Oryza Sativa Cultivars Research Articles

Plant Growth-Promoting Bacillus sp. Cahoots Moisture Stress Alleviation in Rice Genotypes by Triggering Antioxidant Defense System

Drought is considered one of the major obstacles for agricultural productivity worldwide such that greater efforts are required to boost crop production under this stress. One of the methods to overcome this obstacle is to harness the potential of microbe-induced systemic tolerance against moisture stress. The present work evaluated the potential role of two bacterial strains, namely Bacillus altitudinis FD48 and Bacillus methylotrophicus RABA6 and their combination as a co-inoculant for promoting plant growth and moisture stress resilience in two contrast cultivars of Oryza sativa L: CO51 (moderately drought tolerant) and IR64 (drought susceptible) under conditions of terminal moisture stress. B. altitudinis FD48- and B. methylotrophicus-primed rice seeds (CO51 and IR64) significantly influenced the source-sink relationship and reduced the relative water content (RWC). While photosynthetic pigments and proline showed a steady increase owing to the co-inoculant priming, the activity of reactive oxygen species (ROS)-quenching enzymes, such as catalase, superoxide dismutase, ascorbate peroxidase, and peroxidase constitutively increased in plants treated with co-inoculant besides,reducing the trend during the recovery phase. The productive tillers and grain weight were further augmented by the co-inoculant under induced moisture stress. Moreover, the results revealed a 14% and 19% increase in the harvest index (HI) in CO51 and IR64, respectively, attenuated with Bacillus sp. as a co-inoculant. The key mechanism in augmenting energy metabolism by B. altitudinis FD48 and B. methylotrophicus RABA6 could be attributed to the regulation of ROS-quenching enzymes that aid in moisture stress resilience. The results of the present study conclude that these strains may be used as a novel bioinoculant for enhancing the drought tolerance in rice grown under moisture stress regimes.

Comparison of the penetration, development and reproduction of Meloidogyne javanica and M. graminicola on partially resistant Oryza sativa cultivars from East Africa

Summary The host response to Meloidogyne javanica infection of selected Oryza sativa and NERICA (New Rice for Africa) genotypes that are commonly grown in Tanzania and East Africa was examined. The O. sativa genotypes ‘Komboka’ and ‘Supa’ appeared to be partially resistant. A further experiment showed that both genotypes are also partially resistant to M. graminicola infection. The host response of ‘Komboka’ and ‘Supa’ to M. javanica and M. graminicola was further examined and compared in indoor growth chamber conditions. The genotypes ‘TOG5674’, ‘TOG5675’, ‘CG11’ and ‘CG14’ (both O. glaberrima) were included as the resistant reference genotypes for M. graminicola and the genotype ‘UPLRi-5’ (O. sativa) was included as the susceptible reference genotype for both species of root-knot nematodes. Meloidogyne graminicola was more aggressive on ‘Komboka’ and ‘Supa’ than M. javanica. Significantly less root galling was observed on ‘Komboka’ and ‘Supa’ than on ‘UPLRi-5’. In ‘Komboka’ and ‘Supa’ significantly fewer second-stage juveniles (J2) were able to penetrate the roots, to develop into adult females and to reproduce compared with ‘UPLRi-5’. Differential emigration of J2 from the roots of ‘Komboka’ and ‘Supa’ compared with ‘UPLRi-5’ contributed to the observed partial resistance in these genotypes to M. graminicola and M. javanica. Nematodes that successfully penetrated and developed in ‘Komboka’ and ‘Supa’ showed aberrant phenotypes. ‘Supa’ and ‘Komboka’ may be recommended for use by farmers in M. javanica and M. graminicola-infested fields.

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLD\u03b11) of wild Oryza species implies to its low expression in rice bran

Rice bran, a by-product after milling, is a rich source of phytonutrients like oryzanols, tocopherols, tocotrienols, phytosterols, and dietary fibers. Moreover, exceptional properties of the rice bran oil make it unparalleled to other vegetable oils. However, a lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) causes rancidity and ‘stale flavor’ in the oil, and thus limits the rice bran usage for human consumption. To improve the rice bran quality, sequence based allele mining at OsPLDα1 locus (3.6 Kb) was performed across 48 accessions representing 11 wild Oryza species, 8 accessions of African cultivated rice, and 7 Oryza sativa cultivars. From comparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDα1 locus. Phylogenetic analysis revealed 20 OsPLDα1 cDNA variants which further translated into 12 protein variants. The O. officinalis protein variant, when compared to Nipponbare, showed maximum variability comprising 22 amino acid substitutions and absence of two peptides and two β-sheets. Further, expression profiling indicated significant differences in transcript abundance within as well as between the OsPLDα1 variants. Also, a new OsPLDα1 transcript variant having third exon missing in it, Os01t0172400-06, has been revealed. An O. officinalis accession (IRGC101152) had lowest gene expression which suggests the presence of novel allele, named as OsPLDα1-1a (GenBank accession no. MF966931). The identified novel allele could be further deployed in the breeding programs to overcome rice bran rancidity in elite cultivars.

Pathogenicity of the root-lesion nematode, Pratylenchus zeae, on rice genotypes under different hydro-ecologies in Tanzania

Summary The root-lesion nematode, Pratylenchus zeae, is commonly found in upland rice fields. To measure the impact of the nematode on rice production, a screenhouse experiment was conducted using two farmer-adapted Oryza sativa cultivars, ‘Supa’ (‘SurinamV-880’) and ‘SARO-5’ (‘TXD 306’), under flooded, upland and drought water regimes imposed at 7 days post-inoculation of mixed-stage nematodes (200, 500, 1000, 3000 and 10 000 plant−1). Growth and yield parameters were recorded, and the experiment was terminated after 5 months. ‘Supa’ was shown to be resistant to P. zeae, while ‘SARO-5’ was susceptible. Pratylenchus zeae reduced the growth and yield of both cultivars, though more for ‘SARO-5’ than for ‘Supa’. Yield decreased with increasing final nematode densities. Pratylenchus zeae reproduction was highest at 200 and 500 inoculum levels and under upland water conditions. The yield of ‘SARO-5’ was greater than that of ‘Supa’ under flooded conditions and with no or 200 and 500 nematode inoculum levels, but with high P. zeae inoculum ‘Supa’ yield was better than ‘SARO-5’.

Phytostimulation of lowland soil contaminated with imidazolinone herbicides

The phytostimulation is a phytoremediation technique that can be used to remediate area contaminated with herbicides. It is necessary to select plants with high capacity to stimulate soil microbial activity. The present work aimed at evaluating seven plant species regarding their ability to phytostimulate soil and enhance the degradation of the herbicides imazethapyr, imazapic and imazapyr in a lowland soil. An Alfisol Albaqualf was cultivated with the following species, Canavalia ensiformis, Glycine max, Oryza sativa cultivar PUITÁ INTA CL, Lolium multiflorum, Vicia sativa and consortium Lotus corniculatus + Trifolium repens. The rhizosphere of these plants and non-rhizospheric (uncultivated soil) as a control were contaminated in laboratory with analytical standart of the three herbicides, at rates of 0, 150, 300 and 750 g a.i. ha−1, in separate assays. Biodegradation was estimated by quantifying C–CO2 production and through analysis of herbicides residues in soil using liquid chromatography. Results show that biodegradation of herbicides imazethapyr, imazapic and imazapyr was higher in vegetated soil than in unvegetated soil. The leguminous species Canavalia ensiformis, Glycine max, Vicia sativa and consortium of Lotus corniculatus + Trifolium repens showed a great capacity to promote soil microbial, resulting in average biodegradation rates of 91, 92 and 93% for herbicides imazethapyr, imazapic and imazapyr in soil, respectively.

An update of new flood-irrigated rice cultivars in the SimulArroz model

Abstract: The objective of this work was to model, in the SimulArroz model, the three flood-irrigated rice (Oryza sativa) cultivars currently most grown in the state of Rio Grande do Sul, Brazil. The experiments to calibrate and validate the model were conducted in the municipalities of Cachoeirinha, Santa Maria, Uruguaiana, Santa Vitória do Palmar, and Cachoeira do Sul during four crop seasons. The number of leaves, phenology, aboveground dry matter biomass, and yield of each cultivar were evaluated. The results showed a slight overestimate of the R1, R4, and R9 stages; however, overall, the SimulArroz model had a good performance in simulating rice phenology for the three studied genotypes. Furthermore, the model had a reasonable accuracy in simulating aboveground dry matter and yield. The root-mean-square error (RMSE) for aboveground dry matter (leaves, stems, panicles, and grains) ranged from 0.5 to 3.0 Mg ha-1. For yield, the RMSE ranged from 0.8 to 1.3 Mg ha-1. The calibration of the SimulArroz model is efficient in simulating the growth, development, and grain yield of the most important flood-irrigated rice cultivars in Southern Brazil and can be used to estimate harvest forecast and yield potential, as well for yield gap studies.

Macronutrient and mineral contents of five local black rice (Oryza sativa) cultivars in Indonesia

Abstract. Nashrurrokhman M, Sayekti PR, Safitri A, Purwestri YA, Pratiwi R. 2019. Macronutrient and mineral contents of five local black rice (Oryza sativa) cultivars in Indonesia. Biodiversitas 20: 3647-3653. Nutrient composition is important information that can be used to support the development of black rice as functional food. In this study, the macronutrient and mineral compositions of five black rice cultivars were determined by measuring the contents of total carbohydrates, proteins, and lipids, and levels of the minerals Ca, Fe, and Zn of whole rice, refined rice, and rice bran. Rice samples were obtained from farmers who planted the black rice cultivars of Woja Laka, Toraja, Cempo Ireng “Seyegan”, Melik “Bantul” and Wedomartani. Proximate analysis and spectrophotometric methods were performed to measure the contents of macronutrients and minerals. Statistical analysis of all quantitative data was conducted by using One-way analysis of variance (ANOVA) (p<0.05) using the SPSS-25 program. Results showed that the contents of carbohydrates, proteins, and lipids in the five rice cultivars varied in the range of 61.80%-65.58%, 7.13%-9.10%, and 1.98%-3.23%, respectively. Carbohydrates found in refined rice were in the range of 62.71%-67.89%, while rice bran had protein and lipid contents varying in the range of 10.95%-11.48% and 5.70%-6.86%, respectively. Rice bran also had the highest mineral content and the highest mineral content was 30 μg/g Ca compared to Fe and Zn. Therefore, the macronutrient and mineral composition varied among the five black rice cultivars and rice components. The highest carbohydrate content was found in refined rice, while the highest proteins, lipids, and minerals (Ca, Fe, and Zn) contents were found in rice bran.

Natural variation in the expression and catalytic activity of a naringenin 7‐O‐methyltransferase influences antifungal defenses in diverse rice cultivars

Phytoalexins play a pivotal role in plant-pathogen interactions. Whereas leaves of rice (Oryza sativa) cultivar Nipponbare predominantly accumulated the phytoalexin sakuranetin after jasmonic acid induction, only very low amounts accumulated in the Kasalath cultivar. Sakuranetin is synthesized from naringenin by naringenin 7-O-methyltransferase (NOMT). Analysis of chromosome segment substitution lines and backcrossed inbred lines suggested that NOMT is the underlying cause of differential phytoalexin accumulation between Nipponbare and Kasalath. Indeed, both NOMT expression and NOMT enzymatic activity are lower in Kasalath than in Nipponbare. We identified a proline to threonine substitution in Kasalath relative to Nipponbare NOMT as the main cause of the lower enzymatic activity. Expanding this analysis to rice cultivars with varying amounts of sakuranetin collected from around the world showed that NOMT induction is correlated with sakuranetin accumulation. In bioassays with Pyricularia oryzae, Gibberella fujikuroi, Bipolaris oryzae, Burkholderia glumae, Xanthomonas oryzae, Erwinia chrysanthemi, Pseudomonas syringae, and Acidovorax avenae, naringenin was more effective against bacterial pathogens and sakuranetin was more effective against fungal pathogens. Therefore, the relative amounts of naringenin and sakuranetin may provide protection against specific pathogen profiles in different rice-growing environments. In a dendrogram of NOMT genes, those from low-sakuranetin-accumulating cultivars formed at least two clusters, only one of which involves the proline to threonine mutation, suggesting that the low sakuranetin chemotype was acquired more than once in cultivated rice. Strains of the wild rice species Oryza rufipogon also exhibited differential sakuranetin accumulation, indicating that this metabolic diversity predates rice domestication.

Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2′,4,4′-tetrabromodiphenyl ether

2,2′,4,4′-Tetrabromodiphenyl ether (BDE-47), a predominant polybrominated diphenyl ether (PBDE), has received extensive attention for its potential environmental impact. An integrated study of metabolomics and transcriptomics was conducted on two rice (Oryza sativa) cultivars, Lianjing-7 (LJ-7) and Yongyou-9 (YY-9), which have been identified as tolerant and sensitive cultivars to BDE-47, respectively. The objective was to investigate the molecular mechanisms of their different ability to tolerate BDE-47. Both rice plants were cultivated to maturity in soils containing three concentrations of BDE-47 (10, 20, and 50 mg/kg). Metabolomic analyses of rice grains identified 65 metabolites in LJ-7 and 45 metabolites in YY-9, including amino acids, saccharides, organic acids, fatty acids, and secondary metabolites. In the tolerant cultivar LJ-7 exposed to 50 mg/kg BDE-47, concentrations of most of the metabolites increased significantly, with α-ketoglutaric acid increased by 20-fold and stigmastanol increased by 12-fold. In the sensitive cultivar YY-9, the concentrations of most metabolites increased after the plant was exposed to 1 and 10 mg/kg BDE-47 but decreased after the plant was exposed to 50 mg/kg BDE-47. Transcriptomic data demonstrated that regulation of gene expressions was affected most in LJ-7 exposed to 50 mg/kg BDE-47 (966 genes up-regulated and 620 genes down-regulated) and in YY-9 exposed to 10 mg/kg BDE-47 (85 genes up-regulated and 291 genes down-regulated), in good accordance with the observed metabolic alternation in the two cultivars. Analyses of metabolic pathways and KEGG enrichment revealed that many biological processes, including energy consumption and biosynthesis, were perturbed in the two rice cultivars by BDE-47. A majority of metabolites and genes involved in dominating pathways of energy consumption (e.g., tricarboxylic acid cycle) and the biosynthesis (e.g., metabolism of saccharides and amino acids) were enhanced in LJ-7 by BDE-47. In contrast, energy consumption was increased while biosynthetic processes were inhibited in YY-9 by BDE-47, which could lead to the sensitivity of YY-9 to BDE-47. The combined results suggest that the different defensive abilities of these two rice cultivars in response to BDE-47 could be attributed to their differences in energy-consumption strategy and biosynthesis of nutritional components in grains. This study provides a useful reference for rice cultivation in PBDE-polluted areas.

Efficient colonization of the endophytes Herbaspirillum huttiense RCA24 and Enterobacter cloacae RCA25 influences the physiological parameters of Oryza sativa L. cv. Baldo rice.

Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity and production of siderophores and phytohormones, can be assessed as plant growth promotion traits. Our aim was to evaluate the effects of nitrogen fixing and indole-3-acetic acid (IAA) producing endophytes in two Oryza sativa cultivars (Baldo and Vialone Nano). Three bacteria, Herbaspirillum huttiense RCA24, Enterobacter asburiae RCA23 and Staphylococcus sp. 377, producing different IAA levels, were tested for their ability to enhance nifH gene expression and nitrogenase activity in Enterobacter cloacae RCA25. Results showed that H. huttiense RCA24 performed best. Improvement in nitrogen fixation and changes in physiological parameters such as chlorophyll, nitrogen content and shoot dry weight were observed for plants co-inoculated with strains RCA25 and RCA24 in a 10:1 ratio. Based on confocal laser scanning microscopy analysis, strain RCA24 was the best colonizer of the root interior and the only IAA producer located in the same root niche occupied by RCA25 cells. This work shows that the choice of a bio-inoculum having the right composition is one of the key aspects to be considered for the inoculation of a specific host plant cultivar with microbial consortia.

Pyramiding of rapid germination loci from Oryza Sativa cultivar ‘Xieqingzao B’ and cold tolerance loci from Dongxiang wild rice to increase climate resilience of cultivated rice

Rapid and uniform germination of seeds and subsequent high survivability of seedlings in low-temperature environments are two key requirements in the direct-seeding agronomic production system in rice. Dongxiang wild rice (DXWR), the northernmost common wild rice, possesses a number of seedling cold-tolerance loci and is an invaluable genetic resource for the molecular breeding of cold-tolerant rice. However, DXWR has a delayed and desynchronized germination trait in low-temperature environments that is favorable for its adaption to cold environments but is a disadvantage for seedling establishment in the direct-seeding system when integrated into elite cultivars. In the present study, we identified five quantitative trait loci (QTLs) for low-temperature germination in DXWR. All the DXWR alleles delay the germination of DXWR seeds in low-temperature environments. By the pyramiding of QTLs of rapid germination from cultivated rice and QTLs of seedling cold tolerance from high tolerance wild rice DXWR, we obtained a variety numbered DX71 with rapid and uniform germination of seeds and high cold tolerance of seedlings in low-temperature environments. The results could facilitate the understanding of the genetic basis of delayed germination in DXWR, partly explaining how DXWR adapts to low temperatures in its habitat. The identified QTLs provide tightly linked markers for rice breeding in the development of climate-resilient varieties with low input.

Histo-morphological analysis of rice callus cultures reveals differential regeneration response with varying media combinations

Genetic transformation of most indica rice (Oryza sativa) cultivars is hampered by poor in vitro culture performance and low regeneration potential. Histological study of primary calli can provide substantial information on their regeneration potential and can be used for early grading of calli expected to develop plantlets on regeneration media. The study was aimed to undertake histological analysis of primary calli derived from mature seeds of five indica rice cultivars viz. KSK-133, KS-282, Shaheen Basmati, Super Basmati, and DilRosh in order to assess their regeneration potential on different media combinations supplemented with various hormone concentrations (N6 + 2 mg/L 2,4-Dichlorophenoxyacetic acid; N6 + 2 mg/L 2–4 D + 2 mg/L Benzylaminopurine and MS + 2 mg/L 2,4-D). Calli with regeneration capability were subjected to histological assays by examining toulidine blue stained 5–8 μm thin sections for the presence of meristematic zones exhibiting embryogenic callus features. Based on our observations, formation of embryoids or embryoid-like structures was pronounced in KSK-133 and KS-282 calli. However, DilRosh, Super Basmati and Shaheen Basmati did not show these characteristic features. Three-week-old calli of all rice cultivars were transferred into regeneration medium (MS + 2 mg/L BAP + 1 mg/L Naphthaleneacetic acid). KSK-133 and KS-282 showed the highest regeneration potential (81% and 76%, respectively). These data were supported by histological observations where characteristic embryogenic units (EU) were noticed in these genotypes. These meristematic regions displayed high mitotic activity and stained relatively dark. The embryogenic calli cells were found heavily cytoplasmic with prominent nuclei and were located on the callus surface or inside surrounded by parenchymal cells.

Zinc bio-fortification and kernel quality enhancement in elite Basmati rice (Oryza sativa) cultivars of south Asia through legume residue-recycling and zinc fertilization

Basmati-rice (Oryza sativa L.) is a geographical indication and most remunerative foreign-exchange earning crop in Indo-Gangetic-plains-region (IGPR). In current study, summer-mungbean residue-recycling (SMB–RR) and Zn-fertilization through zinc-sulfate-heptahydrate (ZSHH) significantly enhanced the grain yield in basmati rice genotypes by 11.8 and 8.4%, respectively over summer-fallow (SF) and control; besides higher hulling and headrice recovery. Kernel-length before and after cooking enhanced by 3.79 and 5.03%, respectively by SMB–RR over SF. SMB–RR and ZSHH registered higher Zn concentration in rice grains (31.4, 32 mg/kg); besides total Zn uptake (1024.5; 1000.8 g/ha) and Zn harvest index (ZHI), indicating ZSHH offers vital solution to curtail Zn malnutrition. Among basmati-rice cultivars, Pusa–2511 exhibited highest grain yield (5.07 t/ha), hulling (70.9%), kernel-breadth before (0.17 cm) and after cooking (0.24 cm), and Zn concentration in grains (32.8 mg/kg); while Pusa 1121 exhibited highest kernel–length before (0.84 cm) and after cooking (1.6 cm), and kernel L: B ratio after cooking (7.85). The ZSHH supplied plots led to respective significant enhancement in ZHI to the tune of 7.69% over control plots. Overall, SMB–RR and Zn-fertilization assume great significance in improving productivity, kernel-quality and Zn bio-availability in basmati-rice cultivars having global repute as top-quality rice.

The Structural Integrity of Lignin Is Crucial for Resistance against Striga hermonthica Parasitism in Rice.

Striga species are parasitic weeds that seriously constrain the productivity of food staples, including cereals and legumes, in Sub-Saharan Africa and Asia. In eastern and central Africa, Striga spp. infest as much as 40 million hectares of smallholder farmland causing total crop failure during severe infestation. As the molecular mechanisms underlying resistance are yet to be elucidated, we undertook a comparative metabolome study using the Striga-resistant rice (Oryza sativa) cultivar 'Nipponbare' and the susceptible cultivar 'Koshihikari'. We found that a number of metabolites accumulated preferentially in the Striga-resistant cultivar upon Striga hermonthica infection. Most apparent was increased deposition of lignin, a phenylpropanoid polymer mainly composed of p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) aromatic units, around the site of interaction in Nipponbare. The increased deposition of lignin was accompanied by induction of the expression of corresponding enzyme-encoding genes in the phenylpropanoid pathway. In addition, perturbing normal lignin composition by knocking down or overexpressing the genes that regulate lignin composition, i.e. p-COUMARATE 3-HYDROXYLASE or FERULATE 5-HYDROXYLASE, enhanced susceptibility of Nipponbare to S hermonthica infection. These results demonstrate that enhanced lignin deposition and maintenance of the structural integrity of lignin polymers deposited at the infection site are crucial for postattachment resistance against S hermonthica.

Analysis of nutritional composition, antioxidant activity and callus induction of Oryza sativa cultivars Khumthan and Norprae

Analysis of nutritional composition, antioxidant activity and callus induction of Oryza sativa cultivars Khumthan and Norprae

Projected day/night temperatures specifically limits rubisco activity and electron transport in diverse rice cultivars

Ambient temperature has a profound effect on agricultural production. Generally, sub- and supra-optimal temperatures have a negative effect on growth/yield, provided the deviation for optimal is large enough. On average, mean global temperatures are projected to increase by 0.3 to 0.6 °C per decade over the next century. Nighttime temperatures (TN) are projected to increase faster (20%–40% by 2100) than day maximum temperatures (TD). Therefore, an experiment was conducted to determine the effects of projected sub- and supra-optimal day/night temperatures on two diverse rice (Oryza sativa) cultivars, IR6 and Rex, during reproductive growth. At flowering, nine different day/night temperature treatments (TTs) were imposed and maintained until harvesting using sunlit growth chambers (SPAR units). Alterations to plant metabolism were evaluated using CO2 response functions, also, to survey gas exchange readings under ambient conditions. Net photosynthesis (AN) declined under both TD and TN effects. The decline in maximum carboxylation rate allowed by Rubisco (Vcmax) and maximal rate of electron transport allowed by the thylakoid reactions (Jmax), with increasing TN mainly contributed to the decline in AN. Dark respiration rates (RD) declined with increasing temperatures could be a cultivars acclimation mechanism to prevent excessive carbon losses. Cultivars varied mainly for primary photochemistry, with cultivar Rex exhibited significantly higher RD, and pigment contents but lower Jmax than IR6 across TTs. The information on genetic, biochemical and physiological processes in these two diverse cultivars under varied temperature regimes could be useful for developing breeding tools to enhance thermotolerance in US rice cultivars for future climatic conditions.

Nickel and ozone stresses induce differential growth, antioxidant activity and mRNA transcription in Oryza sativa cultivars

ABSTRACT This study evaluates the influences of nickel and ozone exposure individually and/ or in combination on growth performance, antioxidant activity and genes up regulation of two rice cultivars Sakha 101 and Giza 178. Ni treatment at high doses (100 µM Ni) and 75 ppb O3 alone reduced the fresh weight, mineral content, membrane integrity and Rubisco content. There was an increase in SOD and APX activity in the shoots of rice cultivars, whereas, there was a decrease in GR and GST in the roots and shoots. In contrast combined stresses appeared to be stimulatory for growth and mineral contents, Rubisco content and antioxidant enzymes. Nonspecific lipid transfer protein and transmembrane protein genes were up regulation in rice cultivars in response to Ni stress. Carotenoid cleavage dioxygenase is upregulated in response to ozone stress; RNA pseudouridine synthase, heat shock proteins and cytochrome P450-like were upregulated in response to combined stresses. The results revealed that the interactive effects of both stresses were antagonistic on growth parameters and antioxidant activities to overcome the adverse effects of both pollutants.

Extensive allele-level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies.

Epigenetic mechanisms play a major role in heterosis, partly as a result of the remodeling of epigenetic modifications in F1 hybrids. Based on chromatin immunoprecipitation-sequencing (ChIP-Seq) analyses, we show that at the allele level extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F1 hybrids of Oryza sativa (rice) cultivars Nipponbare and 93-11, representing the two subspecies japonica and indica. Globally, the allele modification-altered loci in leaf or root of the reciprocal F1 hybrids involved ˜12-43% or more of the genomic regions carrying either of two typical histone methylation markers, H3K4me3 (>21000 genomic regions) and H3K27me3 (>11000 genomic regions). Nevertheless, at the total modification level, the majority (from ˜43 to >90%) of the modification-altered alleles lay within the range of parental additivity in the hybrids because of concerted alteration in opposite directions, consistent with an overall attenuation of allelic differences in the modifications. Importantly, of the genomic regions that did show non-additivity in total modification level by either marker in the two tissues of hybrids, >80% manifested transgressivity, which involved genes enriched in specific functional categories. Extensive allele-level alteration of H3K4me3 alone was positively correlated with genome-wide changes in allele-level gene expression, whereas at the total level, both H3K4me3 and H3K27me3 remodeling, although affecting just a small number of genes, contributes to the overall non-additive gene expression to variable extents, depending on tissue/marker combinations. Our results emphasize the importance of allele-level analysis in hybrids to assess the remodeling of epigenetic modifications and their relation to changes in gene expression.

Genes Contributing to Domestication of Rice Seed Traits and Its Global Expansion.

Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for the natural survival of wild rice such as seed dormancy and shattering have become favorable ones for human consumption due to the loss-of-function mutations in the genes that are underlying these traits. As a consequence, many genes that are related to these kinds of traits have been fixed with favorable alleles in modern cultivars by artificial selection. After domestication, Oryza sativa cultivars gradually spread to temperate and cool regions from the tropics and subtropics due to the loss of their photoperiod sensitivity. In this paper, we review the characteristics of domestication-related seed traits and heading dates in rice, including the key genes controlling these traits, the differences in allelic diversity between wild rice and cultivars, the geographic distribution of alleles, and the regulatory pathways of these traits. A comprehensive comparison shows that these genes contributed to rice domestication and its global expansion. In addition, these traits have also experienced parallel evolution by artificial selection on the homologues of key genes in other cereals.

Variation in the regulatory region of FZP causes increases in secondary inflorescence branching and grain yield in rice domestication.

Inflorescence branching is a key agronomic trait determining rice yield. The primary branch of the ancestral wild rice (Oryza rufipogon Griff.) bears few grains, due to minimal secondary branching. By contrast, Oryza sativa cultivars have been selected to produce large panicles with more secondary branches. Here we showed that the CONTROL OF SECONDARY BRANCH 1 (COS1) gene, which is identical to FRIZZY PANICLE (FZP), plays an important role in the key transition from few secondary branches in wild rice to more secondary branches in domesticated rice cultivars. A 4-bp tandem repeat deletion approximately 2.7 kb upstream of FZP may affect the binding activities of auxin response factors to the FZP promoter, decrease the expression level of FZP and significantly enhance the number of secondary branches and grain yield in cultivated rice. Functional analyses showed that NARROW LEAF 1 (NAL1), a trypsin-like serine and cysteine protease, interacted with FZP and promoted its degradation. Consistently, downregulating FZP expression or upregulating NAL1 expression in the commercial cultivar Zhonghua 17 increased the number of secondary branches per panicle, grain number per panicle and grain yield per plant. Our findings not only provide insights into the molecular mechanism of increasing grain number and yield during rice domestication, but also offer favorable genes for improving the grain yield of rice.