Sri Lankan Rice Research Articles

Mineral contents of Sri Lankan rice varieties as affected by inorganic fertilization

Application of inorganic fertilizers may incorporate minerals into rice grains. Distribution of minerals in rice grains vary in bran and kernel. The aim of the present study was to compare mineral contents (MCs) of bran and kernels of selected newly improved rice varieties in Sri Lanka with and without fertilizers. Twenty rice varieties were tested. Rice bran and rice kernels were analyzed for Ca, Mg, Mn and Zn using Atomic Absorption Spectrophotometer. Calcium contents of brans and kernels ranged from 952 to 1605 mg/kg and 613 to 1107 mg/kg dry matter in fertilized varieties, respectively. High MCs were observed in fertilizer applied varieties. Higher MCs were found in the bran of rice grains. The MCs of rice grains were significantly different among the varieties and affected by fertilizer application and processing. Applications of inorganic fertilizers strengthened the MCs of rice kernels and bran.

Assessment of the association between yield parameters and polymorphic sites of the Ghd7 locus in a core-set of rice cultivars grown in Sri Lanka

Yield improvement is a major aspect in rice breeding programs. Ghd7 is a pleiotropic gene which regulates yield, plant height, and heading date in rice. Although Ghd7 has been previously cloned and sequenced in several other rice cultivars, none of the studies have been conducted for Sri Lankan rice germplasm. Therefore, in this study, we assessed the yield performance of 12 rice cultivars, genetic polymorphism of Ghd7 locus and associations between DNA markers and yield traits. Breeder seeds of the selected cultivars were obtained from RRDI, Bathalagoda, and established under greenhouse conditions at Peradeniya, Sri Lanka in Maha and Yala seasons, 2017. The cultivars were subjected to morphometric analysis, genotyped for 12 DNA markers and sequenced at Seq7-8 locus. Morphometric data were subjected to single marker analysis using General Linear Model (GLM) in SAS 9.4. Here we reported six marker haplotypes based on the arrangement of 13 DNA maker alleles at Ghd7. Moreover, twenty-three SNP/INDEL variations at Seq7-8 locus revealed close genetic relationships between the rice cultivars Bg 90-2, Bg 352 and At 307, Bg310. Four polymorphic markers (Seq7-8, Seq1-2, RM5436 and RM5346) were significantly associated with rice yield traits so that they could be used in marker assisted selection. The SNPs/INDELs of Ghd7 were significantly associated with all the yield traits except 100 seed weight and 100 endosperm weight. Thus the present study demonstrate the possibility of employing marker assisted breeding to improve rice yield using the polymorphic genomic information at Ghd7 locus.

Molecular characterization and expression of α-gliadin genes from wheat cultivar Dacke in Bg 250 rice variety

ABSTRACTThe main seed storage protein in wheat is gluten. It consists of gliadin and glutenins. Gluten gives high elasticity and extensibility during bread making, facilitating the formation of the dough. Rice is the staple food of Sri Lankans but, it has poor dough making ability compared to wheat. The aim of the present work was to characterize, clone and express α-gliadin in the T0 generation of Bg 250 rice variety as a preliminary step in improving the dough making ability of rice flour. Five α-gliadin recombinant pCR™2.1-TOPO® clones were selected for sequence analysis. Of the five clones, two functional genes and three pseudogenes were identified. Phylogenetic analysis revealed the two functional genes, (accession numbers KC660359 and KC660358) to be closely related to the α-gliadin genes of Triticum monococcum. The α-gliadin gene (KC660359) contained five cysteine residues, one less than the normal occurrence of cysteine residues in α-gliadin genes. To date there are no reports on expression of gliadin gene in transgenic rice. This novel gene was successfully expressed in the Sri Lankan rice variety Bg 250 under the control of the rice GluB-1 endosperm specific promoter.

Forecasting Models Based on Data Analytics for Predicting Rice Price Volatility: A Case Study of the Sri Lankan Rice Market

Paddy rice is a staple food that is common among the Sri Lankan populace. However, the frequent price variation of rice has negatively impacted the Sri Lankan economy. This is due to the Sri Lankan rice market lacking the mechanisms to evaluate and predict future rice price variations, often leaving domestic traders and consumers affected by sudden price spikes. This study identifies the quantifiable economic factors that affect the sudden rice price variations and presents a viable mechanism for forecasting Domestic Rice Price (DRP). In addition, it establishes three different regression models to emphasise the relationship of DRP in Sri Lanka with three economic factors: International Rice Price (IRP), International Crude Oil Price (ICOP), and USD Exchange Rate. Further, a time series model is formulated to forecast future variations in DRP while advancing factors that have a significant, but negative, correlative impact on the DRP. The results presented in this study show that the models proposed can be used by relevant food authorities to predict sudden hikes and dips in DRP, allowing them to establish a robust price control system.

Natural and Induced Glufosinate-resistance in selected Rice (<em>Oryza sativa L</em>.) Varieties in Sri Lanka

Purpose: Herbicide-resistant rice varieties in combination with post-emergent broad-spectrum herbicides improve the effectiveness of weed management in rice fields. Herbicide-resistance can be acquired naturally or induced by classical or modern breeding techniques. In the present study, screening of Sri Lankan rice varieties to glufosinate was examined and attempts were made to develop glufosinate-resistant rice varieties with the help of the breeding technique, mutagenesis.Research Method: Natural glufosinate-resistance was studied in seven (7) traditional and eighteen (18) inbred rice varieties under 0.27, 0.30 and 0.33 kg ha -1 glufosinate concentrations. Induced glufosinate-resistance in seed-derived calli of four glufosinate-susceptible rice varieties using Ethyl Methane Sulfonate was also observed and these were then treated with 0.2% (v/v) glufosinateto to determine induced glufosinate-resistance in seed-derived calli. Findings: Two traditional varieties (Pachchaperumal, Ma Wee) and fifteen inbred varieties (At362, Bg250, Bg300, Bg352, Bg357, Bg358, Bg359, Bg360, Bg366, Bg369, Bg379/2, Bg403, Bg450, Bg454, and Bg94-1) were resistant to glufosinate. Hardly any distinct yield penalty in Bg94-1, Bg403, Bg454, Bg379-2 and Ma Wee was observed under all glufosinate concentrations. Visual symptoms and chlorophyll damages caused by glufosinate for all varieties recovered within 14 days of treatment. Higher glufosinate-resistance was observed in EMS-mutated calli derived from seeds of naturally glufosinate-susceptible varieties. Molecular (AFLP) analysis confirmed in vitromutation and theM31E10 primer combination was a potential AFLP marker to identify glufosinate-resistance in rice varieties.Research Limitation: The study reports the results of screening natural and induced glufosinate-resistance in Sri Lankan rice. Inheritance of glufosinate-resistance is to be tested through several generations in Sri Lankan rice varieties.Original Value: Study provides a screening method applicable to Sri Lankan Rice varieties in identification of herbicide-resistance to permitted concentrations of glufosinate.

Identification and fine mapping of Bph33, a new brown planthopper resistance gene in rice (Oryza sativa L.)

BackgroundHost-plant resistance is the most desirable and economic way to overcome BPH damage to rice. As single-gene resistance is easily lost due to the evolution of new BPH biotypes, it is urgent to explore and identify new BPH resistance genes.ResultsIn this study, using F2:3 populations and near-isogenic lines (NILs) derived from crosses between two BPH-resistant Sri Lankan rice cultivars (KOLAYAL and POLIYAL) and a BPH-susceptible cultivar 9311, a new resistance gene Bph33 was fine mapped to a 60-kb region ranging 0.91–0.97 Mb on the short arm of chromosome 4 (4S), which was at least 4 Mb distant from those genes/QTLs (Bph12, Bph15, Bph3, Bph20, QBph4 and QBph4.2) reported before. Seven genes were predicted in this region. Based on sequence and expression analyses, a Leucine Rich Repeat (LRR) family gene (LOC_Os04g02520) was identified as the most possible candidate of Bph33. The gene exhibited continuous and stable resistance from seedling stage to tillering stage, showing both antixenosis and antibiosis effects on BPH.ConclusionThe results of this study will facilitate map-based cloning and marker-assisted selection of the gene.

<i>In silico</i> promoter analysis reveals rice <i>Wx</i> promoter could be a TATA-less promoter with a putative pyrimidine rich region

Rice waxy gene is one of the major genes, which determines the amylose content of a rice grain. The expression of this gene is regulated by various stimuli such as temperature, light, drought and diseases. Promoter region of a gene is responsible for changing the level of expression with the help of transcription factors and their binding sites, cis-acting regulatory elements found in the promoter region ranging from 2000 bp upstream and 500 bp downstream relative to the transcription start site. Present study investigated the putative transcription factor binding sites in the promoter region and possible expression regulation stimuli using five Sri Lankan rice varieties, two glutinous rice varieties, Arabidopsis thaliana and potato. The promoter regions of the plants were extracted either after mapping selected varieties from rice 3000 genome project or from promoter databases. Signal scan was carried out to capture putative signal sequences, and kappa incidence of coincidence vs guanine cytosine content, guanine cytosine skew, and multiple sequence alignment were also performed. The results revealed that rice Wx promoter could be a TATA-less promoter with a putative pyrimidine patch, and categorized under ATCG middle class of promoters. The possible transcription regulation stimuli of waxy gene include dehydration, light, temperature, and hormones. There were signal sequences related to mesophyll, root nodule, seed and root specific regulation of expression.

Photoperiod sensitivity of very early maturing Sri Lankan rice for flowering time and plant architecture

Abstract Unavailability of information on photoperiod sensitivity of traditional rice is a disadvantage in breeding rice for adaptation to changing climatic conditions and for optimum plant architecture. This experiment was conducted to address the above problem through determination of variation in days to flowering (DF) and morphological traits of twenty eight selected very early maturing Sri Lankan traditional rice accessions under three photoperiod conditions: short day (SD), day neutral (DN) and long day (LD). Although rice is considered to be a facultative short day plant, 12 accessions (2088, 2979, 4615, 3970, 4245, 2091, 3450, 3883, 4217, 6741, 3738 and 3677) flowered significantly late under SD over LD, while accession 4223 flowered significantly late under DN. Fifteen accessions (3943, 4042, 4734, 3693, 4513, 3845, 4390, 4144, 4220, 4223, 4237, 4387, Bg 300, At 308 and Bg 379-2) flowered significantly early under SD over LD. Four accessions (3457, 3884, 6305 and 4358) were non-responsive to photoperiod for flowering time. Plant height significantly increased only in accession 4217 under SD. Higher plant height under DN was obtained from At 308 and accession 3883. Photoperiod did not affect plant height in accession 4237 and Bg 379-2. LD only or both LD and DN conditions produced significantly higher plant height irrespective of photoperiod responsiveness for DF in rest 26 accessions. Variation in response to photoperiod for DF and plant architecture in very early maturing Sri Lankan rice indicates the potential diversity of genetic factors for photoperiod response for future use in rice breeding.

Development of a Sri Lankan rice variety Bg 94-1 harbouring cry2A gene of Bacillus thuringiensis resistant to rice leaffolder [Cnaphalocrocis medinalis (Guenée)

The rice leaffolder (RLF) [ Cnaphalocrocis medinalis (Guenee)] is a major lepidopteran insect pest of rice in Sri Lanka and the larvae cause significant yield losses annually. Insecticidal crystal protein gene, cry2A driven by the 35S cauliflower mosaic virus (CaMV) promoter with a double enhancer sequence was transformed into scutellum derived embryogenic calli of Bg 94-1 via Agrobacterium tumefaciens mediated transformation procedure. Transformation vector pCAMBIA 1305.1 containing the transgene construct CaMV 35S d-cry2A-NOS, hygromycin phosphotransferase and β-glucuronidase (GUS)-Plus was employed in this study. Transformed calli were subjected to 4 ‒ 5 rounds of hygromycin selection. Molecular analysis of the generated plants together with an insect bioassay using RLF larvae confirmed successful transformation and expression of this transgene in T0 generation of rice plants. A total of 19 putative transgenic plants could be confirmed from a total of 60 T0 generation plants examined. Insect feeding bioassay demonstrated that T0 transgenic rice plants are effective against RLF larvae, and showed approximately 89 % larval mortality after 3 days and 100 % mortality after 5 days of feeding. Further molecular analysis of T1 generation of the transgenic lines confirmed the stable integration of cry2A transgene into the Bg 94-1 genome. Findings of this study demonstrated that the cry2A gene of Bacillus thuringiensis ( Bt ) was successfully transformed into Bg 94-1 via Agrobacterium mediated transformation and have developed resistance against the RLF larvae. Thus, this study highlights the importance of developing transgenic rice, which can provide insect resistance against a major lepidopteran insect pest of rice in Sri Lanka.

Screening of Sri Lankan rice (Oryza sativa L.) landraces for drought tolerance

Twenty four (24) traditional Sri Lankan rice landraces were screened for drought tolerance at seedling stage in the greenhouse at the Open University of Sri Lanka, Nawala. Four week old seedlings grown in pots filled with soil were exposed to drought condition by disconnecting water supply for two weeks. Drought tolerance was evaluated by measuring plant height and leaf width after two weeks of recovery. Agro-morphological characterization of rice landraces was made on vegetative characters and yield attributed characters. The Simple Sequence Repeat (SSR) marker analysis was employed to determine the association between allelic diversity and drought tolerance of traditional rice landraces. Comparatively, the landraces Suwandal, Kirimurunga and Suduru samba showed tolerance to drought. Meanwhile, the SSR marker RM252 have shown the potential candidacy for tracing drought tolerance compared to other markers used in the study.

Evaluation of genetic diversity of cis-acting elements of Abscisic acid responsive element binding protein (ABRE-BP) in selected Sri Lankan rice varieties

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.

Developing herbicide resistant Sri-lankan rice (Oryza sativa L.) varieties: An application of Self Organizing Map

Application of high concentrations of post-emergent broad spectrum systemic herbicide, glyphosate is prevalently used to control rice weeds in Asian countries including Sri Lanka. Off target movements of glyphosate adversely affect growth of the rice plant reducing the yield. Inducing herbicide resistance (HR) in cultivated rice is a novel approach to enhance selectivity and crop safety. Studies on induced HR in Sri Lankan rice varieties are limited and studies are required to include HR rice in a cropping program. Ethyl Methyl Sulfonate (EMS), a chemical mutagen is used for functional mutations. The present study is an attempt of raising HR rice lines through conventional breeding methods. A suitable glyphosate concentration was determined by a preliminary study using five rice varieties (Bg300, Bg352, At362, Bg379-2 and H4) and varying glyphosate concentrations (0.25g/l, 0.5g/l, 1g/l, 2g/l and 3g/l). Resistance percentage ≥50% was arbitrary considered as resistant varieties. Complete Randomized Design with three replicates was used in the experiment. Agro-morphological characters were recorded for the survived plants. Twelve varieties (Bg359, At362, Bw364, Ld365, Bg366, Bg369, Bg379-2, Bg403, Bg454 “Pachcha perumal”, “Kalu heenati” and “Kurulu thuda”) showed natural resistance to glyphosate and fourteen varieties have increased resistance after mutagenesis by EMS (S0 – First generation). HR resistance percentage of S​1 (Second generation) plants was similar to S​0 plants indicating HR was transferred to new generation. Conventional statistics was supplemented with Self-Organizing Maps (SOM) to visualize variation of agro-morphological characters under treatment. The result proved that EMS application is an effective method in breeding new rice germplasm with HR and SOM is an important tool for visualizing the multi-dimensional dataset in lower dimensions.

Quantitative genetic assessment of the phosphorus deficiency tolerance in selected F2 progenies of rice (<em>Oryza sativa L.</em>) genotypes in Sri Lanka

Phosphorus deficiency (PD) is a limiting factor in rice farming and hence PD tolerant varieties are essential. The PD tolerant quantitative trait loci (QTL) have been identified using the rice landraces Kasalath and Nipponbare. However, PD tolerant Sri Lankan rice landraces or varieties have not been used for QTL mapping. It is important to study the genetics of the PD tolerance associated traits of the locally grown rice genotypes before mapping QTL. Thus, aim of this study was to unravel the genetics of PD tolerant associated traits in segregating progenies generated by crossing PD tolerant and sensitive rice genotypes. Four F 2 progenies (H-4 × Bg 352, Suduheenati × Bg 352, Mas × Bg 352 and Suduheenati × Bg 357) had been created by crossing PD sensitive genotype Bg 352 with PD tolerant genotypes H-4, Suduheenati and Mas and PD sensitive genotype Bg 357 with PD tolerant genotype Suduheenati, respectively. The F 2 seeds from each cross along with the parents were grown in a greenhouse using a P deficient soil. The growth and quantitative colour parameters were measured at flowering stage. The normality, broad sense heritability and heterosis were calculated for each trait. Goodness of fit tests were conducted for colour metrics considering the common epistatic dihybrid ratios. The growth parameters were normally distributed with higher heritability indicating a potential basis for QTL mapping. The colour metrics were not normally distributed and fitting into the epistatic ratios 9:3:4, 9:6:1, 10:3:3 or 12:3:1 implying that they should be controlled by major genes. All the studied traits showed higher heritability estimates. According to this information, it would be logical to map QTL for growth parameters and colour variation occurred due to PD.

Clustering of selected Sri Lankan rice (Oryza sativa L.) cultivars based on plant architecture and evaluation of their association to relative water content under drought

Certain rice cultivars when get exposed to drought, develop morphology that enables them to acquire drought tolerance. In addition, general morphology of a plant before its exposure to drought may also be a determinant of its final response to drought. Ten Sri Lankan rice cultivars were clustered according to ten morphological parameters under well-watered conditions and their associations to relative water content (RWC) under drought was assessed. The cluster analysis, and the component 1 of principal component (PC) analysis (mainly contributed by plant height (PH), leaf length (LL) and culm length (CL)), grouped the cultivars as traditional and newly-improved (exception Kalu Heenati). No significant (p th , 12 th and 18 th day after imposing drought (DAID). When PC2 (mainly contributed by leaf width (LW) and leaf angle (LA)) and PC1 are considered together, the groups were significantly (p th DAID. Hence, PH, leaf length (LL), CL, LW and LA before exposure to drought has an effect on the RWC of a plant under drought.

Screening of segregating F2 progenies and validation of DNA markers through bulk segregant analysis for phosphorous deficiency tolerance in rice

Phosphorous deficiency (PD) tolerance is a polygenic trait. The underlying genetics of PD tolerance trait is important to provide the basis for detecting Quantitative Trait Loci (QTLs) and validating markers that could be used in Marker Assisted Breeding (MAB) in rice. The PD tolerance of Sri Lankan rice germplasm has been characterized. However, no attempts were taken to develop and validate the DNA markers for the breeding purposes and to understand the genetic basis of the traits. The present research project was conducted to assess the PD related traits and to validate internationally published DNA markers that are linked to PD tolerance using Sri Lankan rice cultivars. A total of 84 crosses were made and advanced to F 2 and higher generations. Out of these crosses, an important subset of three crosses was selected based on the overall PD tolerance and sensitivity, importance as mega production varieties and pedigree connections between the cultivars. The plant height, number of tillers, shoot dry weight, leaf width, flag leaf width and the color metrics L*, a*, b*, hue (h*) and chroma (C*) were measured from 200 individuals each from the three populations grown under P deficient (P o ) soil conditions. Except color traits, other traits were normally distributed and exhibited higher broad sensitivity. The color metrics indicate the presence of possible epistatic interactions between the major underlying loci. From each population, two extreme bulks were selected from the highest and lowest ends of shoot dry weight (SDW) for bulk segregant analyses (BSA) to validate the DNA markers for PD tolerance. It was observed that, DNA marker K46-K1 can be used for MAB of rice for PD tolerance. The genetic information generated in the present study can also be used for larger scale genomic studies such as SNPs, GBS and GWAS mapping.

Overexpression of Arabidopsis BBX 21 Gene in Bg 250 Rice Enhances Its Architecture and Productivity

Arabidopsis BBX21 protein was identified as a transcription activator which can activate the light dependent transcription and positively regulate light mediated development of plants. The productivity of crop plants can be enhanced by over-expressing central regulators of light signaling pathway. The present study was conducted to enhance the productivity of Bg 250 Sri Lankan rice variety by overexpressing Arabidopsis BBX21 gene. The BBX21 gene was cloned into pPZP 200 binary vector and the cloned vector gene construct was transformed into Agrobarcteium tumefaciens GV3101 strain by freeze thaw method. The selected recombinant colonies of A. tumefaciens strain GV3101 harboring BBX 21 gene were transformed into three weeks old Bg 250 rice callus. Selection of the transformed callus was conducted on N6B5 selection medium containing 50 mg/L gentamycin and 500mg/L cefotaxime. A total of putative 83 plants which showed resistant to gentamycin were subjected to PCR analysis and the results showed 69 of the regenerated plants are transgenic. The T1 seeds collected from putative transgenic plants were characterize to check its integration and inheritance. The transgenic plants which showed 3:1 ratio was selected and further grown to obtain its homozygous lines. The expression of BBX21 gene was demonstrated by northern blot analysis and the results showed 4 fold higher expression of BBX21 gene in the transgenic plants compared with its non-transgenic wild type plants. The phenotypic analysis of homozygous BBX21 transgenic plants showed improved plant height, leaf length, leaf area, number of panicles and bushy appearance compared with its non-transgenic plants. Taken together, these results demonstrate an involvement of BBX21 gene in rice modifying architecture and productivity of Bg 250 transgenic plants. Int J Appl Sci Biotechnol, Vol 4(2): 240-246

Validation of K46, a Pup1-linked marker, using a selection of Sri Lankan rice (Oryza sativa L.) germplasm for marker assisted selection towards phosphorous deficiency tolerance

Phosphorous deficiency (PD) tolerance is a pivotal trait that is advantageous if present in modern day high performing rice varieties. However most of the frequently grown mega rice varieties lack this trait leading to expensive application of artificial phosphate fertilizer results secondary consequences such as environmental pollution and higher cost of production. Marker assisted breeding (MAB) for PD tolerance in rice is often hailed as the pragmatic solution to tackle this problem. The genetic basis of PD tolerance in rice has been dissected using a wide cross made between PD tolerant rice landrace Kasalath and a sensitive landrace Nipponbare. A major QTL known as Pup1 has been identified, molecularly characterized and underlying polymorphisms were detected. A major INDEL region within Pup1 QTL within Kasalath background is conferred to control the PD tolerance which is genetically ‘null’ in Nipponbare background. The DNA marker K46 which is present within Pup1 has been developed to identify this INDEL region in Kasalath like genotypes. The PD tolerance in Sri Lankan rice germplasm has been recently studied using a core panel of rice genotypes that are important in rice breeding programs. It is important to figure out the genomic landscape of the INDEL region of Pup1 QTL in these Sri Lankan rice genotypes. Therefore the present study was conducted to characterize the K46 DNA marker locus of the previously characterized for PD tolerance rice cultivars in Sri Lanka. The K46 specific primer-pair was assayed across 30 selected Sri Lankan cultivars and the PCR products were sequenced. The resulted DNA sequences were aligned with the Kasalath reference sequence for K46 locus. Further cluster analysis of the identified SNPs resulted four distinct haplotypes in which nine cultivars were grouped with Kasalath like haplotype, two unique haplotypes and the null haplotype. However, there is no strong association between the haploype class and the PD tolerance score of the cultivars implying the potentially novel PD tolerance mechanisms that require further studies.

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

BackgroundThe development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding. In this study, 135 Sri Lankan accessions, mostly identified as landraces, for which data was available at the International Rice Research Institute on drought scores were genotyped using a 384 SNP array and assessed for root depth using a newly developed buried herbicide method. Roots of 36 accessions were assessed using hydroponics and 12 using soil-filled rhizotrons to establish if variation in herbicide score could be attributed to root traits.ResultsPopulation structure based on the SNPs using STRUCTURE revealed six groups, being tropical japonica, aus and four indica subpopulations. Three of these indica subpopulations do not seem to be represented in the Rice Diversity Panel I (RDP1) of 372 global rice accessions and appear to represent genetic diversity so far poorly studied by the global scientific community. The herbicide score was highly discriminatory between landraces and correlated very strongly with hydroponic and rhizotron root traits. The mean herbicide score strongly differentiated between landraces according to the province and the latitude from which they were collected. It also differed between subpopulations, being high in indica 2 and tropical japonica and low in indica 1 and aus. Drought scores suggest that indica 2 is more drought resistant than the other groups. Correlations indicate that those landraces with high herbicide scores are more drought resistant in the vegetative stage. The landrace Niyan Wee, whose name in Sinhalese means “drought rice” belongs to the indica 2 subgroup, has high herbicide scores and deep roots.ConclusionsNiyan Wee and other cultivars within the indica 2 subgroup should be a valuable source of breeding for drought resistance at least partly because of their superior root traits, not normally associated with the indica rice cultivars.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0092-7) contains supplementary material, which is available to authorized users.

Vegetative Growth and Yield Associated Flowering Time Variation in Sri Lankan Rice “Hondarawala”

Breeding new varieties adaptable for changing climate is an essential need in sustainable rice production. Around 2000 Sri Lankan rice accessions at Plant Genetic Resources Centre (PGRC), Sri Lanka have not been fully characterized for the yield potential and sensitivity to mild photoperiodic differences for days to flowering (DF). DF is a candidate key determinant in yield components in rice and understanding the physiological and molecular nature for DF is important to manipulate crop yield through breeding programmes. The objective of this study was to assess the genetic diversity of 15 Hondarawala accessions from PGRC using selected 37 morphological characters and DF. DF varied from 58-189 days while accession number 3988 did not flower until 200th day of seed germination. Principal Component Analysis (PCA) revealed that four principle components (PA) explained 86.5% of total observed variation. Variation of DF positively associated with most of morphological characters of vegetative growth while a few characters were negatively associated. In the dendogram, 10 clusters formed at rescale distance of 5. Widely variable DF accessions distributed among clusters. The Journal of Agricultural Sciences, vol.11, No 1, January 2016, pp.42-52

Comparative Analysis of Salinity Responsive Candidate Gene Expression in Selected Sri Lankan Rice Varieties

Studying of expression dynamics of salt responsive candidate genes under different genetic background of rice is important to develop resilient salt tolerant rice varieties. The present study was focused to assess the comparative expression of salinity responsive genes which are involved in Na+/K+ homeostasis (OsNHX1), signal transduction pathway (OsMAPK5, OsCDPK7) and synthesis of osmoprotectant (OsTPS1). Comparative expression of selected genes were assessed in At354 (improved), Godawee (traditional) and Kuruwi Perunel (traditional), salinity tolerant varieties and Suwandel, a salinity susceptible traditional variety. The assessment was done before salinization (at 0 h) and after salinization at 24 h and 72 h using semi-quantitative Reverse Transcriptase PCR (RT-PCR). RT-PCR products were analysed using 1.5% agarose gel electrophoresis. Resulted gel profiles were assessed and relative level of gene expression was measured based on the intensity of the PCR product in terms of average pixel values. Relative level of gene expression in four varieties was plotted against the exposure time to salinity. Accordingly, marked variation in expression pattern of the selected genes was detected in four varieties over the tested in Godawee and Suwandel compared to At354 and Kuruwi Perunel. At 24 h, all four genes were up-regulated in At354 and Godawee while they were down-regulated in Suwandel. In Kuruwi Perunel, OsNHX1, OsMAPK5 and OsCDPK7 genes were up-regulated at 24 h while OsTPS1 was up-regulated at 72 h. At 72 h, continuous expression of all genes was observed in Kuruwi Perunel and Godawee, whereas expression was comparatively down-regulated in At354 approximately to the same level under non-stress condition. It could be suggested that At354 might have been adapted to the stress relatively earlier compared to Godawee and Kuruwi Perunel, where expressions of genes were less pronounced. Further experiments with various time period of salinity exposure should be carried out to make detailed inference regarding the expression dynamics in tested rice varieties.