http://repository.wyb.ac.lk/handle/1/3055 Fri, 08 May 2026 14:09:07 GMT 2026-05-08T14:09:07Z http://repository.wyb.ac.lk/handle/1/3576 In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm Terensan, S; Fernando, H.N.S.; Silva, J.N.; Perera, S.A.C.N; Kottearachchi, N.S.; Weerasena, O.V.D.S Pi-ta is a major blast resistant gene, introgressed from indica rice varieties. In this study, diversity of the Pi-ta gene of 47 Sri Lankan rice accessions was studied by bioinformatics, and the results were validated with molecular and disease reaction assays. Sequences of rice accessions at the locus Os12g0281300 were retrieved from Rice SNP-Seek Database, and the coding sequence of reference Pi-ta gene of cultivar Tetep (accession no. GQ918486.1) was obtained from GenBank. Comparisons were made at nucleotide, amino acid, and protein structure level, and the 3D models predicted using Phyre2 software were superimposed using TM-align software. Results: In silico analysis revealed that 10 accessions possessed resistant allele of the Pi-ta gene. The remaining accessions recorded high polymorphism in the leucine-rich domain resulting in 9 allele types, leading to single– amino acid substitutions at 27 different positions including a functional mutation of alanine to serine at the 918th amino acid position. None of the genotypes led to truncations in the amino acid sequence. The in silico analysis results were validated on 23 accessions comprising resistant and susceptible genotypes and another 25 cultivars from Northern Sri Lanka, by molecular assay using YL183/YL87 and YL155/YL87 resistant and susceptible allele specific markers. Resistance of Pi-ta gene for the causal fungus, Magnaporthe oryzae, was further validated through pathogenicity assay. Conclusion: The Pi-ta gene, especially the LRD region, revealed significant variations within Sri Lankan rice cultivars leading to high levels of resistance against blast. This information would be highly useful in breeding programmes for resistance against rice blast Fri, 01 Jan 2021 00:00:00 GMT http://repository.wyb.ac.lk/handle/1/3576 2021-01-01T00:00:00Z http://repository.wyb.ac.lk/handle/1/3575 Development of a CAPS marker for the badh2.7 allele in Sri Lankan fragrant rice (Oryza sativa) DISSANAYAKA, S; KOTTEARACHCHI, N.S.; WEERASENA, J.; PEIRIS, M. Fragrance in rice is caused by mutations in the badh2 (betaine aldehyde dehydrogenase) gene. It was previously reported that exons 1, 2, 7, 10, 13 and 14 of badh2 are hot spots for various mutations leading to fra grance in most aromatic rice. This study was carried out to sequence the 14th exon of badh2 gene of Sri Lankan aromatic rice varieties that lack the badh2.1 allele. The aims of the study were to predict the aberrant protein structure and to develop a functional DNA marker. In view of this, we sequenced the 14th exon of four traditional aromatic accessions and compared with a published sequence. Four accessions contained a nucleotide ‘G’ insertion in the 14th exon. This novel mutation can be classified as the badh2.7 allele. The predicted three-dimensional protein structure of the mutant shows loss of part of the oligomerization and coenzyme binding domains, a change that is predicted to result in fra grance. A CAPS-based novel marker, Bad2.7CAPS, was developed to identify varieties possessing this badh2.7 allele, and it can be utilized in rice breeding programmes. Wed, 01 Jan 2014 00:00:00 GMT http://repository.wyb.ac.lk/handle/1/3575 2014-01-01T00:00:00Z http://repository.wyb.ac.lk/handle/1/3574 Single nucleotide polymorphisms in GBBSI and SSa genes in relation to starch physicochemical properties in selected rice (Oryza sativa L.) varieties Alweera, D; Kottearachchi, N.S.; Gimhani, D. R.; Senarathna, K Starch quality is one of the most important agronomic traits in rice (Oryza sativa L). In this study, we identified single nucleotide polymorphisms (SNPs) in the Waxy and Alk genes of eight rice varieties and their associations with starch physicochemical properties.vi.e.vamylose content (AC) and gelatinization temperature (GT). Seven Sri Lankan rice varieties, Pachchaperumal, Herathbanda, At 354, Bg 352, Balasuriya, H 6 and Bw 295-5 were detected as high amylose varieties while Nipponbare exhibited low amylose content. In silico analysis of the Waxy gene revealed that all tested Sri Lankan varieties possessed ‘G’ (Wxa allele) instead of ‘T’ in the first intron which could explain varieties with high and intermediate amylose content. All Sri Lankan varieties had ‘A’ instead of ‘C’ in exon 6 of the Waxy gene and this fact was tally with the varieties showing high amylose content. Therefore, possessing the Wxa allele in the first intron and ‘A’ in exon 6 could be used as a molecular marker for the selection of high amylose varieties as validated using several Sri Lankan varieties. All Sri Lankan varieties except, Bw 295-5 exhibited the intermediate type of GT which could not be explained using the so far reported allelic differences in the Alk gene. However, Bw 295-5 which is a low GT variety had two nucleotide polymorphisms in the last exon of the Alk gene, i.e. ‘G’ and ‘TT’ that represent low GT class. Therefore, it can be concluded that sequence variations of Waxy and Alk genes reported in this study are useful in breeding local rice varieties with preferential amylose content and GT class. Sat, 09 May 2020 00:00:00 GMT http://repository.wyb.ac.lk/handle/1/3574 2020-05-09T00:00:00Z http://repository.wyb.ac.lk/handle/1/3573 In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice Abhayawickrama, B.; Gimhani, D.; Kottearachchi, N.; Herath, V.; Liyanage, D.; Senadheera, P. Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies. Tue, 11 Feb 2020 00:00:00 GMT http://repository.wyb.ac.lk/handle/1/3573 2020-02-11T00:00:00Z