Selected Rice Varieties in Sri Lanka
(SLIIT, 2022-02-11) Neththasinghe, N. A.S. A; Chandrasekara, E. D. C.T; Ekanayake, E. M.S; Madushan, N. D.R; Rathnayake, W. M. U. K; Sirisena, D. N; Suriyagoda, L. D. B
Rice (Oryza sativa L.) is the staple food for Sri Lankans, and it serves as a key source of essential mineral elements. The variation of grain nutrient concentrations as affected by genetic factors (variety, grain color and age group) are not known, and those were tested in the current study. Total of 200 rice grain samples were collected using a stratified random sampling approach, representing all agro-climatic zones in Sri Lanka. Grain nitrogen (N), phosphorus (P) and potassium (K) concentrations were measured using Kjeldahl, Colorimetric, and General methods, respectively. Grain N P and K concentrations were significantly different among rice varieties (P<0.1). Grain N concentration varied between 4-19 mg g−1 . The highest grain N concentration was recorded in Bg 307 (14 mg g−1 ) while the lowest (i.e., < 10 mg g−1 ) in Bg 367, Bg 374, Bg 358, Bg 310 and Bg 379-2. Grain P concentration varied in the range 0.6- 1.7 mg g−1 . Grain P concentration in At 406 was the highest (1.6 mg g-1), followed by Bg 307, Bg 94-1, Bg 367 i.e., >1.3 mg g-1 and the lowest in Bg 403, Ld 365 and Bg 310 i.e., < 1 mg g−1 . Bg 357, Ld 365, Bg 406, Ld 368 and Bg 310 rice varieties showed significantly lower P concentration than other varieties (P<0.1) Grain N, P and K concentrations were similar among different age classes of rice varieties (P>0.05). Moreover, grain N and P concentrations between the red and white grain varieties were similar (P>0.05). However, varieties with white color grains had higher K concentration than in red rice varieties. There was a significant correlation between grain P and K concentrations (r =0.496, P<0.001). This information would be useful when selecting rice varieties with high and low nutritional qualities and implementing sustainable nutrient management practices in rice-based cropping systems in Sri Lanka.
Embargo
Identification of SNP-Allelic Polymorphism Based Changes in Two Salt Responsive Proteins, Na+ H+ ANTIPORTER 4 and GLUTAREDOXIN 24 Between Two Rice Varieties
(Faculty of Humanities and Sciences - SLIIT, 2021-03-26) Abhayawickrama, B.P.; Hanchapola, C.R.; Kottearachchi, N.S.; Gimhani, D.R.
Rice is identified as a salinity vulnerable crop. To avoid the salinity stress problem, advanced steps have been taken, including developing novel plant sources with genetic variation associated with stress tolerance. Therefore, developing salt-tolerant varieties by combining different salt-tolerant mechanisms is a long-term solution to withstand salinity stress. Subsequently, single nucleotide polymorphisms (SNPs) are largely utilized in crop improvement including rice. This study was focused on analyzing the SNP variations discovered in two key salt responsive genes: Na+ H+ antiporter 4 (OsNHX4) and Glutaredoxin 24 (OsGRX24). The OsNHX4 and OsGRX24 gene sequences of At354 and Bg352 were retrieved from the Next Generation Sequencing derived whole genomes of two rice varieties. The gene sequences were aligned along with the Nipponbare reference gene sequences and the SNP variants present in the coding regions were identified. The amino acid sequences of each gene were obtained and their physiochemical parameters and protein structures were predicted. Results showed that OsNHX4 had 4 and 9 SNPs in At354 and Bg352 while OsGRX24 had 3 and 5 SNPs in At354 and Bg352 respectively. The secondary protein structure of OsNHX4 in Bg352 was modified due to an amino acid residue substitution, causing an alpha-helix to beta-sheet transition. In OsGRX24 of Bg352, two different alpha-helix regions were affected due to amino acid substitutions. Consequently, it could be speculated that these amino acid differences between the two varieties might be one of the causal factors for their phenotypic differences in salinity responsiveness.

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