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A major challenge in modern rice production is to achieve the dual goals of high yield and good quality with low environmental costs. This study was designed to determine whether optimized nitrogen (N) fertilization could fulfill these multiple goals. In two-year experiments, two high yielding ‘super’ rice cultivars were grown with different N fertilization management regimes, including zero N input, local farmers’ practice (LFP) with heavy N inputs, and optimized N fertilization (ONF). In ONF, by reducing N input, increasing planting density, and optimizing the ratio of urea application at different stages, N use efficiency and the physicochemical and textural properties of milled rice were improved at higher yield levels. Compared with LFP, yield and partial factor productivity of applied N (PFP) under ONF were increased (on average) by 1.70 and 13.06%, respectively. ONF increased starch and amylose content, and significantly decreased protein content. The contents of the short chains of A chain (degree of polymerization (DP) 6–12) and B1 chain (DP 13–25) of amylopectin were significantly increased under ONF, which resulted in a decrease in the stability of rice starch crystals. ONF increased viscosity values and improved the thermodynamic properties of starch, which resulted in better eating and cooking quality of the rice. Thus, ONF could substantially compensate the negative effects caused by N fertilizer and achieve the multiple goals of higher grain quality and nitrogen use efficiency (NUE) at high yield levels. These results will be useful for applications of high quality rice production at high yield levels.

Abstract To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core accessions collected from 25 countries were evaluated for 13 traits associated with salt tolerance (ST) at the germination and seedling stages. The rice panel showed tremendous variation for all measured ST traits and eight accessions showing high levels of ST at either and/or both the germination and seedling stages. Using 395,553 SNP markers covering ~372 Mb of the rice genome and multi-locus mixed linear models, 20 QTN associated with 11 ST traits were identified by GWAS, including 6 QTN affecting ST at the germination stage and 14 QTN for ST at the seedling stage. The integration of bioinformatic with haplotype analyses for the ST QTN lets us identify 22 candidate genes for nine important ST QTN (qGR3, qSNK1, qSNK12, qSNC1, qSNC6, qRNK2, qSDW9a, qSST5 and qSST9). These candidate genes included three known ST genes (SKC1, OsTZF1 and OsEATB) for QTN qSNK1 qSST5 and qSST9. Candidate genes showed significant phenotypic differences in ST traits were detected between or among 2–4 major haplotypes. Thus, our results provided useful materials and genetic information for improving rice ST in future breeding and for molecular dissection of ST in rice.

Grain minerals in rice, especially those in milled grains, are important sources of micro-nutrition elements, such as iron (Fe), zinc (Zn), manganese (Mn), copper (Cu), and selenium (Se), and of toxic heavy metal elements, especially cadmium (Cd), for populations consuming a rice diet. To date, the genetic mechanism underlying grain mineral concentrations (GMCs) in milled grain remains largely unknown. In this report, we adopted a set of 698 germplasms consisting of two subsets [indica/Xian (X-set) and japonica/Geng (G-set)], to detect quantitative trait loci (QTL) affecting GMC traits of Fe, Zn, Cd, Mn, Cu, and Se in milled grains. A total of 47 QTL regions, including 18 loci and 29 clusters (covering 62 Cd loci), responsible for the GMCs in milled grains were detected throughout the genome. A joint exploration of favorable haplotypes of candidate genes was carried out as follows: (1) By comparative mapping, 10 chromosome regions were found to be consistent with our previously detected QTL from linkage mapping. (2) Within eight of these regions on chromosomes 1, 4, 6, 7, and 8, candidate genes were identified in the genome annotation database. (3) A total of 192 candidate genes were then submitted to further haplotype analysis using million-scale single nucleotide polymorphisms (SNPs) from the X-set and the G-set. (4) Finally, 37 genes (19.3%) were found to be significant in the association between the QTL targeting traits and the haplotype variations by pair-wise comparison. (5) The phenotypic values for the haplotypes of each candidate were plotted. Three zinc finger (like) genes within two candidate QTL regions (qFe6-2 and qZn7), and three major GMC traits (Fe, Zn, and Cd) were picked as sample cases, in addition to non-exhausted cross validations, to elucidate this kind of association by trait value plotting. Taken together, our results, especially the 37 genes with favorable haplotype variations, will be useful for rice biofortification molecular breeding.

In a breeding effort to develop salt tolerant (ST) rice varieties by designed QTL pyramiding, large numbers of progenies derived from four crosses between salt- or drought- tolerant BC2F5 IR64 introgression lines, were subjected to severe salt stress, resulting in 422 ST plants. The progeny testing of the selected F3 lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of ST. Genetic characterization of the 422 ST F3 progeny and 318 random F2 plants from the same four crosses using 105 segregating SSR markers lead to three interesting discoveries: (1) salt stress can induce genome-wide epigenetic segregation (ES) characterized by complete loss of heterozygosity (LOH) and nearly complete loss of an allele (LOA) in the F3 progenies of four rice populations in a single generation; (2) ∼25% of the stress-induced ES loci were transgenerational and inherited from their salt- and drought- selected parents; and (3) the salt-induced LOH and LOA loci (regions) appeared to contain genes/alleles associated with ST and/or drought tolerance. 32 genomic regions that showed one or more types of salt-induced ES in the random and salt-selected progenies from these crosses. The same or different types of ES were detected with two large genomic regions on chromosomes 1 and 6 where more and the strongest ES were found across different populations. 14 genomic regions were found where the salt-induced ES regions were overlapping with QTL affecting ST related traits. The discovery of the three types of salt-induced ES showed several interesting characteristics and had important implications in evolution and future breeding for developing stress-resilient rice and crops.

To develop superior rice varieties with improved yield in most rainfed areas of Asia/Africa, we started an introgression-breeding program for simultaneously improving yield and tolerances of multiple abiotic stresses. Using eight BC1 populations derived from a widely adaptable recipient and eight donors plus three rounds of phenotypic selection, we developed 496 introgression lines (ILs) with significantly higher yield under drought, salt and/or non-stress conditions in 5 years. Six new varieties were released in the Philippines and Pakistan and many more are being evaluated in multi-location yield trials for releasing in several countries. Marker-facilitated genetic characterization revealed three interesting aspects of the breeding procedure: (1) the donor introgression pattern in specific BC populations was characteristic; (2) introgression frequency in different genomic regions varied considerably, resulting primarily from strong selection for the target traits; and (3) significantly lower heterozygosity was observed in BC progenies selected for drought and salinity tolerance. Applying strong phenotypic selection under abiotic stresses in early segregating generations has major advantages for not only improving multiple abiotic stress tolerance but also achieving quicker homozygosity in early generations. This breeding procedure can be easily adopted by small breeding programs in developing countries to develop high-yielding varieties tolerant of abiotic stresses. The large set of trait-specific ILs can be used for genetic mapping of genes/QTL that affect target and non-target traits and for efficient varietal development by designed QTL pyramiding and genomics-based recurrent selection in our Green Super Rice breeding technology.

Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating rice diseases worldwide. The development and use of disease-resistant cultivars have been the most effective strategy to control bacterial blight. Identifying the genes mediating bacterial blight resistance is a prerequisite for breeding cultivars with broad-spectrum and durable resistance. We herein describe a genome-wide association study involving 172 diverse Oryza sativa ssp. indica accessions to identify loci influencing the resistance to representative strains of six Xoo races. Twelve resistance loci containing 121 significantly associated signals were identified using 317,894 single nucleotide polymorphisms, which explained 13.3-59.9% of the variability in lesion length caused by Xoo races P1, P6, and P9a. Two hotspot regions (L11 and L12) were located within or nearby two cloned R genes (xa25 and Xa26) and one fine-mapped R gene (Xa4). Our results confirmed the relatively high resolution of genome-wide association studies. Moreover, we detected novel significant associations on chromosomes 2, 3, and 6-10. Haplotype analyses of xa25, the Xa26 paralog (MRKc; LOC_Os11g47290), and a Xa4 candidate gene (LOC_11g46870) revealed differences in bacterial blight resistance among indica subgroups. These differences were responsible for the observed variations in lesion lengths resulting from infections by Xoo races P1 and P9a. Our findings may be relevant for future studies involving bacterial blight resistance gene cloning, and provide insights into the genetic basis for bacterial blight resistance in indica rice, which may be useful for knowledge-based crop improvement.

Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the whole-plant growth duration salt tolerance (ST) was genetically dissected by phenotyping two sets of BC2F5 introgression lines (ILs) for four yield traits under severe natural salt stress and non-stress filed conditions using SSR markers and the methods of advanced backcross QTL (AB-QTL) analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and non-stress conditions were identified, most (>90%) of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan (HHZ) ILs with favorable donor alleles at multiple QTLs and significantly improved yield traits under salt stress and non-stress conditions were identified, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection (MAS) or genome selection.

How to overcome yield stagnation is a big challenge to rice breeders. An effective method for quickly developing new cultivars is to further improve an outstanding cultivar. In this study, three advanced backcross populations under yield selection that consist of 123 BC2F2:4 introgression lines (ILs) were developed by crossing Minghui 86 (recurrent parent, RP) with three high-yielding varieties (donors), namely, ZDZ057, Fuhui 838, and Teqing, respectively. The progeny testing allowed the identification of 12 promising ILs that had significantly higher mean grain yields than Minghui 86 in two environments. A total of 55 QTLs that affect grain yield and its related traits were identified, which included 50 QTLs that were detected using the likelihood ratio test based on stepwise regression (RSTEP-LRT) method, and eight grain yield per plant (GY) QTLs were detected using chi-squared (c2) test. Among these QTLs, five QTLs were simultaneously detected in different populations and 22 QTLs were detected in both environments. The beneficial donor alleles for increased GY and its related traits were identified in 63.6% (35 out of 55) of the QTLs. These promising ILs and QTLs identified will provide the elite breeding materials and genetic information for further improvement of the grain yield for Minghui 86 through pyramiding breeding.

A set of 240 introgression lines derived from the advanced backcross population of a cross between a japonica cultivar, Xiushui 09, and an indica breeding line, IR2061, was developed to dissect QTLs affecting cold tolerance (CT) at seedling stage and heat tolerance (HT) at anthesis. Survival rate of seedlings (SRS) and spikelet fertility (SF), the index traits of CT and HT, showed significant differences between the two parents under stresses. A total of four QTLs (qSRS1, qSRS7, qSRS11a and qSRS11b) for CT were identified on chromosomes 1, 7, 11, and the Xiushui 09 alleles increased SRS at all loci except qSRS7. Four QTLs for SF were identified on chromosomes 4, 5, 6, and 11. These QTLs could be classified into two major types based on their behaviors under normal and stress conditions. The first was QTL expressed only under normal condition; and the second QTL was apparently stress induced and only expressed under stress. Among them, two QTLs (qSF4 and qSF6) which reduced the trait difference between heat stress and normal conditions must have contributed to HT because of their obvious contribution to trait stability, and the IR2061 allele at the qSF6 and the Xiushui 09 allele at the qSF4 improved HT, respectively. No similar QTL was found between CT at seedling stage and HT at anthesis. Therefore, it is possible to breed a new variety with CT and HT by pyramiding the favorable CT- and HT-improved alleles at above loci from Xiushui 09 and IR2061, respectively, through marker-assisted selection (MAS).

Source leaf/sink capacity (SS) traits are important determinants of grain yield (GY) of rice. To understand the genetic basis of the SS relationship in rice, five SS and GY traits of rice were genetically dissected using two reciprocal introgression populations. Seventy-three QTL affecting the SS and GY traits were identified, most of which were detected in one of the parental genetic backgrounds (GBs). Two major QTL at bins 4.7 (SS1) and 3.12 (SS2) were associated consistently with all measured SS and yield traits in both GBs across two contrasting environments. Strong interactions between SS1/SS2 and the detected QTL led us to the discovery of genetic networks affecting the SS and GY traits. The SS1 acted as a regulator controlling two groups of downstream QTL affecting the source leaf width and grain number per panicle (GNP). SS2 functioned as a regulator positively regulating different groups of downstream QTL affecting the source leaf length, GNP, grain weight, and GY. Map-based cloning of SS1 indicates that SS1 is NAL1 involved in polar auxin/IAA transport. Different alleles at NAL1 were apparently able to qualitatively and/or quantitatively control the IAA transport from the apical meristem to different plant tissues and thus regulate those downstream loci/pathways controlling different SS traits of rice. There was a functional allele and a non-functional mutation in the parents at each of the QTL downstream of SS1 or SS2, which were detectable only in the presence of the functional allele of SS1 or SS2. Our results provided direct evidence that SS and yield traits in rice are controlled by complex signaling pathways and suggest further improvement of rice yield potential with enhanced and balanced SS relationships can be achieved by accurately manipulating allelic combinations at loci in the SS1 and SS2 mediated pathways.

In the modern world, the grain mineral concentration (GMC) in rice (Oryza sativa L.) not only includes important micronutrient elements such as iron (Fe) and zinc (Zn), but it also includes toxic heavy metal elements, especially cadmium (Cd) and lead (Pb). To date, the genetic mechanisms underlying the regulation of GMC, especially the genetic background and G × E effects of GMC, remain largely unknown. In this study, we adopted two sets of backcross introgression lines (BILs) derived from IR75862 (a Zn-dense rice variety) as the donor parent and two elite indica varieties, Ce258 and Zhongguangxiang1, as recurrent parents to detect QTL affecting GMC traits including Fe, Zn, Cd and Pb concentrations in two environments. We detected a total of 22 loci responsible for GMC traits, which are distributed on all 12 rice chromosomes except 5, 9 and 10. Six genetic overlap (GO) regions affecting multiple elements were found, in which most donor alleles had synergistic effects on GMC. Some toxic heavy metal-independent loci (such as qFe1, qFe2 and qZn12) and some regions that have opposite genetic effects on micronutrient (Fe and Zn) and heavy metal element (Pb) concentrations (such as GO-IV) may be useful for marker-assisted biofortification breeding in rice. We discuss three important points affecting biofortification breeding efforts in rice, including correlations between different GMC traits, the genetic background effect and the G × E effect.

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many 'downstream' loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and "co-adapted" gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.

Abstract Non-Hermitian physics has emerged as a new paradigm that profoundly changes our understanding of non-equilibrium systems, introducing novel concepts such as exceptional points, spectral topology, and non-Hermitian skin effects (NHSEs). Most existing studies focus on non-Hermitian eigenstates, whereas dynamic properties have been discussed only recently, and the dynamic NHSEs are not yet confirmed in experiments. Here, we report the experimental observation of non-Hermitian skin dynamics using tunable one-dimensional nonreciprocal double-chain mechanical systems with glide-time symmetry. Remarkably, dynamic NHSEs are observed with various behaviors in different dynamic phases, which can be understood via the generalized Brillouin zone and the related concepts. Moreover, the observed dynamic NHSEs, amplifications, bulk unidirectional wave propagation, and boundary wave trapping provide promising ways to manipulate waves in a controllable and robust way. Our findings open a new pathway toward non-Hermitian dynamics, which will fertilize the study of non-equilibrium phases of matter.

Abstract Entanglement entropy is a fundamental concept with rising importance in various fields ranging from quantum information science, black holes to materials science. In complex materials and systems, entanglement entropy provides insight into the collective degrees of freedom that underlie the systems’ complex behaviours. As well-known predictions, the entanglement entropy exhibits area laws for systems with gapped excitations, whereas it follows the Gioev-Klich-Widom scaling law in gapless fermion systems. However, many of these fundamental predictions have not yet been confirmed in experiments due to the difficulties in measuring entanglement entropy in physical systems. Here, we report the experimental verification of the above predictions by probing the nonlocal correlations in phononic systems. We obtain the entanglement entropy and entanglement spectrum for phononic systems with the fermion filling analog. With these measurements, we verify the Gioev-Klich-Widom scaling law. We further observe the salient signatures of topological phases in entanglement entropy and entanglement spectrum.

Abstract Branched flows occur ubiquitously in various wave systems, when the propagating waves encounter weak correlated scattering potentials. Here we report the experimental realization of electrical tuning of the branched flow of light using a nematic liquid crystal (NLC) system. We create the physical realization of the weakly correlated disordered potentials of light via the inhomogeneous orientations of the NLC. We demonstrate that the branched flow of light can be switched on and off as well as tuned continuously through the electro-optical properties of NLC film. We further show that the branched flow can be manipulated by the polarization of the incident light due to the optical anisotropy of the NLC film. The nature of the branched flow of light is revealed via the unconventional intensity statistics and the rapid fidelity decay along the light propagation. Our study unveils an excellent platform for the tuning of the branched flow of light which creates a testbed for fundamental physics and offers a new way for steering light.

Abstract Topologically protected photonic edge states offer unprecedented robust propagation of photons that are promising for waveguiding, lasing, and quantum information processing. Here, we report on the discovery of a class of hybrid topological photonic crystals that host simultaneously quantum anomalous Hall and valley Hall phases in different photonic band gaps. The underlying hybrid topology manifests itself in the edge channels as the coexistence of the dual-band chiral edge states and unbalanced valley Hall edge states. We experimentally realize the hybrid topological photonic crystal, unveil its unique topological transitions, and verify its unconventional dual-band gap topological edge states using pump-probe techniques. Furthermore, we demonstrate that the dual-band photonic topological edge channels can serve as frequency-multiplexing devices that function as both beam splitters and combiners. Our study unveils hybrid topological insulators as an exotic topological state of photons as well as a promising route toward future applications in topological photonics.

Abstract Using 3D sonic crystals as acoustic higher‐order topological insulators (HOTIs), 2D surface states described by spin‐1 Dirac equations at the interfaces between the two sonic crystals with distinct topology but the same crystalline symmetry are discovered. It is found that the Dirac mass can be tuned by the geometry of the two sonic crystals. The sign reversal of the Dirac mass reveals a surface topological transition where the surface states exhibit zero refractive index behavior. When the surface states are gapped, 1D hinge states emerge due to the topology of the gapped surface states. The zero refractive index behavior and the emergent topological hinge states are confirmed experimentally. This study reveals a multidimensional Wannier orbital control that leads to extraordinary properties of surface states and unveils an interesting topological mechanism for the control of surface waves.

Higher-order topological phenomenologies are usually observed separately, with each system giving rise to a specific type of topological insulator. Here, the authors realise a nonsymmorphic acoustic metacrystal where the first and the second band gap host dipole and quadrupole topology respectively.

To understand the physiological and molecular mechanisms underlying seedling salt tolerance in rice (Oryza sativa L.), the phenotypic, metabolic, and transcriptome responses of two related rice genotypes, IR64 and PL177, with contrasting salt tolerance were characterized under salt stress and salt+abscisic acid (ABA) conditions. PL177 showed significantly less salt damage, lower Na+/K+ ratios in shoots, and Na+ translocation from roots to shoots, attributed largely to better salt exclusion from its roots and salt compartmentation of its shoots. Exogenous ABA was able to enhance the salt tolerance of IR64 by selectively decreasing accumulation of Na+ in its roots and increasing K+ in its shoots. Salt stress induced general and organ-specific increases of many primary metabolites in both rice genotypes, with strong accumulation of several sugars plus proline in shoots and allantoin in roots. This was due primarily to ABA-mediated repression of genes for degradation of these metabolites under salt. In PL177, salt specifically up-regulated genes involved in several pathways underlying salt tolerance, including ABA-mediated cellular lipid and fatty acid metabolic processes and cytoplasmic transport, sequestration by vacuoles, detoxification and cell-wall remodeling in shoots, and oxidation-reduction reactions in roots. Combined genetic and transcriptomic evidence shortlisted relatively few candidate genes for improved salt tolerance in PL177. [ABSTRACT FROM AUTHOR]

Background Cold stress is an important factor limiting rice yield in many areas of high latitude and altitude. Considerable efforts have been taken to genetically dissect cold tolerance (CT) in rice using DNA markers. Because of possible epistasis and gene × environment interactions associated with identified quantitative trait loci, the results of these genetic studies have unfortunately not been directly applicable to marker-assisted selection for improved rice CT. In this study, we demonstrated the utility of a selective introgression strategy for simultaneous improvement and genetic dissection of rice seedling CT. Results A set of japonica introgression lines (ILs) with significantly improved seedling CT were developed from four backcross populations based on two rounds of selection. Genetic characterization of these cold-tolerant ILs revealed two important aspects of genome-wide responses to strong phenotypic selection for rice CT: (1) significant over-introgression of donor alleles at 57 loci in 29 functional genetic units (FGUs) across the rice genome and (2) pronounced non-random associations between or among alleles at many unlinked CT loci. Linkage disequilibrium analyses of the detected CT loci allowed us to construct putative genetic networks (multi-locus structures) underlying the seedling CT of rice. Each network consisted of a single FGU, with high introgression as the putative regulator plus two to three groups of highly associated downstream FGUs. A bioinformatics search of rice genomic regions harboring these putative regulators identified a small set of candidate regulatory genes that are known to be involved in plant stress response. Conclusions Our results suggest that CT in rice is controlled by multiple pathways. Genetic complementarity between parental-derived functional alleles at many loci within a given pathway provides an appropriate explanation for the commonly observed hidden diversity and transgressive segregation of CT and other complex traits in rice. [ABSTRACT FROM AUTHOR]

Abstract Photonic topological states have revolutionized the understanding of the propagation and scattering of light. The recent discovery of higher‐order photonic topological insulators opens an emergent horizon for 0D topological corner states. However, the previous realizations of higher‐order topological insulators in electromagnetic‐wave systems suffer from either a limited operational frequency range due to the lumped components involved or a bulky structure with a large footprint, which are unfavorable for achieving compact photonic devices. To overcome these limitations, a planar surface‐wave photonic crystal realization of 2D higher‐order topological insulators is hereby demonstrated experimentally. The surface‐wave photonic crystals exhibit a very large bulk bandgap (a bandwidth of 28%) due to multiple Bragg scatterings and host 1D gapped edge states described by massive Dirac equations. The topology of those higher‐dimensional photonic bands leads to the emergence of in‐gap 0D corner states, which provide a route toward robust cavity modes for scalable compact photonic devices.

An indica pyramiding line, DK151, and its recurrent parent, IR64, were evaluated under drought stress and non-stress conditions for three consecutive seasons. DK151 showed significantly improved tolerance to drought. The DNA methylation changes in DK151 and IR64 under drought stress and subsequent recovery were assessed using methylation-sensitive amplified polymorphism analysis. Our results indicate that drought-induced genome-wide DNA methylation changes accounted for ∼12.1% of the total site-specific methylation differences in the rice genome. This drought-induced DNA methylation pattern showed three interesting properties. The most important one was its genotypic specificity reflected by large differences in the detected DNA methylation/demethylation sites between DK151 and IR64, which result from introgressed genomic fragments in DK151. Second, most drought-induced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of the sites at which drought-induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought-induced DNA demethylation/methylation changes remain even after recovery. Third, the drought-induced DNA methylation alteration showed a significant level of developmental and tissue specificity. Together, these properties are expected to have contributed greatly to rice response and adaptation to drought stress. Thus, induced epigenetic changes in rice genome can be considered as a very important regulatory mechanism for rice plants to adapt to drought and possibly other environmental stresses. [ABSTRACT FROM PUBLISHER]

Background: Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown. Results: A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. Conclusions: In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes. [ABSTRACT FROM AUTHOR]

Rice bacterial leaf blight (BB) caused by Xanthomonas oryzae pv. oryzae and bacterial leaf streak (BLS) caused by X. oryzae pv. oryzicola ( Xoc) are two important diseases of rice that often outbreak simultaneously and constrain rice production in much of Asia and parts of Africa. Developing resistant cultivars has been the most effective approach to control BB, however, most single resistance genes have limited value in breeding programs because of their narrow-spectrum of resistance to the races of the pathogen. By contrast, there is little progress in breeding varieties resistant to Xoc since BLS resistance in rice was a quantitative trait and so far only a few quantitative resistance loci have been identified. We reported here the development of a high yield elite line, Lu-You-Zhan highly resistant to both BB and BLS by pyramiding Xa23 with a wide-spectrum resistance to BB derived from wild rice and a non-host maize resistance gene, Rxo1, using both marker assisted selection (MAS) and genetic engineering. Our study has provided strong evidence that non-host R genes could be a valuable source of resistance in combating those plant diseases where no single R gene controlling high level of resistance exists and demonstrated that MAS combined with transgenic technologies are an effective strategy to achieve high level of resistance against multiple plant diseases. [ABSTRACT FROM AUTHOR]

Genetic load in the genome of the model species, rice, was genetically dissected by mapping quantitative trait loci (QTLs) affecting the radiosensitivity of 226 recombinant inbred lines (RILs) to γ-ray- and spaceflight-induced radiation. The parents and RILs varied considerably in their radiosensitivity to γ-ray irradiation. A total of 28 QTLs affecting the two index traits, seedling height (SH) and seed fertility (SF), of radiosensitivity were identified. The japonica parent, Lemont, was much more sensitive to γ-ray irradiation than the indica parent, Teqing, and its alleles at almost all QTLs were associated with increased radiosensitivity, suggesting a much higher genetic load in the japonica genome of rice. Six QTLs (QSh2a, QSh2b, QSh5a, QSh7, QSf3b, and QSf10b) were located in the genomic regions particularly sensitive to radiation and thus might represent possible ‘mutation hot spots’ in the japonica genome. Detailed characterization of these genomic regions may shed light on the evolution and subspecific differentiation of rice. [ABSTRACT FROM PUBLISHER]

Abstract Tremendous efforts have been taken worldwide to develop genome-wide genetic stocks for rice functional genomic (FG) research since the rice genome was completely sequenced. To facilitate FG research of complex polygenic phenotypes in rice, we report the development of over 20 000 introgression lines (ILs) in three elite rice genetic backgrounds for a wide range of complex traits, including resistances/tolerances to many biotic and abiotic stresses, morpho-agronomic traits, physiological traits, etc., by selective introgression. ILs within each genetic background are phenotypically similar to their recurrent parent but each carries one or a few traits introgressed from a known donor. Together, these ILs contain a significant portion of loci affecting the selected complex phenotypes at which allelic diversity exists in the primary gene pool of rice. A forward genetics strategy was proposed and demonstrated with examples on how to use these ILs for large-scale FG research. Complementary to the genome-wide insertional mutants, these ILs opens a new way for highly efficient discovery, candidate gene identification and cloning of important QTLs for specific phenotypes based on convergent evidence from QTL position, expression profiling, functional and molecular diversity analyses of candidate genes, highlights the importance of genetic networks underlying complex phenotypes in rice that may ultimately lead to more complete understanding of the genetic and molecular bases of quantitative trait variation in rice. [ABSTRACT FROM AUTHOR]

Examines the similarities of dominant and recessive plant disease resistance genes. Association between rice components and R genes properties; Dominance of Xa4 and Xa21 genes against avirulent Xoo races; Involvement of Xoo races on different pathways of the rice defensive system.

Investigates the genetic basis of inbreeding depression and heterosis in rice. Description of the mapping populations; Determination of the hybrid testcross performance; Identification of epistatic QTL pairs; Implications of results in rice evolution and improvement.