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To evaluate the feasibility of subsequent elective nodal radiotherapy (ENRT) for nodal recurrences after previous radiotherapy with a defined planning approach for a gapless radiation field junction.Patients with 1) previous radiotherapy of prostate or prostatic fossa and subsequent pelvic ENRT or 2) previous pelvic radiotherapy and subsequent ENRT to paraaortic lymph nodes (LN) and gapless junction of both radiation fields were analyzed. The cumulative maximum dose (DTwenty-two patients with PSMA-PET/CT-staged nodal oligorecurrence after prior radiotherapy were treated with pelvic (14 patients) or paraaortic ENRT (9 patients). One patient was treated sequentially at both locations. Median time between first and second RT was 20.2 months. Median doses to the lymphatic pathways and to PET-positive LN were 47.5 Gy and 64.8 Gy, respectively. The planning constraint of an estimated DENRT for nodal recurrences after a previous radiotherapy with gapless junction of radiation fields seems to be feasible, applying the dose constraints D

f5 locus in rice (Oryza sativa L.) confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotypes were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. A total of 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs f5-j/j, f5-j/j vs f5-i/i, and f5-i/j vs f5-i/i, respectively. 145 DEGs were identified simultaneously in f5-i/j vs f5-j/j and f5-i/j vs f5-i/i. Enrichment analysis indicated that stress and cell control related processes were enriched. The expression of ascorbate peroxidase (APX) and most of the heat shock proteins (HSPs) were decreased, which might result in higher sensitivity to various stresses in pollen cells. A model was proposed to summarize the underlying process for f5-caused hybrid male sterility. These results would provide significant clues to further dissecting the molecular mechanism of f5-caused inter-subspecific reproductive isolation.

Additional file 1: Figure S1. Detection of ORF5+ transgenic plants. Figure S2. Genetic linkage map of the F2 population derived from the cross between Dular and BalillaORF5+. Figure S3. Additional mapping of qSIG3.1. Figure S4 Genotype of BC3F3 individuals with high SF. Figure S5. Rice genome 6 K-microarray analysis of 18MR47–17 and 18MR47–19. Table S1. Detailed information of primers. Table S2. Detailed information of NILs for each locus. Table S3. Genotypes of 173 F2 individual plants for two flank markers of qSIG5.1. Table S4. SF and genotypes of plants in different generations.

Perennial crops have some advantages over annuals in soil erosion prevention, lower labor and water requirements, carbon sequestration, and maintenance of thriving soil ecosystems. Rhizome, a kind of root-like underground stem, is a critical component of perenniality, which allows many grass species to survive through harsh environment. Identification of rhizome-regulating genes will contribute to the development of perennial crops. There have been no reports on the cloning of such genes until now, which bring urgency for identification of genes controlling rhizomatousness. Using rhizomatous Oryza longistaminata and rhizome-free cultivated rice as male and female parents, respectively, genetic populations were developed to identify genes regulating rhizome. Both entire population genotyping and selective genotyping mapping methods were adopted to detect rhizome-regulating quantitative trait loci (QTL) in 4 years. Results showed that multiple genes regulated development of rhizomes, with over 10 loci related to rhizome growth. At last, five major-effect loci were identified including qRED1.2, qRED3.1, qRED3.3, qRED4.1, and qRED4.2. It has been found that the individual plant with well-developed rhizomes carried at least three major-effect loci and a certain number of minor-effect loci. Both major-effect and minor-effect loci worked together to control rhizome growth, while no one could work alone. These results will provide new understanding of genetic regulation on rhizome growth and reference to the subsequent gene isolation in rice. And the related research methods and results in this study will contribute to the research on rhizome of other species.

Compared with annual cultivated rice, perennial rice had great advantages of soil erosion control, labor saving, water and fertilizer management, etc. As the key organ for perenniality, rhizome can help grasses to achieve rapid expansion to occupy more environmental resources, and withstand the harsh environmental conditions. Oryza longistaminata, a perennial wild relative of rice with vigorous rhizomes, is an ideal donor for transferring perenniality to Asian cultivated rice (Oryza sativa). However, some hybrid F1 between O. longistaminata and cultivated rice didn’t have rhizomes. Obtaining rhizomatous hybrid progeny becomes a prerequisite for the rhizomes study. In this work, four varieties of O. sativa and three accessions of O. longistaminata were used to carry out an incomplete diallel cross experiment. It was found that most F1 hybrids had rhizomes with varying length and numbers. Data analysis showed that the general combining ability (GCA) of the female parents had significant effect on rhizome-related trait of the F1s. Nevertheless, the GCA of the male parents and special combining ability of the hybrid combination played minor effect. And we speculated that the appropriate choice for female parents is more crucial to obtain rhizomatous hybrid. As the first incomplete diallel cross between O. longistaminata and O. sativa, this work would be benefit to appropriate parent selection for genetic research and breeding of perennial rice.

Background Asian cultivated rice (Oryza sativa L.) comprises two subspecies, O. sativa subsp. indica and subsp. japonica, and the hybrids between them display strong heterosis. However, hybrid sterility (HS) limits practical use of the heterosis between these two subspecies. S5 is a major-effect locus controlling the HS of female gametes in rice, consisting of three closely-linked genes ORF3, ORF4 and ORF5 that act as a killer-protector system. The HS effects of S5 are inconsistent for different genetic backgrounds, indicating the existence of interacting genes within the genome. Results In the present study, the S5-interacting genes (SIG) and their effects on HS were analyzed by studying the hybrid progeny between an indica rice, Dular (DL) and a japonica rice, BalillaORF5+ (BLORF5+), with a transgenic ORF5+ allele. Four interacting quantitative trait loci (QTL): qSIG3.1, qSIG3.2, qSIG6.1, and qSIG12.1, were genetically mapped. To analyze the effect of each interacting locus, four near-isogenic lines (NILs) were developed. The effect of each specific locus was investigated while the other three loci were kept DL homozygous (DL/DL). Of the four loci, qSIG3.1 was the SIG with the greatest effects in which the DL allele was completely dominant. Furthermore, the DL allele displayed incomplete dominance at qSIG3.2, qSIG6.1, and qSIG12.1. qSIG3.1 will be the first choice for further fine-mapping. Conclusions Four S5-interacting QTL were identified by genetic mapping and the effect of each locus was analyzed using advanced backcrossed NILs. The present study will facilitate elucidation of the molecular mechanism of rice HS caused by S5. Additionally, it would provide the basis to explore the origin and differentiation of cultivated rice, having practical significance for inter-subspecific hybrid rice breeding programs.

A review on photoperiod and temperature-sensitive genic male sterility in rice. Male sterility in plants, facilitating the development of hybrid crops, has made great contribution to crop productivity worldwide. Environment-sensitive genic male sterility (EGMS), including photoperiod-sensitive genic male sterility (PGMS) and temperature-sensitive genic male sterility (TGMS), has provided a special class of germplasms for the breeding of “two-line” hybrids in several crops. In rice, the finding of the PGMS NK58S mutant in 1973 started the journey of research and breeding of two-line hybrids. Genetic and molecular characterization of these germplasms demonstrated diverse genes and molecular mechanisms of male sterility regulation. Two loci identified from NK58S, PMS1 and PMS3, both encode long noncoding RNAs. A major TGMS locus, TMS5, found in the TGMS line Annong S-1, encodes an RNase Z. A reverse PGMS mutant carbon starved anther encodes an R2R3 MYB transcription factor. Breeding efforts in the last three decades have resulted in hundreds of EGMS lines and two-line hybrids released to rice production, which have greatly elevated the yield potential and grain quality of rice varieties. The enhanced molecular understanding will offer new strategies for the development of EGMS lines thus further improving two-line hybrid breeding of rice as well as other crops.

Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.

Hybrid rice has been cultivated worldwide since Yuan LongPing initially proposed the idea of developing and applying hybrid rice in rice production 50 years ago. Hybrid rice has provided a strong guarantee for the food security in China. The application of hybrid rice was firstly based on cytoplasmic male sterility using a 3-line system, including the sterile line, the maintainer line, and the restorer line. Later, the discovery of some environment-sensitive genic male sterile lines whose fertility changed in different environments, indicated their strong application potential in hybrid rice production. Shi MingSong accidentally found a natural male sterile mutant Nongken 58S in the field when planting normal japonica variety Nongken 58. The pollen of Nongken 58S was sterile under long-day conditions, while was fertile under short-day conditions. Based on this special property, Nongken 58S could be developed as a photoperiod-sensitive genic male sterile line for hybrid rice: it would be a sterile line at longdays, meanwhile served as a maintainer line at shortdays. Since then, the theory of 2-line system has been improving. Furthermore, the discovery of some other thermosensitive genic male sterile lines such as 5460S, Annong S-1 and Hengnong S-1 enriched this system. They were sterile under high temperatures, but converted to fertility under low temperatures. The 2-line hybrid rice based on the photoperiod thermo-sensitive genic male sterile lines has played important roles in the hybrid rice production. From 1996 to 2013, the proportion of 2-line hybrid rice increased from 0.92% to 33.59%. Some early genetic analysis indicated that the fertility of most photoperiod thermo-sensitive genic male sterile lines was controlled by a recessive allele. And the genetic linkage map of these loci has been established. But only until recent years, with the completion of rice genome and the development of new sequencing technologies and rice transgenic techniques, several genes controlling photoperiod- sensitive genic male sterility or thermo-sensitive genic male sterility in rice have been cloned. Among them, pms3 was the first reported, the mutation of which caused Nongken 58S. pms3 encodes a long non-coding RNA LDMAR. A SNP of LDMAR altered its RNA secondary structure, resulting in increased siRNA-directed DNA methylation in the promoter, which reduced the expression of LDMAR in Nongken 58S under long-day conditions. Another group found that the SNP was located in a siRNA (termed as osa-smR5864m); loss-of-function of this siRNA may fail to suppress the expression of its target genes. Shortly after, tms5 , a thermosensitive genic male sterility gene in Annong S-1 was charactered to encode RNase ZS1 processing Ub L40 mRNAs. Overaccumulation of Ub L40 mRNAs resuting from a premature stop codon of RNase ZS1 gene created by a SNP in the tms5 mutant caused the male sterility under high temperatures. Elucidation of the molecular mechanism of these genes have important implications for breeding new types of excellent and stable two-line male sterile lines in the future.

Functional genomics research is the core field in plant scientific research. As a staple food crop and a reference of monocot plant, tremendous progress has been made in rice functional genomics in China. Various methods and technical platforms have been developed to enable high-throughput analyses and effective determination of gene functions, including: large T-DNA insertion mutant libraries; global gene expression profiles for the entire life cycle of rice growth and development, abiotic and/or biotic conditions; full-length cDNA clones; high-throughput genotyping by whole-genome resequencing; large-scale analyses of metabolome and reliable high- throughput phenotyping platforms, etc. With those enabling tools and genetic resources, large efforts have been focused on identifying genes controlling yield, fertility, superior quality, resistances to biotic and abiotic stresses, and high nutrient-use efficiency. The combination of approaches based on the advances in genomic research has been formulated to develop rice cultivars referred to as Green Super Rice (GSR). We briefly summarize these advances and call for the prospects in future proposed by Chinese scientists: the RICE2020 Project and the RICE 4D Genome Program.

Pms1, a locus for photoperiod sensitive genic male sterility in rice, was identified and mapped to chromosome 7 in previous studies. Here we report an effort to identify the candidate genes for Pms1 by comparative sequencing of BAC clones from two cultivars Minghui 63 and Nongken 58, the parents for the initial mapping population. Annotation and comparison of the sequences of the two clones resulted in a total of five potential candidates which should be functionally tested. We also conducted comparative analysis of sequences of these two cultivars with two other cultivars, Nipponbare and 93-11, for which sequence data were available in public databases. The analysis revealed large differences in sequence composition among the four genotypes in the Pms1 region primarily due to retroelement activity leading to rapid recent growth and divergence of the genomes. High levels of polymorphism in the forms of indels and SNPs were found both in intra-and inter-subspecific comparisons. Dating analysis using LTRs of the retroelements in this region showed that the substitution rate of LTRs was much higher than reported in the literature. The results provided strong evidence for rapid genomic evolution of this region as a consequence of natural and artificial selection.