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Fulltext Genetic diversity of upland rice germplasm in Malaysia based on quantitative traits

Sohrabi M, Rafii MY, Hanafi MM, Siti Nor Akmar A, Latif MA

ScientificWorldJournal, 2012;2012:416291.
PMID: 22654604 DOI: 10.1100/2012/416291

Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

Matched MeSH terms: Oryza/classification*
Flowering response and crop duration of aromatic rices in diverse environments

Shahidullah SM, Hanafi MM, Ashrafuzzaman M, Salam MA, Khair A

C. R. Biol., 2009 Oct;332(10):909-16.
PMID: 19819411 DOI: 10.1016/j.crvi.2009.07.003

Crop duration of a rice plant, essentially dictated by flowering response, is an important selection criterion. It is determined by the interaction of genotype and environment. A field experiment was conducted with 40 rice genotypes to assess the fluctuation and/or stability of crop duration in a series of 16 environmental conditions. The effects of genotype, environment and all the components of G x E interaction were highly significant. Among the genotypes Benaful and Gandho kasturi were most sensitive to environmental changes, and indicating lower adaptability over the environments. Crop durations of 17 genotypes were comparatively stable against environmental changes. Four genotypes viz. Basmati PNR346, BR28, Neimat and Sarwati showed only nonlinear sensitivity and thus unpredictable fluctuation. Seventeen genotypes indicated average stability over the environments. The AMMI analysis identified Badshabhog, Basmati Tapl-90, Bhog ganjia, BR38, Elai, Jata katari and Radhuni pagal as most stable genotypes over the environment series. It also advocated three comparatively stable environments for all the genotypes.

Matched MeSH terms: Oryza/classification
Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Song BK, Chuah TS, Tam SM, Olsen KM

Mol Ecol, 2014 Oct;23(20):5003-17.
PMID: 25231087 DOI: 10.1111/mec.12922

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.

Matched MeSH terms: Oryza/classification
Effect of salt stress on morpho-physiology, vegetative growth and yield of rice

Hakim MA, Juraimi AS, Hanafi MM, Ali E, Ismail MR, Selamat A, et al.

J Environ Biol, 2014 Mar;35(2):317-26.
PMID: 24665756

Selection of salt tolerant rice varieties has a huge impact on global food supply chain. Five Malaysian rice (Oryza sativa L.) varieties, MR33, MR52, MR211, MR219 and MR232 were tested in pot experiment under different salinity levels for their response in term of vegetative growth, physiological activities, development of yield components and grain yield. Rice varieties, BRRI dhan29 and IR20 were used as a salt-sensitive control and Pokkali was used as a salt-tolerant control. Three different salinity levels viz. 4, 8, and 12 dS m(-1) were used in a randomized complete block design with four replications under glass house conditions. Two Malaysia varieties, MR211 and MR232 performed better in terms of vegetative growth (plant height, leaf area plant(-1), number of tillers plant(-1), dry matter accumulation plant(-1)), photosynthetic rate, transpiration rate, yield components, grain yield and injury symptoms. While, MR33, MR52 and MR219 verities were able to withstand salinity stress over salt-sensitive control, BRRI dhan29 and IR20.

Matched MeSH terms: Oryza/classification
Fulltext Grain sterility in relation to dry mass production and distribution in rice (Oryza sativa L.)

Puteh AB, Mondal MM, Ismail MR, Latif MA

Biomed Res Int, 2014;2014:302179.
PMID: 24895563 DOI: 10.1155/2014/302179

The experiment was conducted to investigate potential causes of grain sterility in widely cultivated rice variety in Malaysia, MR219 and its two mutant lines (RM311 and RM109) by examining the source-sink relations. RM311 produced increased dry matter yield both at heading and maturity and also showed higher grain yield with greater proportion of grain sterility than the other two genotypes (RM109 and MR219) resulting in the lowest harvest index (49.68%). In contrast, harvest index was greater in RM109 (53.34%) and MR219 (52.76%) with less grain sterility percentage than MR311 indicating that dry matter partitioning to economic yield was better in RM109 and MR219 than in MR311. Results indicated that dry matter allocation per spikelet from heading to maturity was important for reducing grain sterility in rice. The greater above-ground crop dry matter per spikelet was observed in RM109 and MR219 as compared to high dry matter producing genotype; RM311 implies that poor grain filling may not have resulted from dry matter production or source limitation. These findings suggest that grain sterility or poor grain filling in rice is the result of poor translocation and partitioning of assimilates into grains (sink) rather than of limited biomass production or source limitation.

Matched MeSH terms: Oryza/classification*
Fulltext Viability and Antioxidant Effects of Traditional Cooling Rice Powder (bedak sejuk) Made from Oryza sativa ssp. Indica and Oryza sativa ssp. japonica on UVB-Induced B164A5 Melanoma Cells

Ghazali AR, Muralitharan RV, Soon CK, Salyam T, Ahmad Maulana NN, Mohamed Thaha UAB, et al.

Asian Pac J Cancer Prev, 2020 Nov 01;21(11):3381-3386.
PMID: 33247699 DOI: 10.31557/APJCP.2020.21.11.3381

BACKGROUND: Traditional cooling rice powder (bedak sejuk) is a fermented rice-based cosmetic that is applied topically on one's skin, as an overnight facial mask. According to user testimonies, bedak sejuk beautifies and whitens skin, whereby these benefits could be utilised as a potential melanoma chemopreventive agent.
OBJECTIVE: Hence, this study aimed to determine the effects of bedak sejuk made from Oryza sativa ssp. indica (Indica) and Oryza sativa ssp. japonica (Japonica) on UVB-induced B164A5 melanoma cells, and also identify the antioxidant capacities of both types of bedak sejuk.
METHODS: The optimum dose of Indica and Japonica bedak sejuk to treat the cells was determined via the MTT assay. Then, the antioxidant capacities of both types of bedak sejuk were determined using the FRAP assay.
RESULTS: From the MTT assay, it was found that Indica and Japonica bedak sejuk showed no cytotoxic effects towards the cells. Hence, no IC50 can be obtained and two of the higher doses, 50 and 100 g/L were chosen for treatment. In the FRAP assay, Indica bedak sejuk at 50 and 100 g/L showed FRAP values of 0.003 ± 0.001 μg AA (ascorbic acid)/g of bedak sejuk and 0.004 ± 0.0003 μg AA/g of bedak sejuk. Whereas Japonica bedak sejuk at 50 g/L had the same FRAP value as Indica bedak sejuk at 100 g/L. As for Japonica bedak sejuk at 100 g/L, it showed the highest antioxidant capacity with the FRAP value of 0.01 ± 0.0007 μg AA/g of bedak sejuk which was statistically significant (p < 0.05) when compared to other tested concentrations.
CONCLUSION: In conclusion, Japonica bedak sejuk has a higher antioxidant capacity compared to Indica bedak sejuk despite both being not cytotoxic towards the cells. Regardless, further investigations need to be done before bedak sejuk could be developed as potential melanoma chemoprevention agents.

Matched MeSH terms: Oryza/classification*
Fulltext Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

Cui Y, Song BK, Li LF, Li YL, Huang Z, Caicedo AL, et al.

G3 (Bethesda), 2016 Dec 07;6(12):4105-4114.
PMID: 27729434 DOI: 10.1534/g3.116.035881

Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.

Matched MeSH terms: Oryza/classification
Cross-species bacterial artificial chromosome (BAC) library screening via overgo-based hybridization and BAC-contig mapping of a yield enhancement quantitative trait locus (QTL) yld1.1 in the Malaysian wild rice Oryza rufipogon

Song BK, Nadarajah K, Romanov MN, Ratnam W

Cell Mol Biol Lett, 2005;10(3):425-37.
PMID: 16217554

The construction of BAC-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. Here, we describe our initial efforts to apply an overgo approach to screen a BAC library of the Malaysian wild rice species, Oryza rufipogon. Overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. Pairs of 24-bp oligos that contain an 8-bp overlap were developed from the publicly available genomic sequences of the cultivated rice, O. sativa, to generate 20 overgo probes for a 1-Mb region that encompasses a yield enhancement QTL yld1.1 in O. rufipogon. The advantages of a high similarity in melting temperature, hybridization kinetics and specific activities of overgos further enabled a pooling strategy for library screening by filter hybridization. Two pools of ten overgos each were hybridized to high-density filters representing the O. rufipogon genomic BAC library. These screening tests succeeded in providing 69 PCR-verified positive hits from a total of 23,040 BAC clones of the entire O. rufipogon library. A minimal tilling path of clones was generated to contribute to a fully covered BAC-contig map of the targeted 1-Mb region. The developed protocol for overgo design based on O. sativa sequences as a comparative genomic framework, and the pooled overgo hybridization screening technique are suitable means for high-resolution physical mapping and the identification of BAC candidates for sequencing.

Matched MeSH terms: Oryza/classification*
The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers

Golestan Hashemi FS, Rafii MY, Ismail MR, Mohamed MT, Rahim HA, Latif MA, et al.

Gene, 2015 Jan 25;555(2):101-7.
PMID: 25445269 DOI: 10.1016/j.gene.2014.10.048

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars.

Matched MeSH terms: Oryza/classification
Identification and quantification of phenolic and flavonoid components in straw and seed husk of some rice varieties (Oryza sativa L.) and their antioxidant properties

Karimi E, Mehrabanjoubani P, Keshavarzian M, Oskoueian E, Jaafar HZ, Abdolzadeh A

J Sci Food Agric, 2014 Aug;94(11):2324-30.
PMID: 24415452 DOI: 10.1002/jsfa.6567

Plant foods are rich sources of bioactive compounds that can act as antioxidants to prevent heart disease, reduce inflammation, reduce the incidence of cancers and diabetes. This study aimed to determine the phenolics and flavonoids profiling in three varieties of rice straw and five varieties of the seed husk of Iranian rice using high-performance liquid chromatography (HPLC). Furthermore, the antioxidant activities of the extracts were evaluated by using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and nitric oxide assays.

Matched MeSH terms: Oryza/classification
Fulltext Simple and rapid molecular techniques for identification of amylose levels in rice varieties

Cheng A, Ismail I, Osman M, Hashim H

Int J Mol Sci, 2012;13(5):6156-66.
PMID: 22754356 DOI: 10.3390/ijms13056156

The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)(10), (CT)(11), (CT)(16), (CT)(17), and (CT)(18) were identified. Of these, (CT)(11) and (CT)(17) were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)(10) and (CT)(11), while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5'-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE.

Matched MeSH terms: Oryza/classification
Fulltext Compositional analyses of white, brown and germinated forms of popular Malaysian rice to offer insight into the growing diet-related diseases

Abubakar B, Yakasai HM, Zawawi N, Ismail M

J Food Drug Anal, 2018 04;26(2):706-715.
PMID: 29567241 DOI: 10.1016/j.jfda.2017.06.010

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.

Matched MeSH terms: Oryza/classification
Laboratory study of Vibrio cholerae O1 survival on three types of boiled rice (Oryza sativa L.) held at room temperature

Huat JT, Leong YK, Lian HH

J Food Prot, 2008 Dec;71(12):2453-9.
PMID: 19244898

This study examined whether the survival of Vibrio cholerae O1 on contaminated cooked rice was influenced by the type of rice. Vibrios survived unchanged on clumps of glutinous white rice (wet, grains adhered) held at room temperature for 24 h. On nonglutinous white rice (slightly moist, grains separate), 30% viable vibrios remained at 24 h. On nonglutinous brown rice (moist, separate, covered with a mucus-like substance), the number of vibrios increased 2.7-fold at 24 h. Survival rates of vibrios on the surfaces of a row of five cooked rice grains after 2 h of exposure at room temperature were 86, 29, 12, and 4% for glutinous rice, white rice, and the endosperm and pericarp of brown rice, respectively. (Each boiled brown rice grain surface was partly pericarp and partly endosperm, which became exposed by a rupture of the pericarp.) Covering each inoculated grain with a similar cooked rice grain surface increased the corresponding figures to 93, 99, 60, and 94%. Scanning electron microscopy revealed that each type of cooked grain surface possessed a distinct microtopography. For example, the surfaces of glutinous rice grains consisted of separated overlapping strips with many holes, while the pericarps of brown rice were flat interspersed with small pits. In conclusion, each type of boiled rice produced a distinct survival pattern of V. cholerae O1 caused by both the distinct gross features and the fine surface characteristics of the rice. The significance of this finding is that the type of rice consumed can be a factor in cholera transmission by contaminated rice.

Matched MeSH terms: Oryza/classification
Fulltext Molecular identification of Fusarium species in Gibberella fujikuroi species complex from rice, sugarcane and maize from Peninsular Malaysia

Hsuan HM, Salleh B, Zakaria L

Int J Mol Sci, 2011;12(10):6722-32.
PMID: 22072914 DOI: 10.3390/ijms12106722

The objective of this study was to identify Fusarium species in the Gibberella fujikuroi species complex from rice, sugarcane and maize as most of the Fusarium species in the species complex are found on the three crops. Isolates used were collected from the field and obtained from culture collection. The Fusarium isolates were initially sorted based on morphology and identifications confirmed based on the DNA sequence of the translation elongation factor 1-α (TEF-1α) gene. Based on the closest match of BLAST analysis, five species were recovered, namely, F. sacchari, F. fujikuroi, F. proliferatum, F. andiyazi and F. verticillioides. This is the first report regarding F. andiyazi from rice in Malaysia and Southeast Asia. The phylogenetic tree generated by using the neighbor joining method showed that isolates from the same species were grouped in the same clade. The present study indicated that Fusarium species in the G. fujikuroi species complex are widespread in rice, sugarcane and maize in Peninsular Malaysia. The findings also suggest that the use of morphological characters for identification of Fusarium species in the G. fujikuroi species complex from the three crops will lead to incorrect species designation.

Matched MeSH terms: Oryza/classification
The role of digestive factors in determining glycemic response in a multiethnic Asian population

Tan VM, Ooi DS, Kapur J, Wu T, Chan YH, Henry CJ, et al.

Eur J Nutr, 2016 Jun;55(4):1573-81.
PMID: 26160548 DOI: 10.1007/s00394-015-0976-0

PURPOSE: There are wide inter-individual differences in glycemic response (GR). We aimed to examine key digestive parameters that influence inter-individual and ethnic differences in GR in healthy Asian individuals.
METHODS: Seventy-five healthy male subjects (25 Chinese, 25 Malays, and 25 Asian-Indians) were served equivalent available carbohydrate amounts (50 g) of jasmine rice (JR) and basmati rice (BR) on separate occasions. Postprandial blood glucose concentrations were measured at fasting (-5 and 0 min) and at 15- to 30-min interval over 180 min. Mastication parameters (number of chews per mouth and chewing time per mouthful), saliva α-amylase activity, AMY1 gene copy numbers and gastric emptying rate were measured to investigate their relationships with GR.
RESULTS: The GR for jasmine rice was significantly higher than for basmati rice (P 0.05).
CONCLUSION: Mastication parameters contribute significantly to GR. Eating slowly and having larger food boluses before swallowing (less chewing), both potentially modifiable, may be beneficial in glycemic control.

Matched MeSH terms: Oryza/classification

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