Malaysian Rice Cultivars Research Articles

Physicochemical and Rheological Properties of Rice Flour and Starch from Malaysian Rice Cultivars

Physicochemical and Rheological Properties of Rice Flour and Starch from Malaysian Rice Cultivars

Identification and Evaluation of Regulatory Role of miR164b in Malaysian Rice Variety (MR303) under Drought Stress

MR303 is a newly released Malaysian rice cultivar that comes with special traits as it can be cultivated in less fertile soils. Previous studies stated that miR164b is a key molecule that is responsible for regulating drought stress tolerance in many rice varieties. Thus, this study aims to identify the presence and regulatory role of miR164b in the MR303 variety using both computational and experimental approaches. The stem-loop structure of miR164b (pre-miR164b) was identified through reverse-transcriptase PCR (RT-PCR) with a size of ~ 100 bp. The target prediction by psRNA target revealed that the target gene of miR164b is the NAM protein of the NAC transcription factor. A gene expression study by RT-PCR followed by Image J analysis in both control and drought-treated plants demonstrated low expression of miR164b was observed in the drought sample, which led to the accumulation of its target, NAM1. This study provides preliminary knowledge of the presence of miR164b and its regulatory role in the MR303 rice variety.

Callogenesis and somatic embryogenesis of <i>Oryza sativa</i> L. (cv. MARDI Siraj 297) under the influence of 2, 4-dichlorophenoxyacetic acid and kinetin

<abstract> <p>Callogenesis and embryogenesis are integral parts of many tissue culture procedures for genetic manipulation in rice. However, the efficiency of both processes is largely dependent on the media constituent especially the plant growth regulators (PGRs) due to the genotype-dependent nature of <italic>in vitro</italic> culture protocols. Therefore, this study investigates the effect of two PGRs; 2, 4-dichlorophenoxyacetic acid (2, 4-D) and kinetin (Kin) on callus growth and somatic embryogenesis of an important Malaysian rice cultivar (<italic>Oryza sativa</italic> L. cv. MARDI Siraj 297). Mature rice seeds explants were inoculated in Murashige & Skoog (MS) medium supplemented with different combinations of 2, 4-D (0 to 3.5 mg/L) and Kin (0 to 0.5 mg/L) to induce callogenesis. Parameters for callus growth such as fresh weight (FW), callus induction frequency (CIF), embryogenic callus frequency (ECF), regeneration frequency (RF), number of plantlets per callus (PPC), callus texture and callus color were observed after 35 days of inoculation. The results show that the maximum callus growth was achieved in MS medium supplemented with combination of 2.0 mg/L 2, 4-D and 0.2 mg/L Kin, represented by the highest FW (211 mg), CIF (95%), ECF (90%), RF (100%) and PPC (22 plantlets); along with friable callus texture. Low concentration of 2, 4-D (0 to 0.5 mg/L) in the presence or absence of Kin promotes root growth instead of callus, while high concentrations (above 3.0 mg/L) retard the callus formation. The embryogenic calli from this optimized PGRs combination were successfully formed shoots in MS medium supplemented with 2 mg/L BAP and 1 mg/L NAA, followed by rooting in PGRs-free MS medium. This finding provides an efficient protocol for callogenesis and somatic embryogenesis of MARDI Siraj 297, since this is the first published report regarding somatic embryogenesis induction of this cultivar.</p> </abstract>

Perfil molecular da resistência à ferrugem bacteriana em cultivares de arroz da Malásia

Bacteria blight is one of the most serious bacterial diseases of rice worldwide. The identification of genetic potential against bacterial blight in the existing rice resources is a prerequisite to develop multigenic resistance to combat the threat of climate change. This investigation was conducted to evaluate alleles variation in 38 Malaysian cultivars using thirteen Simple Sequences Repeats markers and one Sequence Tagged Sites (STS) marker which were reported to be linked with the resistance to bacterial blight. Based on molecular data, a dendrogram was constructed which classified the rice cultivars into seven major clusters at 0.0, 0.28 and 0.3 of similarity coefficient. Cluster 5 was the largest group comprised of ten rice cultivars where multiple genes were identified. However, xa13 could not be detected in the current rice germplasm, whereas xa2 was detected in 25 cultivars. Molecular analysis revealed that Malaysian rice cultivars possess multigenic resistance.

Susceptibility of Malaysian Rice (Oryza sativa L.) Cultivar to Saline Water Submergence Based on the Morphological Traits

Saline water submergence is a newly emerge abiotic stress jeopardizing rice production especially for the rice fields located nearby or alongside coastal areas. The stress was caused by the intrusion of sea water into those rice fields causing flash flood mainly during monsoon season. The present study was conducted to evaluate susceptibility level of selected Malaysian rice cultivars to saline water submergence at seedling stage based on the morphological traits and survival rate. There were six genotypes involved in the study mainly IR64-Sub1 as submergence tolerant control, Pokkali as salinity tolerant control, IR64 as susceptible control and MR297, MR284 and MR253 as local rice cultivars, respectively. The experiment was conducted using split plot design with three replications. On the day 14 after germination, all rice seedlings were totally submerged of about one-meter depth in a polyethylene tank containing saline water at 0, 4, 8 and 12 dS/m for 14 days while the non-submerged plant was control of the experiment. Seedling growth attributes and survival rate were recorded before, right after de-submerged and 14 days after de-submerged. All genotypes however were susceptible to saline water submergence at 4, 8 and 12 dS/m. In contrast, under 0 dS/m, IR64-Sub1 recorded significantly higher survival rate at 83% as compared to MR284 (17%), MR297 (17%), Pokkali (8%), MR253 (0%) and IR64 (0%). All genotypes were not survived under saline submergence. Therefore, further phenotypic screening of rice genetic resources originated from or nearby coastal areas could be suggested in order to increase chance of identifying potentially tolerant genotype to saline water submergence.

Combination of Plant Growth Regulators, Maltose, and Partial Desiccation Treatment Enhance Somatic Embryogenesis in Selected Malaysian Rice Cultivar.

The development of efficient tissue culture protocol for somatic embryo would facilitate the genetic modification breeding program. The callus induction and regeneration were studied by using different parameters i.e., auxins, cytokinins, and desiccation treatment. Scanning electron microscopy and histological analysis were performed to identify the embryogenic callus for regeneration. The callus percentage results showed that MS (Murashige and Skoog) basal medium supplemented with 3 mg/L 2, 4-D and 30g/L maltose were the optimal callus induction medium for MR220 (80%) and MR220-CL2 (95%). The morphology of the embryogenic callus was confirmed by the SEM (Scanning Electron Microscopy) (presence of extracellular matrix surface network) and later by histological analysis. Finally, MS media supplemented with 0.5 mg/L NAA (Naphthalene Acetic Acid), 2 mg/L kin, and 1 mg/L BAP were selected as the optimum regeneration media treatment while callus desiccated for 48 h was proved to produce more plantlets in MR220 (60%) and MR220-CL2 (73.33%) compared to control treatment (without desiccation). The protocol presented here showed the necessity for the inclusion of partial desiccation as an important step in the tissue culture protocol of Malaysian indica rice genotypes in order to enhance their regeneration potential.

The Effects of Temperature on Callus Induction and Regeneration in Selected Malaysian Rice Cultivar Indica

The development of an efficient tissue culture protocol for somatic embryo would facilitate the genetic modification in breeding program. The present study describes the reproducible protocols for three wetland Malaysian rice cultivars (MR232, MR220 and MR220-CL2) and upland rice (Bario) via somatic embryogenesis. In the present study, four pre-heat treatments (35, 40, 45 and 50°C) were applied to mature seeds with different imbibition periods (3, 5 and 7 days) prior to culture on MS media with 3 mg/L 2,4-D. The results showed that the cultivars exhibited the highest callus induction percentage from 45°C pre-heated seeds and 3 days imbibition (100%, 96%, 100% and 95% for MR232, MR220, MR220-CL2 and Bario, respectively). Callus was induced early ranging from 3 to 12 days compared to without pre-heat treatment. The regeneration efficiency for MR220 and MR220-CL2 cultivars was significantly higher compared to the control treatment. However, both 45°C and 25°C (control) treatments produced higher plantlet regeneration for MR232 and Bario. This study observed that pre-heat treated seeds prior to callus induction did promote callusing and hence regeneration. These findings can be used to establish a suitable protocol for the in vitro regeneration system for several genetic improvements in the numerous stress tolerances of Malaysian rice.

Compositional analyses of white, brown and germinated forms of popular Malaysian rice to offer insight into the growing diet-related diseases

Diet-related metabolic diseases, and especially obesity, are metabolic disorders with multifactorial aetiologies. Diet has been a cornerstone in both the aetiology and management of this metabolic disorders. Rice, a staple food for over half of the world's population, could be exploited as part of the solution to check this menace which has been skyrocketing in the last decade. The present study investigated nine forms of rice from three widely grown Malaysian rice cultivars for in vitro and in vivo (glycaemic index and load) properties that could translate clinically into a lower predisposition to diet-related diseases. The germinated brown forms of MRQ 74 and MR 84 rice cultivars had high amylose content percentages (25.7% and 25.0%), high relative percentage antioxidant scavenging abilities of 85.0% and 91.7%, relatively low glycaemic indices (67.6 and 64.3) and glycaemic load (32.3 and 30.1) values, and modest glucose uptake capabilities of 33.69% and 31.25%, respectively. The results show that all things being equal, rice cultivars that are germinated and high in amylose content when compared to their white and low amylose counterparts could translate into a lower predisposition to diet-related diseases from the dietary point of view in individuals who consume this cereal as a staple food.

Enhancing somatic embryogenesis of Malaysian rice cultivar MR219 using adjuvant materials in a high-efficiency protocol

Enhancing of the efficient tissue culture protocol for somatic embryos would facilitate the engineered breeding plants program. In this report, we describe the reproducible protocol of Malaysian rice (Oryza sativa L.) cultivar MR219 through somatic embryogenesis. Effect of a wide spectrum of exogenesis materials was assessed in three phases, namely callogenesis, proliferation and regeneration. Initially, rice seeds were subjected under various auxin treatments. Secondly, the effect of different concentrations of 2,4-D on callus induction was evaluated. In the next step, the efficiency of different explants was identified. Subsequently, the effects of different auxins, cytokinins, l-proline, casein hydrolysate and potassium metasilicate concentrations on the callus proliferation and regeneration were considered. For the callogenesis phase, 2 mg L−1of 2,4-D and roots were chosen as the best auxin and explant. In the callus proliferation stage, the highest efficiency was observed at week eight in the MS media supplemented with 2 mg L−1 of 2,4-D, 2 mg L−1 of kinetin, 50 mg L−1 of l-proline, 100 mg L−1 of casein hydrolysate and 30 mg L−1 of potassium metasilicate. In the last phase of the research, the MS media added with 3 mg L−1 of kinetin, 30 mg L−1of potassium metasilicate and 2 mg L−1 of NAA were selected. Meanwhile, to promote the roots of regenerated explants, 0.4 mg L−1 of IBA has shown potential as an appropriate activator.

Epigenetic of DNA Methylation Patterns in Lowland and Upland Malaysian Rice Cultivars under Induced Drought and Salinity

Epigenetic of DNA Methylation Patterns in Lowland and Upland Malaysian Rice Cultivars under Induced Drought and Salinity

Exogenous proline significantly affects the plant growth and nitrogen assimilation enzymes activities in rice (Oryza sativa) under salt stress

Salinity has been shown to be a major factor contributing to low nitrogen availability in plants. To verify the changes in nitrogen metabolism activity as affected by the exogenous application of proline under salt stress and its relation to salt tolerance, in vitro rice shoot apices were used as a model to study the growth performance and changes in nitrogen assimilation activities in two Malaysian rice cultivars MR 220 and MR 253. Results revealed that salt stress greatly reduced the plant height, shoot nitrate (NO3 −) content, shoot glutamine synthetase (GS), and root nitrate reductase (NR) activities in both cultivars. Supplementation of proline significantly increased the plant height, number of roots, root NO3 − content, root NR, and root GS activities under salt stress in both cultivars with greater enhancement in MR 253 than MR 220. The results also indicated that MR 253 possessed higher nitrite reductase (NiR) and glutamate synthase (NADH–GOGAT) activities as compared with MR 220 in all tested treatments. It was suggested that the NO3 − content, NR, and GS activities played important roles in regulating nitrogen metabolism under salt stress. Taken together, it was concluded that the ability of proline in mitigating salt stress-induced damages was correlated with the changes in nitrogen assimilation activities.

Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought.

BackgroundWith the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY2.2, qDTY3.1, and qDTY12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY2.2, qDTY3.1, and qDTY12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI.ResultsThe GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha−1 under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha−1 under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY2.2 +qDTY12.1) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY2.2 and qDTY12.1 in the MRQ74 background.ConclusionDrought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha−1 under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.

English

A collection of 42 Malaysian rice cultivars which consists of 40 traditional rice varieties and two Malaysian elite varieties were genotyped using a set of 96 SNP markers to understand their diversity levels. Forty of the traditional rice cultivars originated from Peninsular Malaysia, Sabah and Sarawak. Out of 96 SNPs genotyped, only 67 SNPs were used for statistical analysis since the rest of the markers were either monomorphic or could not amplify most of the samples. The polymorphism information content (PIC) values ranged from 0.0232 to 0.3748 with an average of 0.1496. The gene diversity and heterozygosity values ranged from 0.0235 to 0.4997 and 0.0000 to 0.1429 with an average of 0.1703 and 0.0362, respectively. These low values of gene diversity and heterozygosity suggested low genetic diversity in the studied collections. The UPGMA dendogram showed the cultivar collections could be clustered into two major groups. The results were further supported by principal co-ordinate analysis (PCoA). The results from this study allow the characterization of germplasm collections which can aid in better genetic conservation management and selection of parental lines for breeding programs.

Marker assisted pyramiding of drought yield QTLs into a popular Malaysian rice cultivar, MR219.

BackgroundThree drought yield QTLs, qDTY2.2, qDTY3.1, and qDTY12.1 with consistent effect on grain yield under reproductive stage drought stress were pyramided through marker assisted breeding with the objective of improving the grain yield of the elite Malaysian rice cultivar MR219 under reproductive stage drought stress. Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selection were performed. BC1F3-derived lines with different combinations of qDTY2.2, qDTY3.1, and qDTY12.1 were evaluated under both reproductive stage drought stress and non-stress during the dry seasons of 2013 and 2014 at IRRI.ResultsThe grain yield reductions in the stress trials compared to non-stress trials ranged from 79 to 93 %. In the stress trials, delay in days to flowering and reduction in plant height were observed. In both seasons, MR219 did not produce any yield under stress, however it produced a yield of 5917 kg ha−1 during the 2013 dry season and 8319 kg ha−1 during the 2014 dry season under non-stress. Selected introgressed lines gave a yield advantage of 903 to 2500 kg ha−1 over MR219 under reproductive stage drought stress and a yield of more than 6900 kg ha−1 under non-stress during the 2014 dry season. Among lines with single qDTY, lines carrying qDTY2.2 provided a higher yield advantage under reproductive stage drought stress in the MR219 background. Two-qDTY combinations (qDTY3.1+qDTY2.2 and qDTY3.1+qDTY12.1) performed better than lines with three qDTY combinations, indicating the absence of positive interactions between the three qDTYs.ConclusionWe successfully developed drought-tolerant MR219 pyramided lines with a yield advantage of more than 1500 kg ha−1. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs. This is the first report on the successful effect of qDTYs in increasing the yield under drought in genetic backgrounds other than those in which the qDTYs were earlier identified.

EVALUATION OF THREE RNA EXTRACTION METHODS FROM THREE CULTIVARS OF MALAYSIAN UPLAND RICE

Rice (Oryza sativa L.) can be divided into two major categories, which is upland rice and lowland rice. Apart from being the staple food for more than half of the world population, it is also known as model plant for functional genomics study. However, it possess high amount of starch and polysaccharide that makes the isolation of good quality RNA for downstream purposes often a difficult task. While there are many studies being carried out for lowland rice extraction, none has been reported for upland rice. This study is the first to report on evaluation of three RNA extraction methods for three Malaysian upland rice cultivars in order to determine the best method to isolate high grade RNA. The result obtained demonstrated that good quality RNA in terms of integrity, purity and quality can be isolated from young leaves of these cultivars by using guanidine isothiocyanate based extraction method that is fast, simple and efficient and had been proven suitable for further downstream applications.

Effects of Ageing on Selected Cooking Quality Parameters of Rice

Ageing can improve cooking quality of rice by influencing major cooking quality parameters i.e., kernel expansion, water absorption, alkali digestion value, and gelatinization temperature along with changes in internal structure of rice grains. In this research, the effects of natural and artificial ageing on the selected cooking quality parameters of two Malaysian rice cultivars, named Mahsuri and Puteri, were studied. A relation was observed between water absorption and elongation ratio in both varieties under different aging conditions. Alkali digestion value and gelatinization temperature were also influenced by varieties and ageing conditions. This study revealed the potentiality of ageing for the improvement of rice cooking quality.

In vitro rice shoot apices as simple model to study the effect of NaCl and the potential of exogenous proline and glutathione in mitigating salinity stress

This study was conducted using in vitro rice shoot apices cultures of two Malaysian rice cultivars—MR 220 and MR 253 to investigate the effect of NaCl and the exogenous application of proline and glutathione in mitigating the salt-induced damages. The results showed that high NaCl concentrations (150, 200, 250 and 300) mM significantly impeded plant growth resulted in reduction in plant height, root length, biomass and chlorophyll content. Results showed that the supplementation of proline and glutathione effectively ameliorates salt stress induced damages. The plant height recorded at 150 mM NaCl (control) were 9.8 and 10.3 cm for MR 220 and MR 253. With the supplementation of 5 mM proline, the plant height of MR 220 and MR 253 increased to 14.8 and 15.0 cm respectively. Similarly, the plant height of MR 220 and MR 253 was further increased to 20.3 and 21.3 cm when 10 mM glutathione was added exogenously. Fresh weight was recorded as 0.06 g in 150 mM NaCl media for both cultivars and increased to 0.13, 0.26, 0.16, 0.23 g (MR 220) and 0.11, 0.14, 0.27, 0.32 (MR 253) with the supplementation of 5, 10, 15 and 20 mM proline respectively. It was noted that supplementation of 5 mM proline successfully increase the endogenous proline content from 9.05 to 58.4 and 15.8 to 70.5 μmol/g for both MR 220 and MR 253 respectively. In addition, supplementation of 5 and 10 mM glutathione increased chlorophyll content from 7.0 mg/g (NaCl) for both cultivars to 13.09, 17.06 mg/g for MR 220 and 14.7, 12.6 mg/g for MR 253 respectively. These results highlighted the potential role of exogenously applied proline and glutathione in mitigating the detrimental effect of salt stress.

Effect of 2,4-D on Embryogenic Callus Induction of Malaysian indica Rice (Oryza sativa L.) Cultivars MR123 and MR127

The aim of this study is to study the effect of various concentrations of 2,4-D on embryogenic callus induction of indica rice MR123 cultivar and MR127 cultivar using mature seeds. Optimal media for induction of callus of both cultivars was MS basal media supplemented with 30g/L sucrose, 500mg/L glutamine and 500mg/L proline supplemented with 2.5 mg/L 2,4-D. The highest percentage of callus induction was 70% and 76% for MR123 and MR127 respectively. Both cultivars produced an embryogenic callus from scutellum after a week in culture with white-yellowish in color. The viability tested using Evans blue show callus obtained was embryogenic. This simple protocol using staining method could be used for screening embryogenic callus before further experiments can be conducted.

Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers

A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.

Amylose Content and Grain Length of New Rice Transgressive Variants Derived from a Cross Between O. rufipogon and Malaysian Rice Cultivar MR219

Amylose content is one of the important grain quality properties of rice. A total of 10 new rice genotypes (BC2F7 generation) derived from a cross between O. rufipogon Griff. accession IRGC105491 and O. sativa subspecies indica cv. MR219 with high yield were evaluated for amylose content in three environments in Peninsular Malaysia. One of the parents, a popular high yielding Malaysian rice cultivar MR219 was used as a check. Based on the average amylose content across the environments, the genotype G13 showed significantly (p < 0.05) different amylose content (23.88 %) in comparison to other genotypes. Two genotypes G13 (25.7%) and G15 (25.6%) were higher than MR219 (25.1%) in terms of amylose content in Sungai Besar environment. There was a positive (r2=0.018) but no significant correlation between amylose content and grain length.