A novel allele of Days to Heading 8 promotes heading, potentially widening indica rice adaptation in Japan

Single nucleotide polymorphisms in GBBSI and SSIIa genes in relation to starch physicochemical properties in selected rice (Oryza sativa L.) varieties

The aim of this study was to decipher the reprogramming of protective machineries and sulfur metabolism, as responses to time-dependent effect of fluoride stress for 10 and 20 days in two indica rice (Oryza sativa) varieties. Unregulated accumulation of fluoride via chloride channels (CLC1 and CLC2) in 10-day-old (cv. Khitish) and 20-day-old (cv. MTU1010) seedlings caused higher accumulation of H2O2 and superoxide anion that eventually incited chlorophyll loss and electrolyte leakage, along with the formation of malondialdehyde and methylglyoxal. Higher fluoride accumulation also enhanced lipoxygenase and NADPH oxidase activities, which further aggravated the oxidative damages. However, for stressed 20-day-old Khitish and 10 day-old MTU1010 seedlings, plant growth was maintained with lesser oxidative damages due to upregulated expression of H+-ATPase and FEX along with the elevated level of cysteine and H2S, which could be linked with higher activity of ATP-S, OASTL, and DES. The activity of the enzymatic antioxidants (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and glutathione peroxidase) and level of non-enzymatic antioxidants (anthocyanins and flavonoids) were also enhanced that strengthened the antioxidative potential of the seedlings. Our work demonstrated that differential reprogramming of the protective metabolites and sulfur assimilation pathways is responsible for the differential pattern of adaptive strategies against fluoride stress in the two indica rice varieties, with Khitish exhibiting tolerance against long-term fluoride stress, whilst MTU1010 showing high susceptibility to the same.

DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers. To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species, we studied 49 Indica, 43 Japonica, and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs. Results indicated that of the 45 InDel primer pairs, 41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%. The scatter plotting data of the principal component analysis (PCA) indicated that: (i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties, in addition to revealing their genetic differentiation; (ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties; and (iii) the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types. It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying Indica and Japonica rice varieties, and for studying genetic relationships of wild rice species, particularly in terms of the Indica-Japonica differentiation.

Aroma and cooked kernel elongation (CKE) are the two most important quality traits, which differentiate the highly valued Basmati rice from other rice types. Previous studies on genetic analysis have shown that genes/QTLs for these two traits are linked and present on chromosome number 8. We have evaluated the genetic diversity in 33 rice genotypes representative of the traditional Basmati (TB), cross-bred Basmati derived from indica × Basmati rice crosses and non-Basmati (indica and japonica) rice varieties for chromosome number 8 using 26 SSR markers including a specific marker (SCU-SSR1) for RG28 locus; the results have been compared with whole genome based SSR allelic data. The 26 SSR markers (24 polymorphic and 2 monomorphic) amplified a total of 106 alleles; 21 of these alleles were detected to be unique, present in only one genotype. The number and size of the alleles, and polymorphism information content (PIC) values ranged between 1–8, 87–312 and 0–0.736 bp, respectively. SCU-SSR1 marker amplified a total of three alleles (128, 129 and 130 bp). All the TB varieties except Basmati 217 (129 bp) and 7/13 cross-bred Basmati varieties had the 130 bp allele. Alleles of 129 and 128 bp were present in majority of the indica and japonica varieties, respectively. The average pair-wise Jaccard similarity coefficients for TB, indica and japonica varieties were 0.512, 0.483 and 0.251, respectively. Average similarity coefficient between TB and japonica was higher (0.236) compared to that between TB and indicas (0.150). Genetic relationships as determined by Principal Component Analysis (PCA, NTSYS-pc), PowerMarker tree, and Structure analyses, clearly showed high-level differentiation between TB and indica rice varieties, which formed two distinct clusters. The cross-bred Basmati and japonica rice genotypes were placed between these two clusters. Basmati 217 and Ranbir Basmati were quite divergent from rest of the TB varieties. Some of cross-bred Basmati varieties including Super, CSR30 and kernel were closer to TB. Indica rice varieties, CSR10 (salt tolerant variety) and Pokkali (salt tolerant landrace) formed a separate distinct cluster. The Pritchard structure analysis divided the rice genotypes in four major sub-populations of TB, cross-bred Basmati, indica and japonica (including Ranbir Basmati and Basmati 217) rice varieties. Chromosome 8 data-set showed a positive correlation (Mantel test, r = 0.739) with the allelic data-set for 30 SSR markers well-distributed on 12 rice chromosomes indicating a higher level of similarity between the two. The study demonstrates the distinctness of TB from other rice types (indica and japonica) and also provides several novel markers for differentiation between TB rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.

Alteration of soil pH induced by submerging/drainage and application of peanut straw biochar and its impact on Cd(II) availability in an acidic soil to indica-japonica rice varieties

Variation and Distribution of Vitamin E and Composition in Seeds Among Different Rice Varieties

The present study considered transcriptional profiles and protein expression analyses from shoot and/or root tissues under three abiotic stress conditions, namely, salinity, dehydration, and cold, as well as following exogenous abscisic acid treatment, at different time points of stress exposure in three indica rice varieties, IR-29 (salt sensitive), Pokkali, and Nonabokra (both salt tolerant). The candidate genes chosen for expression studies were HKT-1, SOS-3, NHX-1, SAPK5, SAPK7, NAC-1, Rab16A, OSBZ8, DREBP2, CRT/DREBP, WRKY24, and WRKY71, along with the candidate proteins OSBZ8, SAMDC, and GST. Gene expression profile revealed considerable differences between the salt-sensitive and salt-tolerant rice varieties, as the expression in the latter was higher even at the constitutive level, whereas it was inducible only by corresponding stress signals in IR-29. Whether in roots or shoots, the transcriptional responses to different stressors peaked following 24 h of stress/ABA exposure, and the transcript levels enhanced gradually with the period of exposure. The generality of stress responses at the transcriptional level was therefore time dependent. Heat map data also showed differential transcript abundance in the three varieties, correlating the observation with transcript profiling. In silico analysis of the upstream regions of all the genes represented the existence of conserved sequence motifs in single or multiple copies that are indispensable to abiotic stress response. Overall, the transcriptome and proteome analysis undertaken in the present study indicated that genes/proteins conferring tolerance, belonging to different functional classes, were overrepresented, thus providing novel insight into the functional basis of multiple stress tolerance in indica rice varieties. The present work will pave the way in future to select gene(s) for overexpression, so as to generate broad spectrum resistance to multiple stresses simultaneously.

Bioinformatics analyses of rice calmodulin-lysine N-methyltransferases gene (OsCaM KMT) and characterization of its promoter from Oryza sativa L. sub sp. indica through transgenic approach

Plant roots provide important support for plant growth, acquiring water and nutrients, and anchoring the plants. Rice varieties have been cultivated and improved through crossbreeding of japonica rice and indica rice varieties, which have various contrasting characteristics in important traits including root development. In this study, we performed genome-wide transcriptome analysis between Dongjin (japonica) and IR64 (indica) rice varieties to identify genes associated with important agricultural traits in rice roots. Using Agilent 44K array analysis, we isolated 564 genes from Dongjin that were significantly upregulated relative to expression in IR64 and 251 genes upregulated in IR64 compared with Dongjin. Gene ontology (GO) enrichment analysis revealed that genes related to glycine, cellular amino acid, carbohydrate metabolism, hydrogen peroxide, chitin, cell wall macromolecule catabolism, and response to oxidative stress are over-represented in Dongjin compared with IR64. Conversely, in IR64, enterobactin biosynthesis, response to oxidative stress, oxidation reduction, and metabolic process genes were upregulated. Through MapMan analysis, we determined that four ascorbate peroxidase (APX) and glutathione peroxidase (GPX)-related genes closely associated with response to oxidative stress from GO enrichment analysis were more important in the roots of Dongjin than in IR64. We further confirmed that the APX and GPX enzyme activities under cold stress were higher in Dongjin than in IR64. These results explain why the japonica cultivar is more resistant to cold stress than the indica cultivar. Our results can be used as an important basis for future studies on useful traits related to root development and abiotic stress tolerance in rice.

Dissimilarity of ascorbate–glutathione (AsA–GSH) cycle mechanism in two rice (Oryza sativa L.) cultivars under experimental free-air ozone exposure

Differential responses of antioxidative system to chilling and drought in four rice cultivars differing in sensitivity

Arsenic (As) is a worldwide concern because of its toxic effects on crop yield and prevalence in the food chain. Rice is consumed by half of the world's population and is known to accumulate As. The present study reviews the available literatures on As accumulation in different subspecies of rice grains (indica, japonica and aromatic) and performs meta-analyses for grain size and texture; these data include 120 studies conducted over the last 15 years across different parts of the world. Aromatic rice varieties accumulate less As with its 95% confidence interval (CI) being 73.90 - 80.94 μg kg-1 which is significantly lower than the As accumulation by either indica or japonica rice varieties with their overall 95% CI being 135.48 - 147.78 μg kg-1 and 204.71 - 212.25 μg kg-1, respectively. Japonica rice varieties accumulate higher As than indica rice grains and within each subspecies polished and/or shorter rice grains accumulated significantly lower As compared to larger and/or unpolished grains; 95% CIs for the polished indica and japonica rice varieties are seen to be 96.33 - 111.11 μg kg-1 and 203.34 - 211.09 μg kg-1, respectively, whereas the same for unpolished varieties are seen to be 215.99 - 238.18 μg kg-1 and 215.27 - 248.63 μg kg-1, respectively. This shows that rice-based As bioaccumulation in humans could be lowered by increased use of aromatic or polished indica rice varieties, followed by the cultivation of shorter polished grains of japonica rice. These findings will be important to inform policy on rice cultivation and dietary uptake of As for a large portion of the global population.

Indica–japonica variation represents the most significant genetic differentiation in Asian cultivated rice (Oryza sativa L. subsp. indica Kato or subsp. japonica Kato). Understanding the differentiation and distribution patterns of cultivated rice along altitude gradients will facilitate strategic utilization and conservation of rice germplasm from mountainous regions. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the “InDel molecular index” developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region: indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indica–japonica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.

Effect of rice (Oryza sativa L.) genotype on yield: Evidence from recruiting spatially consistent rhizosphere microbiome

The purpose of this study was found out to investigate the response of some rice (Oryza sativa L.) cultivars to germination parameters under salinity stress. This study was carried out to confirm rice seedling growth performance and to examine a range of genetic variability for salinity tolerance among ten rice cultivars under seven salinity levels. A laboratory experiment was accompanied at Giza Central Seed Testing laboratory (CASC), Egypt. The results showed that rice cultivars significantly varied in means of Final Germination Percentage (FGP), Germination Rate (GR), Germination Index (GI), Vigor Index (VI), Root Length, Shoot Length, Root Fresh Weight, Shoot Fresh Weight, Root Dry Weight, Relative Dry Weight and Seedling Height Reduction. Sakha 102 and Sakha 106 had positive effects in most of studied characters while, Giza 181 cultivar had negative effects in most of germination parameters under study. Salinity levels significantly varied in all germination parameters under study except shoot dry weight character. Increasing salinity concentration from 0 to 14% NaCl gradually reduced averages of germination and seedling characters. All studied characters were significantly affected by the interaction between cultivars and salinity stress, vice versa, shoot, root fresh weight and root dry weight didn't affect by interaction. It could be established that for exploiting rice germination percentage and seedling parameters under salinity stress are recognized by using rice Sakha 102, Sakha 106, Sakha 104 and Egyptian Yasmin cultivars with increasing salinity levels up to 14% NaCl. These cultivars were more tolerant to salinity and suggested to use in breeding program for attractive rice production in Egypt . Key wordsOryza sativa, salinity concentration, germination characters, rice cultivars, seedling parameters International Journal of Agriculture Sciences ISSN: 0975-3710 & E-ISSN: 0975-9107, Volume 4, Issue 6, 2012 Introduction Rice is considered as a major cereal crop for more than 50% of the world population. There is a great shortage in rice production more than 25% of the recent production may be needed [1]. Moreover, rice ranks second after wheat crop as the national income is concerned. The excessive increase in population in Egypt needs to increase the total yield of this crop in order to overcome this lack in production through its cultivation in the newly reclaimed lands especially under saline conditions of such soil. Rice is one of the most effective and commercial means of reclaiming hundreds of thousands of hectares of saline lands in Egypt. Growth characters including shoot height, fresh weight, dry weight and leaf area of salt-stressed seedlings were inhibited, depending on rice genotypes [2]. Rice varieties showed a great variation in germination due to salinity effects. Many investigators concluded that differences among rice cultivars in germination characters and seedling parameters[3,15,17,22]. Salinity is one of the major obstacles in enhancing rice production in growing areas in Egypt. Salinity decreases final germination percentage, speed of germination and led to reduction in shoot and root length and dry weight in all varieties and the magnitude of reduction increased with increasing salinity stress [11]. Therefore, development of salt tolerance varieties has been considered as one of strategies to increase rice production in saline prone Citation: Kandil A.A., Sharief A.E. and Nassar E.S.E. (2012) Response of Some Rice (Oryza sativa L.) Cultivars to Germination Under Salinity Stress. International Journal of Agriculture Sciences, ISSN: 0975-3710 & E-ISSN: 0975-9107, Volume 4, Issue 6, pp-272-277. Copyright: Copyright©2012 Kandil A.A., Sharief A.E. and Nassar E.S.E. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.