http://www.thericejournal.com The latest research articles published by Rice 2013-05-21T00:00:00Z Background: Bacterial grain rot (BGR), caused by the bacterial pathogen Burkholderia glumae, is a destructive disease of rice. Because BGR tends to be highly affected by environmental conditions such as temperature and humidity, it is difficult to evaluate BGR resistance of diverse cultivars with different heading dates by using field inoculation. Molecular tagging of genes involved in BGR is an important objective for rice breeding. Results: In this study, we mapped a quantitative trait locus (QTL) for BGR resistance by a modified cut-panicle inoculation method. First, we assessed the levels of BGR resistance in 84 cultivars by a standard cut-panicle inoculation technique, in which panicles are harvested and inoculated in the laboratory under controlled conditions. For the genetic analysis, we selected two cultivars: Kele, a resistant traditional lowland cultivar (indica) that originated in India, and Hitomebore, a susceptible modern lowland cultivar (temperate japonica) from Japan. Second, by comparing the susceptibility of Kele and Hitomebore spikelets before and up to 3 days after anthesis, we found a dramatic decline in susceptibility at 1 day after anthesis in Kele but not in Hitomebore. Thus, we applied a modified method by inoculating spikelets at 1 day after anthesis for further analysis. To search for QTLs associated with BGR resistance, we measured the ratio of diseased spikelets (RDS, an index reflecting both quantity and severity of infection) and the ratio of diseased spikelet area (RDSA) in 110 backcrossed inbred lines (BILs) derived from a cross between Kele and Hitomebore. One major QTL associated with both RDS and RDSA was detected on the long arm of chromosome 1. This QTL explained 25.7% and 12.1% of the total phenotypic variance in RDS and RDSA in the BILs, respectively, and the Kele allele increased BGR resistance. Conclusions: We mapped a major QTL for BGR resistance on the long arm of chromosome 1. These results clearly demonstrated that genetic analysis of BGR resistance in rice can be effectively performed and that this trait could be a target of marker-assisted selection in rice breeding programs. http://www.thericejournal.com/content/6/1/13 Ritsuko Mizobuchi Hiroyuki Sato Shuichi Fukuoka Takanari Tanabata Seiya Tsushima Tokio Imbe Masahiro Yano Rice 2013, null:13 2013-05-21T00:00:00Z doi:10.1186/1939-8433-6-13 /content/figures/1939-8433-6-13-toc.gif Rice 1939-8433 ${item.volume} 13 2013-05-21T00:00:00Z PDF Background: Phytic acid (InsP6) is considered as the major source of phosphorus and inositol phosphates in cereal grains. Reduction of phytic acid level in cereal grains is desirable in view of its antinutrient properties to maximize mineral bioavailability and minimize the load of phosphorus waste management. We report here RNAi mediated seed-specific silencing of myo-inositol-3-phosphate synthase (MIPS) gene catalyzing the first step of phytic acid biosynthesis in rice. Moreover, we also studied the possible implications of MIPS silencing on myo-inositol and related metabolism, since, first step of phytic acid biosynthesis is also the rate limiting step of myo-inositol synthesis, catalyzed by MIPS. Results: The resulting transgenic rice plants (T3) showed a 4.59 fold down regulation in MIPS gene expression, which corresponds to a significant decrease in phytate levels and a simultaneous increment in the amount of inorganic phosphate in the seeds. A diminution in the myo-inositol content of transgenic plants was also observed due to disruption of the first step of phytic acid biosynthetic pathway, which further reduced the level of ascorbate and altered abscisic acid (ABA) sensitivity of the transgenic plants. In addition, our results shows that in the transgenic plants, the lower phytate levels has led to an increment of divalent cations, of which a 1.6 fold increase in the iron concentration in milled rice seeds was noteworthy. This increase could be attributed to reduced chelation of divalent metal (iron) cations, which may correlate to higher iron bioavailability in the endosperm of rice grains. Conclusion: The present study evidently suggests that seed-specific silencing of MIPS in transgenic rice plants can yield substantial reduction in levels of phytic acid along with an increase in inorganic phosphate content. However, it was also demonstrated that the low phytate seeds had an undesirable diminution in levels of myo-inositol and ascorbate, which probably led to sensitiveness of seeds to abscisic acid during germination. Therefore, it is suggested that though MIPS is the prime target for generation of low phytate transgenic plants, down-regulation of MIPS can have detrimental effect on myo-inositol synthesis and related pathways which are involved in key plant metabolism. http://www.thericejournal.com/content/6/1/12 Nusrat Ali Soumitra Paul Dipak Gayen Sailendra Sarkar Swapan Datta Karabi Datta Rice 2013, null:12 2013-05-15T00:00:00Z doi:10.1186/1939-8433-6-12 /content/figures/1939-8433-6-12-toc.gif Rice 1939-8433 ${item.volume} 12 2013-05-15T00:00:00Z XML Background: This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents -- 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community. Results: The indica MAGIC population is the most advanced of the MAGIC populations developed thus far and comprises 1328 lines produced by single seed descent (SSD). At the S4 stage of SSD a subset (200 lines) of this population was genotyped using a genotyping-by-sequencing (GBS) approach and was phenotyped for multiple traits, including: blast and bacterial blight resistance, salinity and submergence tolerance, and grain quality. Genome-wide association mapping identified several known major genes and QTLs including Sub1 associated with submergence tolerance and Xa4 and xa5 associated with resistance to bacterial blight. Moreover, the genome-wide association study (GWAS) results also identified potentially novel loci associated with essential traits for rice improvement. Conclusion: The MAGIC populations serve a dual purpose: permanent mapping populations for precise QTL mapping and for direct and indirect use in variety development. Unlike a set of naturally diverse germplasm, this population is tailor-made for breeders with a combination of useful traits derived from multiple elite breeding lines. The MAGIC populations also present opportunities for studying the interactions of genome introgressions and chromosomal recombination. http://www.thericejournal.com/content/6/1/11 Nonoy Bandillo Chitra Raghavan Pauline Muyco Ma Sevilla Irish Lobina Christine Dilla-Ermita Chih-Wei Tung Susan McCouch Michael Thomson Ramil Mauleon Rakesh Singh Glenn Gregorio Edilberto Redoña Hei Leung Rice 2013, null:11 2013-05-06T00:00:00Z doi:10.1186/1939-8433-6-11 /content/figures/1939-8433-6-11-toc.gif Rice 1939-8433 ${item.volume} 11 2013-05-06T00:00:00Z PDF Background: MiRNAs are key regulators in the miRNA-mediated regulatory networks. Single nucleotide polymorphisms (SNPs) that occur at miRNA-related regions may cause serious phenotype changes. To gain new insights into the evolution of miRNAs after SNP variation, we performed a genome-wide scan of miRNA-related SNPs, and analyzed their effects on the stability of miRNAs structure and the alteration of target spectrum in rice. Results: We find that the SNP density in pre-miRNAs is significantly higher than that in the flanking regions, owing to the rapid evolution of a large number of species-specific miRNAs in rice. In contrast, it is obvious that deeply conserved miRNAs are under strong purifying selection during evolution. In most cases, the SNPs in stem regions may result in the miRNA hairpin structures changing from stable to unstable status; And SNPs in mature miRNAs have great potential to have either newly created or disrupted the miRNA-target interactions. However, the total number of gained targets is over 2.5 times greater than that are lost after mutation. Notably, 12 putative domestication-related miRNAs have been identified, where the SNP density is significantly lower. Conclusions: The present study provides the first outline of SNP variations occurred in rice pre-miRNAs at the whole genome-wide level. These analyses may deepen our understanding on the effects of SNPs on the evolution of miRNAs in the rice genome. http://www.thericejournal.com/content/6/1/10 Qingpo Liu Hong Wang Leyi Zhu Haichao Hu Yuqiang Sun Rice 2013, null:10 2013-04-23T00:00:00Z doi:10.1186/1939-8433-6-10 /content/figures/1939-8433-6-10-toc.gif Rice 1939-8433 ${item.volume} 10 2013-04-23T00:00:00Z XML Background: Plant growth regulators play important roles in plant growth and development, but little is known about roles of plant growth regulators in yield, grain qualities and antioxidant enzyme activities in super hybrid rice. In this study, gibberellic acid(GA3), paclobutrazol (PBZ), 6-Benzylaminopurine(6-BA) treatments and distilled water (control) were sprayed to two hybrid rice cultivars (Peizataifeng and Huayou 86) at the heading stage in the field experiments in both early and late season in 2007. Treatments were arranged in a split-plot design with four replications. Cultivars treatments with two newly developed super hybrid rice Peizataifeng and Huayou86 were the main plots and plant growth regulators treatments were the subplots. Subplot treatments included (1) plots sprayed with distilled water(CK), (2) plots sprayed with 20 mg L-1 GA3 prepared using 95% ethanol as surfactant(GA3), (3) plots sprayed with 50 mg L-1 PBZ(PBZ), (4) plots sprayed with 30 mg L-1 6-BA(6-BA). Results: Spraying PBZ with 50 mg L-1 or 6-BA with 30 mg L-1 at the heading stage could increase the number of spikelets per panicle, seed setting rate and grain yields in Peizataifeng and Huayou86 in both seasons. PBZ treatment also significantly improved head rice rate and amylose content in Peizataifeng and Huayou86 in early season. Furthermore, it was observed that spraying PBZ or 6-BA could increase super oxide dismutase (SOD) and peroxidase (POD) activities, decrease accumulation of malendialdehyde (MDA) in flag leaves at the late growth stage. Conclusions: Application of PBZ or 6-BA partially alleviated the detrimental effects of rice senescence by modulating the activity of enzymatic antioxidants, and improving antioxidant system, which helped in sustaining plant growth. Therefore, spraying PBZ with 50 mg L-1 or 6-BA with 30 mg L-1 at the heading stage could increase grain yields and improve grain qualities in the two super hybrid rice. http://www.thericejournal.com/content/6/1/9 Shenggang Pan Fahd Rasul Wu Li Hua Tian Zhaowen Mo Meiyang Duan Xiangru Tang Rice 2013, null:9 2013-04-16T00:00:00Z doi:10.1186/1939-8433-6-9 /content/figures/1939-8433-6-9-toc.gif Rice 1939-8433 ${item.volume} 9 2013-04-16T00:00:00Z XML Background: In plant cells, most microRNAs (miRNAs) perform cleavages of target mature mRNAs in the cytoplasm. A recent report of a miRNA pathway involved in DNA methylation in the rice nucleus raises the possibility that plant miRNAs could cleave intron-containing pre-mRNAs (the precursor of messenger RNAs) located in the nucleus. Results: In this study, we searched for the miRNA binding sites present within the introns of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genes. All miRNA—intron interactions predicted to result in cleavages were validated by using the public degradome sequencing data. As a result, 40 miRNA—intron pairs involving 25 miRNAs in Arabidopsis and 1912 pairs involving 91 miRNAs in rice were identified. For several rice genes, not all transcription forms (alternative splicing variants) were under similar regulation by specific miRNAs. Certain transcripts could escape cleavages due to the absence of intronic miRNA binding sites within these sequences. In some instances, specific cleaved intron remnants could be converted to double-stranded RNAs (dsRNAs) by RNA-dependent RNA polymerase 2. These dsRNAs could then be processed into 21- and 24-nt phased sRNAs by the activity of Dicer-like 1 and 3, respectively. The resultant siRNAs have the potential to be incorporated into Argonaute (AGO)-associated silencing complexes and result in cleavages of target pre-mRNA sequences. Conclusions: A regulatory model, miRNA—targeting of intron-containing pre-mRNAs—phased sRNAs—targeting of mature mRNAs is proposed, which further expands the potential modes of action of plant miRNAs. http://www.thericejournal.com/content/6/1/8 Yijun Meng Chaogang Shao Xiaoxia Ma Huizhong Wang Rice 2013, null:8 2013-04-15T00:00:00Z doi:10.1186/1939-8433-6-8 /content/figures/1939-8433-6-8-toc.gif Rice 1939-8433 ${item.volume} 8 2013-04-15T00:00:00Z XML Background: Normal development of chloroplast is vitally important to plants, but its biological mechanism is still far from fully being understood, especially in rice. Results: In this study, a novel yellow-green leaf mutant, ygl138, derived from Nipponbare (Oryza sativa L. ssp. japonica) treated by ethyl methanesulfonate (EMS), was isolated. The mutant exhibited a distinct yellow-green leaf phenotype throughout development, reduced chlorophyll level, and arrested chloroplast development. The phenotype of the ygl138 mutant was caused by a single nuclear gene, which was tentatively designed as YGL138(t). The YGL138(t) locus was mapped to chromosome 11 and isolated into a confined region of 91.8 kb by map-based cloning. Sequencing analysis revealed that, Os11g05552, which was predicted to encode a signal recognition particle 54 kDa (SRP54) protein and act as a chloroplast precursor, had 18 bp nucleotides deletion in the coding region of ygl138 and led to a frameshift. Furthermore, the identity of Os11g05552 was verified by transgenic complementation. Conclusions: These results are very valuable for further study on YGL138(t) gene and illuminating the mechanism of SRP54 protein involving in chloroplast development of rice. http://www.thericejournal.com/content/6/1/7 Fantao Zhang Xiangdong Luo Biaolin Hu Yong Wan Jiankun Xie Rice 2013, null:7 2013-03-27T00:00:00Z doi:10.1186/1939-8433-6-7 /content/figures/1939-8433-6-7-toc.gif Rice 1939-8433 ${item.volume} 7 2013-03-27T00:00:00Z XML Background: Anther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin). Results: A total of 1,165 × 106 raw reads were generated with over 58× coverage that detected 1,154,063 DNA polymorphisms between the Korean rice accessions and Nipponbare. We observed that in Hwayeong and its progenies, 0.64 SNP was found per one kb of Nipponbare genome, while Dongjin, bred by a conventional breeding method, had a lower number of SNPs (0.45 SNP/kb). Among 1,154,063 DNA polymorphisms, 29,269 non-synonymous SNPs located on 30,013 genes and these genes were functionally classified based on gene ontology (GO). We also analyzed line-specific SNPs which were estimated 1 ~ 3% of the total SNPs. The frequency of non-synonymous SNPs in each accession ranged from 26 SNPs in Hwayeong to 214 SNPs in HY-04. Conclusions: The genetic difference we detected between the progenies derived from anther culture and their mother cultivar is due to somaclonal variation during tissue culture process, such as karyotype change, chromosome rearrangement, gene amplification and deletion, transposable element, and DNA methylation. Detection of genome-wide DNA polymorphisms by high-throughput sequencer enabled to identify sequence diversity derived from anther culturing and genomic locations of heritable traits. Furthermore, it will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance. http://www.thericejournal.com/content/6/1/6 In-Seon Jeong Ung-Han Yoon Gang-Seob Lee Hyeon-So Ji Hyun-Ju Lee Chang-Deok Han Jang-Ho Hahn Gynheung An Tae-Ho Kim Rice 2013, null:6 2013-03-14T00:00:00Z doi:10.1186/1939-8433-6-6 /content/figures/1939-8433-6-6-toc.gif Rice 1939-8433 ${item.volume} 6 2013-03-14T00:00:00Z XML Background: The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality. Results: Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL. Conclusions: The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will have a high impact on the yield stability and sustainability of rice productivity. http://www.thericejournal.com/content/6/1/5 Jung-Pil Suh Ji-Ung Jeung Tae-Hwan Noh Young-Chan Cho So-Hyun Park Hyun-Su Park Mun-Sik Shin Chung-Kon Kim Kshirod Jena Rice 2013, null:5 2013-02-08T00:00:00Z doi:10.1186/1939-8433-6-5 /content/figures/1939-8433-6-5-toc.gif Rice 1939-8433 ${item.volume} 5 2013-02-08T00:00:00Z XML Background: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. http://www.thericejournal.com/content/6/1/4 Yoshihiro Kawahara Melissa de la Bastide John Hamilton Hiroyuki Kanamori W McCombie Shu Ouyang David Schwartz Tsuyoshi Tanaka Jianzhong Wu Shiguo Zhou Kevin Childs Rebecca Davidson Haining Lin Lina Quesada-Ocampo Brieanne Vaillancourt Hiroaki Sakai Sung Lee Jungsok Kim Hisataka Numa Takeshi Itoh C Buell Takashi Matsumoto Rice 2013, null:4 2013-02-06T00:00:00Z doi:10.1186/1939-8433-6-4 /content/figures/1939-8433-6-4-toc.gif Rice 1939-8433 ${item.volume} 4 2013-02-06T00:00:00Z XML