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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. [ABSTRACT FROM AUTHOR]

Three genetically modified (GM) rice varieties were developed: drought-tolerant, insect-resistant, and marker-free transgenic Bt rice. The metabolomic approaches were applied to the seeds and leaves of three GM rice plants to comparatively investigate the effects of genetic modification on GM and non-GM rice. Among the non-GM rice, commercial rice consisting of japonica, indica, and japonica × indica (hybrid) subspecies was grown in a greenhouse together with GM rice. Multivariate analysis revealed that natural genotypes (japonica, indica, and hybrids) had a much stronger effect on rice seed and leave compositions than genetic modifications. Compared to japonica rice, raffinose and inositol were higher in the seeds and leaves of indica and hybrid rice, suggesting a metabolic phenotype for the genetic diversity of subspecies with different origins. Our results demonstrated that metabolomics approaches can be used to evaluate the unintended effects of GM and non-GM rice ingredients. Furthermore, metabolic profiling reflects the natural variability of the metabolites associated with their origins. [ABSTRACT FROM AUTHOR]

Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169 bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties. [ABSTRACT FROM AUTHOR]

The objective of this study was to preliminarily analyze the differences in pathogenicity and physiologic races between Pyricularia oryzae isolates from indica and japonica rice varieties. Five to 7 isolates of P. oryzae from indica and japonica, having good sporulation capacity, were screened out in each experimental year. To determine the pathogenicity of P. oryzae, different kinds of rice varieties were inoculated with mixtures of indica and japonica isolates. A total of 46 isolates, including 23 indica isolates and 23 japonica isolates, were screened out in four years. In total, 1252 rice varieties, including 490 indica, 296 japonica and 466 indica-japonica hybrid rice varieties, were inoculated. Our results suggested that the degree of disease was more severe in most indica varieties infected with indica isolates than in those infected with japonica isolates. That is, indica isolates were more inclined to infect indica varieties. A majority of japonica and indica-japonica hybrid rice varieties infected with japonica isolates showed more severe infection than those infected with indica isolates. In other words, japonica isolates more easily infected japonica and indica-japonica hybrid rice varieties. The differences in quantity among the varieties indicated high resistance to rice blast in the corresponding kinds of rice inoculated with indica and japonica isolates, fully explaining the above viewpoint. Most of the 23 indica isolates belonged to indica races. Among the 23 japonica isolates, half were indica races and half were japonica races. In addition, there were significant differences between the isolates selected in the first two years and those selected in the second two years. The isolates in the first two years were all of indica races, and those of japonica races all appeared in the second two years. The results showed that the race of isolates shared little association with the kind of rice variety collected but was associated with the year of neck blast sample collection. [ABSTRACT FROM AUTHOR]

Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indica–japonica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4–5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice. [ABSTRACT FROM AUTHOR]

Exhaustive studies on mitogen-activated protein kinase (MAPK) have reported the importance in regulating a variety of responses during plant growth and development. In particular, the potential MAPK genes, MPK3 and MPK6, seem to regulate a plethora of responses, conferring tolerance to varied abiotic, biotic, and developmental stimuli. This makes both MPK3 and MPK6 potential targets for further studies. It would be an important concern to overexpress and knock out these pivotal proteins and then, in turn, to monitor the plant response which is expected to correlate action of a gene to a trait in cellular and organismal contexts. However, overexpression of MAPK genes has remained a puzzle in plants. In the present study, we report the generation of stable transgenic lines overexpressing OsMPK3 in indica and japonica cultivars and OsMPK6 in japonica cultivar under the control of an inducible promoter. We also establish the crucial steps and troubleshooting for each of the indicated rice transformation medium components. Later, we study the potential role of these MAPKs in high-throughput analysis of root system architectural (RSA) traits. It was observed that OsMPK6 overexpression lines had a more robust and spread out root architectural system while OsMPK3 overexpression lines had a typical bushy phenotype. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. Results: To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/−50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes. Conclusions: The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation. [ABSTRACT FROM AUTHOR]

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

Flag leaves in crops are one of the key organs determining grain yield, which significantly affects total yield. However, our understanding of the molecular and genetic regulation of flag leaves is very limited. To provide a genome-wide view of gene expression in flag leaves associated with grain yield, we compared the flag leaves of rice varieties with different yield potentials, such as Hwacheong (moderate yield), Milyang23 (high yield), Dasan (high yield), and IR64 (high yield), using an Agilent 8x60K microarray. As a result, we identified 245 genes that were up-regulated in high yield potential varieties compared to Hwacheong, along with 293 genes that were up-regulated in Hwacheong. GO enrichment analysis of the selected candidate genes revealed that the thiamin biosynthetic process and the sucrose metabolic process were the most enriched terms in flag leaves from the high yield potential varieties, while phosphate transport and the chitin catabolic process terms were the most significant in flag leaves of Hwacheong. In addition, MapMan analysis suggested that the biotic stress response and auxin signaling are important in Hwacheong, while the heat stress response, calcium and G-protein signaling are necessary in other high yield potential varieties. The functions of 11 of our candidate genes have been previously characterized in genetic and molecular biological studies and most of them are related to tolerance against environmental challenges or yield, thereby indicating the potential significance of our candidate genes in further applications. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is a major food for more than half of the world’s population and serves as a model monocot plant. DEP1 (dense and erect panicle 1), corresponding to an erect-panicle architecture, may bring the third breakthrough in rice breeding after the introduction of the semi-dwarf trait and the application of heterosis in hybrid rice. The aim of this study was to determine the effects of DEP1 on yield components and vascular bundle-related traits under indica and japonica genetic backgrounds. We analyzed a series of recombinant inbred lines, which were derived from a cross between the japonica variety SN265 with an erect panicle and the indica variety R99 with a curved panicle. The results showed that effects of the DEP1/dep1 allele were much stronger than the effects of the indica/japonica genetic background on vascular bundle-related traits and yield components. As the frequency of indica alleles increased, the grain yield per plant and the harvest index significantly increased in lines with the dep1 allele. Among the indica-type lines, those with the dep1 allele showed superior values for almost all of the vascular bundle-related traits and yield components. Our results provide new insights into the use of a high-yield-related gene derived from japonica in the indica genetic background. [ABSTRACT FROM AUTHOR]

Key message: Japonica and indica have different non-host resistance (NHR) abilities to Puccinia striiformis f. sp. tritici ( Pst ), and hydrogen peroxide (H O ) has a positive function in NHR to japonica against Pst. Abstract: Non-host interactions between Puccinia striiformis f. sp. tritici ( Pst) and two rice subspecies were characterized using 23 rice varieties, including 11 japonica and 12 indica. Results showed that the infected fungal structures were easily produced in the leaves of indica, whereas only several substomatal vesicles and primary infection hyphae were observed in the leaves of japonica. This result indicated that indica is less resistant or more susceptible to Pst than japonica. Hydrogen peroxide accumulated in the initial phase of japonica- Pst interaction but not in indica- Pst interaction. A set of reactive oxygen species (ROS)-related genes was also induced in response to Pst infection, suggesting that ROS activation is one of the major mechanisms of non-host resistance of rice to Pst. [ABSTRACT FROM AUTHOR]

Aminotransferases are pyridoxal 5′-phosphate-dependent enzymes that play crucial roles in plant growth, development, and responses to abiotic stress. The class III aminotransferase family ( ATIII family) is an important subfamily. However, no characterization of rice ATIII genes has been previously reported. Using available rice genome sequence information, we identified 12 japonica and 13 indica ATIII genes that were randomly localized on chromosomes 2, 3, 4, 5, 7, 8, and 11. Information provided by the Plant Genome Duplication Database revealed that four japonica and four indica ATIII genes are the results of segmental duplications, and two japonica and six indica genes resulted from tandem duplications. A phylogenetic analysis of the ATIII genes in japonica, indica and Arabidopsis enabled the classification of the genes into six different groups, and the characteristics were established before the monocot-dicot and japonica- indica split. An analysis of the Ka/Ks, divergence time and average indel length suggested the diverse selection styles of the duplicated gene pairs. Gene structure and motif analyses revealed that the ATIII gene family has experienced extensive divergence. Real-time PCR was performed to examine the expression pattern of the japonica ATIII genes in response to various abiotic stresses including drought, salt, and cold. The results suggested that most of the genes were differentially up- or down-regulated in rice seedlings in response to at least one stress factor, which indicates the key role of the rice ATIII gene family in responding to abiotic stresses. These results provide a basis for elucidating the roles of the ATIII genes and their further functional analysis under abiotic stresses. [ABSTRACT FROM AUTHOR]

Indica is not only an important rice subspecies widely planted in Asia and the rest of the world, but it is also the genetic background of the majority of hybrid varieties in China. Studies on genetic structure and genetic diversity in indica germplasm resources are important for the classification and utilization of cultivated rice in China. Using a genetically representative core collection comprising 1482 Chinese indica landraces, we analysed the genetic structure, geographic differentiation and diversity. Model-based structure analysis of varieties within three ecotypes revealed nine eco-geographical types partially accordant with certain ecological zones in China. Differentiation of eco-geographical types was attributed to local ecological adaption and physical isolation. These groups may be useful for developing heterotic groups of indica. To facilitate the identification of different ecotypes and eco-geographical types, we identified characteristic SSR alleles of each ecotype and eco-geographical type and a rapid index of discrimination based on characteristic alleles. The characteristic alleles and rapid discrimination index may guide development of heterotic groups, and selection of hybrid parents. [ABSTRACT FROM AUTHOR]

Water scarcity and drought have seriously threatened traditional rice cultivation practices in several parts of the world including India. In the present investigation, experiments were conducted to see if the water-efficient aerobic rice genotypes developed at UAS, Bangalore (MAS25, MAS26 and MAS109) and IRRI, Philippines (MASARB25 and MASARB868), are endowed with drought tolerance or not. A set of these aerobic and five lowland high-yielding (HKR47 and PAU201, Taraori Basmati, Pusa1121 and Pusa1460) indica rice genotypes were evaluated for: (i) yield and yield components under submerged and aerobic conditions in field, (ii) root morphology and biomass under aerobic conditions in pots in the nethouse, (iii) PEG-6000 (0, −1, −2 and −3 bar) induced drought stress at vegetative stage using a hydroponic culture system and (iv) polymorphism for three SSR markers associated with drought resistance traits. Under submerged conditions, the yield of aerobic rice genotypes declined by 13.4-20.1 % whereas under aerobic conditions the yield of lowland indica/Basmati rice varieties declined by 23-27 %. Under water-limited conditions in pots, aerobic rice genotypes had 54-73.8 % greater root length and 18-60 % higher fresh root biomass compared to lowland indica rice varieties. Notably, root length of MASARB25 was 35 % shorter than MAS25 whereas fresh and dry root biomass of MASARB25 was 10 % and 64 % greater than MAS25. The lowland indica were more sensitive to PEG-stress with a score of 5.9-7.6 for Basmati and 6.1-6.7 for non-aromatic indica rice varieties, than the aerobic rice genotypes (score 2.7-3.3). A set of three microsatellite DNA markers (RM212, RM302 and RM3825) located on chromosome 1 which has been shown to be associated with drought resistance was investigated in the present study. Two of these markers (RM212 and RM302) amplified a specific allele in all the aerobic rice genotypes which were absent in lowland indica rice genotypes. [ABSTRACT FROM AUTHOR]

Two subspecies in rice, japonica and indica, have their own ecotypic traits. However, reproductive barriers such as spikelet sterility in hybrid progenies between subspecies have been an obstacle in breeding programs for combining desirable traits from both subspecies through inter-subspecific hybridization. The 166 F RILs and two BCFs' were analyzed for spikelet and pollen fertility with the parents and F between Dasanbyeo (DS, indica) / TR22183 (TR, japonica). A frame map was constructed using a total of 218 polymorphic STS and SSR markers. In both BCFs' of DS//DS/TR and TR//DS/TR, clusters of significant QTLs for spikelet and pollen fertility were identified on the short arm of chromosome 5 and chromosome 8. Nine and ten digenic epistatic interactions for DS//DS/TR and TR//DS//TR were identified, respectively. HF-QTLs were detected at the similar position with subspecies-specific markers and segregation distortion loci, implying that HF-QTLs might be associated with the differentiation of indica and japonica. Hybrid fertility/sterility and its relationship with other traits are discussed in relation to the reproductive barriers between subspecies of rice. [ABSTRACT FROM AUTHOR]

Studies on microsatellite distribution and divergence in related genomes contribute towards understanding of genome evolution in eukaryotes. Despite the availability of whole genome sequences of four rice genomes, occurrence and significance of microsatellites in the rice genome has remained a relatively unexplored area of research. We have aligned genomes of two rice subspecies i.e. indica and japonica to understand the trends of microsatellite conservation and divergence in the rice genome. Nearly 62% of the indica microsatellites were also found in the japonica genome. Occurrence of microsatellites showed a negative association with that of retrotransposons. Microsatellites repeat unit length and sequence showed direct influence on the microsatellite locus length. Further, microsatellite allele length was also influenced by the sequence characteristics of the neighbouring regions. CCG repeats were most conserved microsatellite sequences across the different syntenic regions in the two rice genomes and often showed association with CpG islands. Our study suggested that microsatellite distribution is not only governed by a balance between replication slippage and point mutations as proposed earlier, but also by the microsatellite motif sequence and characteristics of microsatellite neighbouring regions in the genome. Thus, this study is likely to prove an important reference for understanding the process of microsatellite evolution and dynamics in the two rice subspecies. [ABSTRACT FROM AUTHOR]

The cultivated rice ( Oryza sativa L.) has two subspecies, indica and japonica. The japonica rice germplasm has a narrower genetic diversity compared to the indica subspecies. Rice breeders aim to develop new varieties with a higher yield potential, with enhanced resistances to biotic and abiotic stresses, and improved adaptation to environmental changes. In order to face some of these challenges, japonica rice germplasm will have to be diversified and new breeding strategies developed. Indica rice improvement could also profit from more “genepool mingling” for which japonica rice could play an important role. Interesting traits such as low-temperature tolerance, and wider climate adaptation could be introgressed into the indica subspecies. In the past decade, huge developments in rice genomics have expanded our available knowledge on this crop and it is now time to use these technologies for improving and accelerating rice breeding research. With the full sequence of the rice genome, breeders may take advantage of new genes. Also new genes may be discovered from the genepool of wild relatives, or landraces of the genus Oryza, and incorporated into elite japonica cultivars in a kind of “gene revolution” program. Expectedly, new technologies that are currently being optimized, aiming for novel gene discovery or for tracking the regions under selection, will be suggested as new breeding approaches. This paper revisits breeding strategies successfully employed in indica rice, and discusses their application in japonica rice improvement (e.g. ideotype breeding, wide hybridization and hybrid performance). [ABSTRACT FROM AUTHOR]

Submergence is a major stress causing yield losses particularly in the direct-seeded rice cultivation system and necessitates the development of a simple, rapid and reliable bioassay for a large scale screening of rice germplasms with tolerance against submergence stress. We developed two new bioassay methods that were based primarily on the seedling vigor evaluated by the ability of fast shoot elongation under submerged conditions, and compared their effectiveness with two other available methods. All four bioassay methods using cultivars of 7 indica and 6 japonica types revealed significant and consistent cultivar differences in seedling vigor under submergence and/or submergence tolerance. Japonica cultivars were more vigorous than indica cultivars, with Nipponbare being the most vigorous. The simplest test tube method showed the highest correlations to all other methods. Our results suggest that seedling vigor serves as a submergence avoidance mechanism and confers tolerance on rice seedlings to flooding during early crop establishment. A possible relationship is discussed between seedling vigor based on fast shoot elongation and submergence tolerance defined by recovery from submergence stress. [ABSTRACT FROM AUTHOR]

Rice ( Oryza sativa) is one of three predominant grain crops, and its nuclear and organelle genomes have been sequenced. Following genome analysis revealed many exchanges of DNA sequences between the nuclear and organelle genomes. In this study, a total of 45 chloroplast DNA insertions more than 2 kb in length were detected in rice nuclear genome. A homologous recombination mechanism is expected for those chloroplast insertions with high similarity between their flanking sequences. Only five chloroplast insertions with high sequence similarity between two flanking sequences from an insertion were found in the 45 insertions, suggesting that rice might follow the non-homologous end-joining (NHEJ) repair of double-stranded breaks mechanism, which is suggested to be common to all eukaryotes. Our studies indicate that the most chloroplast insertions occurred at a nuclear region characterized by a sharp change of repetitive sequence density. One potential explanation is that regions such as this might be susceptible target sites or “hotspots” of DNA damage. Our results also suggest that the insertion of retrotransposon elements or non-chloroplast DNA into chloroplast DNA insertions may contribute significantly to their fragmentation process. Moreover, based on chloroplast insertions in nuclear genomes of two subspecies ( indica and japonica) of cultivated rice, our results strongly suggest that they diverged during 0.06–0.22 million years ago. [ABSTRACT FROM AUTHOR]

An investigation was made to exploit an innovative tool viz., thermosensitive genic male sterile (TGMS) system in twoline inter-subspecies rice hybrids using 132 hybrids involving four TGMS lines viz., TS15, TS16, TS18 and TS29 and thirty three testers viz., 17 indicas, 7 japonicas and 9 javanicas by line × tester method at Paddy Breeding Station, Tamil Nadu Agricultural University, India. Pre-ponderence of non-additive gene action for yield and yield attributing traits was observed by analysing combining ability. TGMS lines TS18, TS29 and the testers CB96073, CB96026, CB94247, TNAU 94241 ( indicas), Gohykumangoku ( japonica), Dular, PRR16 ( javanicas) were good general combiners. The hybrids TS29 × TNAU 94241 ( indica/indica), TS 18 × Yamadanishiki ( indica/japonica) and TS29 × Dular, TS29 × PRR16 ( indica/javanica) were promising for heterosis breeding programme. The japonica tester Gohykumangoku and javanica testers Dular and CPSL0-17 exhibited strong heterosis for spikelet fertility when crossed with TGMS lines TS 16, TS 18, TS 29 indicated that these lines may possess wide compatible gene (WCG) for spikelet fertility. Based on mean performance, standard heterosis and sca for yield and yield traits, the inter – subspecies hybrids viz., TS29 × TNAU 94241, TS18 × TNAU 94241, TS29 × CB96073, TS29 × CB94247, TS29 × CB96026 ( indica/indica) TS18 × Yamadanishiki, TS29 × Gohykumangoku ( indica/japonica), TS29 × Dular, TS29 × PRR16 ( indica/javanica) exhibited high heterosis over check hybrid CORH2 and the above hybrids can be exploited commercially. The present investigation revealed that the TGMS system may utilized as an innovative tool for developing inter subspecies two line hybrids with strong heterosis in rice. [ABSTRACT FROM AUTHOR]

This paper describes the relative efficiency of three marker systems, RAPD, ISSR, and AFLP, in terms of fingerprinting 14 rice genotypes consisting of seven temperate japonica rice cultivars, three indica near-isogenic lines, three indica introgression lines, and one breeding line of japonica type adapted to high-altitude areas of the tropics with cold tolerance genes. Fourteen RAPD, 21 ISSR, and 8 AFLP primers could produce 970 loci, with the highest average number of loci (92.5) generated by AFLP. Although polymorphic bands in the genotypes were detected by all marker assays, the AFLP assay discriminated the genotypes effectively with a robust discriminating power (0.99), followed by ISSR (0.76) and RAPD (0.61). While significant polymorphism was detected among the genotypes of japonica and indica through analysis of molecular variance (AMOVA), relatively low polymorphism was detected within the genotypes of japonica rice cultivars. The correlation coefficients of similarity were significant for the three marker systems used, but only the AFLP assay effectively differentiated all tested rice lines. Fingerprinting of backcross-derived resistant progenies using ISSR and AFLP markers easily detected progenies having a maximum rate of recovery for the recurrent parent genome and suggested that our fingerprinting approach adopting the ‘undefined-element-amplifying’ DNA marker system is suitable for incorporating useful alleles from the indica donor genome into the genome of temperate japonica rice cultivars with the least impact of deleterious linkage drag. [ABSTRACT FROM AUTHOR]

We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies. [ABSTRACT FROM AUTHOR]

The somatic chromosomes of standard indica diploid rice, IR 36, were squashed on glass slides and stained with Giemsa. The condensation patterns (CP) of prometaphase chromosomes were quantitatively analysed using CHIAS III software. The relative length and centromeric index (CI) were converted from CHIAS III to numerical data and calculated by EXCEL program. The ideogram based on CP of indica rice was established. There were 2 pairs of satellite chromosomes and the result was confirmed by fluorescence in situ hybridization using 45S rDNA as a probe. [ABSTRACT FROM AUTHOR]

Fertile rice plants have been regenerated from protoplasts of two japonica rice varieties (Radon and Baldo) using a protocol initially developed for plant regeneration from protoplasts of an indica rice. Embryogenic calli were developed from immature embryos of Radon and Baldo rice on a callus induction medium, and then used to establish cell suspensions. Protoplasts were isolated from the cell suspensions, and cultured on a Millipore filter placed on a Kao/agarose medium that contained cell clusters from suspensions of IR52 or IR45. The protoplasts grew vigorously on Kao medium and developed into embryogenic calli within two to three weeks. Somatic embryo development occurred during a subsequent transfer of the calli to an LS medium for two to three weeks. The calli were then transferred to MS or N6 plant regeneration medium, and within one to three weeks, plants regenerated from 21 to 32% of the Radon calli, and 33 to 35% of the Baldo calli. Based upon these results and the previous success in regenerating an indica variety from protoplasts, this procedure has great promise for regenerating a range of rice varieties, and probably for regeneration of other monocotyledonous plants from protoplasts [ABSTRACT FROM AUTHOR]

Plant regeneration from protoplasts of two commercially cultivated Indian indica rice varieties, Pusa Basmati 1 and Java, has been accomplished by plating embryogenic cell suspension-derived protoplasts on the surface of filter membranes overlying agarose-embedded feeder cells of Lolium multltiflorum and Oryza ridleyi, combined with the use of a maltose-containing shoot regeneration medium. Embryogenic cell suspension cultures of Pusa Basmati 1 and Jaya were initiated from mature seed scutellum-derived calli in liquid R medium modified by the addition of 560 mg l of proline and 1.0 % (w/v) maltose. In both varieties, protoplast plating efficiencies up to 0.4 % were obtained, depending on the nature of the feeder cells. L. multiflorum feeder cells induced a 6-fold higher plating efficiency than feeder cells of O. ridleyi. In combination, O. ridleyi and L. multiflorum feedercells further enhanced protoplast plating efficiency. Protoplast-derived cell colonies were not obtained from protoplasts of either indica varieties in the absence of feeder cells. MS-based medium containing kinetin (2.0 mg l) and α-naphthaleneacetic acid (0.5 mg 1), together with sucrose and maltose both at 1.5 % (w/v), induced green shoot regeneration in 44 % of protoplast-derived tissues, depending on the feeder cells used for protoplast culture. In both varieties, tissues obtained using O. ridleyi feeder cells were more morphogenic than tissues obtained using L. multiflorum feeder cells, either alone or in combination with cells of O. ridleyi. In the japonica rice variety Taipei 309, this new procedure resulted in a 30-fold increase in plant regeneration from protoplasts compared to previous published procedures. [ABSTRACT FROM AUTHOR]

Degenerated oligonucleotide primers were used to amplify, clone, and analyze sequence heterogeneity and chromo-somal distribution of 23 PCR fragments corresponding to the reverse transcriptase domain of copia-like retrotrans-posons in rice. Of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were divided into 6 groups according to the phylogenetic and Southern blot analyses. Amino acid sequence differences among the 22 aligned fragments ranged from 1 to 64%. Southern blot analysis of 10 rice accessions including indica, japonica and common wild rice, using these 23 fragments as probes, showed that copia-like retrotransposons were present in moderate to high copy numbers in all the rice genome although the exact copy number cannot be determined. The major difference revealed by southern analysis is a differentiation between the four indica varieties as one group and the four japonica varieties and the two wild rice accessions as another group. Polymorphisms were also detected among the indica and japonica varieties by major bands and repeatable minor bands. Five hybridization bands were mapped to chromosomes 3, 4, 8, and 9, respectively. All the five bands were inherited in a dominant Mendelian fashion and were not allelic with each other, indicating that the same element did not reside on the same location in different rice accessions. No transcript of the copia-like reverse transcriptase was detected on northern blot. The results suggest that the sequence heterogeneity and distributional variability of retrotransposons may be one of contributory factors causing genetic diversity in rice. [ABSTRACT FROM AUTHOR]

In a previous study, we compared chloroplast DNAs (ctDNAs) from four species of Oryza and detected two independent deletions of DNA fragments in the ctDNAs (Kanno and Hirai 1992a). These deletions were genotype-specific variations. Since short direct-repeat sequences were detected at the borders of both deletions, the deletions were apparently the result of intramolecular recombination mediated by these direct-repeat sequences. In the present study, we examined whether or not this type of variation exists within a single species. Ishii et al. demonstrated three types of ctDNA in O. Sativa (1988), and the source of the variations that they identified seemed to be deletions. We determined the precise locations of the deletions and the sequences around them. As expected, our results showed that these variations were the results of deletions that were mediated by short direct-repeat sequences. While the deletions that had been found previously were located on spacer regions, those found in this study were located within open reading frames (ORFs). Northern hybridization analysis showed that one of the ORFs was-transcribed. In the case of this deletion, the amino acid sequence encoded by the C-terminal region of the ORF was altered and the short inverted-repeat sequences downstream of the ORF were deleted. In addition, there were other short inverted-repeat sequences downstream of the altered ORF. [ABSTRACT FROM AUTHOR]

Background: The domestication process of Asian rice (Oryza sativa L.) is complicated. It's well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. Results: A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (FST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima's D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. Conclusions: Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication. [ABSTRACT FROM AUTHOR]

Background: While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. Results: Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. Conclusions: This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications. [ABSTRACT FROM AUTHOR]