The genetic basis and process of inbreeding depression in an elite hybrid rice.

Inbreeding depression refers to the reduced performance arising from increased homozygosity, a phenomenon that is the reverse of heterosis and exists among plants and animals. As a natural self-pollinated crop with strong heterosis, the mechanism of inbreeding depression in rice is largely unknown. To understand the genetic basis of inbreeding depression, we constructed a successive inbreeding population from the F2 to F4 generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each generation. The expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle, 11 for primary branches, and 12 for secondary branches, and these loci constitute the main correlation between heterosis and inbreeding depression. However, the genetic basis of inbreeding depression is also distinct from that of heterosis, such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected depression. Noticeably, two-locus interactions may change the extent and direction of the depression effects of the target loci, and overall interactions would promote inbreeding depression among generations. Using an F2:3 variation population, the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after inbreeding. We found inconsistent or various degrees of background depression from the F2 to F3 generation assuming different genotypes of the target locus, which may affect the actual depression effect of the locus due to epistasis. The results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms, which expand our understanding of the whole-genome architecture of inbreeding depression.

Bridge synergy and simplicial interaction in complex contagions.

Modeling complex contagion in networked systems is an important topic in network science, for which various models have been proposed, including the synergistic contagion model that incorporates coherent interference and the simplicial contagion model that involves high-order interactions. Although both models have demonstrated success in investigating complex contagions, their relationship in modeling complex contagions remains unclear. In this study, we compare the synergy and the simplest form of high-order interaction in the simplicial contagion model, known as the triangular one. We analytically show that the triangular interaction and the synergy can be bridged within complex contagions through the joint degree distribution of the network. Monte Carlo simulations are then conducted to compare simplicial and corresponding synergistic contagions on synthetic and real-world networks, the results of which highlight the consistency of these two different contagion processes and thus validate our analysis. Our study sheds light on the deep relationship between the synergy and high-order interactions and enhances our physical understanding of complex contagions in networked systems.

The effects of respiratory muscle training on respiratory function and functional capacity in patients with early stroke: a meta-analysis.

BACKGROUND: Respiratory muscle training is a continuous and standardized training of respiratory muscles, but the evidence of the effects on early stroke patients is not clear. This meta-analysis aimed to investigate the effects of respiratory muscle training on respiratory function and functional capacity in patients with early stroke. METHODS: PubMed, Embase, PEDro, ScienceDirect, AMED, CINAHL, and China National Knowledge Infrastructure databases were searched from inception to December 8, 2023 for articles about studies that 1) stroke patients with age ≥ 18 years old. Early stroke < 3 months at the time of diagnosis, 2) respiratory muscle training, including inspiratory and expiratory muscle training, 3) the following measurements are the outcomes: respiratory muscle strength, respiratory muscle endurance, pulmonary function testing, dyspnea fatigue score, and functional capacity, 4) randomized controlled trials. Studies that met the inclusion criteria were extracted data and appraised the methodological quality and risk of bias using the Physiotherapy Evidence Database scale and the Cochrane Risk of Bias tool by two independent reviewers. RevMan 5.4 with a random effect model was used for data synthesis and analysis. Mean differences (MD) or standard mean differences (SMD), and 95% confidence interval were calculated (95%CI). RESULTS: Nine studies met inclusion criteria, recruiting 526 participants (mean age 61.6 years). Respiratory muscle training produced a statistically significant effect on improving maximal inspiratory pressure (MD = 10.93, 95%CI: 8.51-13.36), maximal expiratory pressure (MD = 9.01, 95%CI: 5.34-12.69), forced vital capacity (MD = 0.82, 95%CI: 0.54-1.10), peak expiratory flow (MD = 1.28, 95%CI: 0.94-1.63), forced expiratory volume in 1 s (MD = 1.36, 95%CI: 1.13-1.59), functional capacity (SMD = 0.51, 95%CI: 0.05-0.98) in patients with early stroke. Subgroup analysis showed that inspiratory muscle training combined with expiratory muscle training was beneficial to the recovery of maximal inspiratory pressure (MD = 9.78, 95%CI: 5.96-13.60), maximal expiratory pressure (MD = 11.62, 95%CI: 3.80-19.43), forced vital capacity (MD = 0.87, 95%CI: 0.47-1.27), peak expiratory flow (MD = 1.51, 95%CI: 1.22-1.80), forced expiratory volume in 1 s (MD = 0.76, 95%CI: 0.41-1.11), functional capacity (SMD = 0.61, 95%CI: 0.08-1.13), while inspiratory muscle training could improve maximal inspiratory pressure (MD = 11.60, 95%CI: 8.15-15.05), maximal expiratory pressure (MD = 7.06, 95%CI: 3.50-10.62), forced vital capacity (MD = 0.71, 95%CI: 0.21-1.21), peak expiratory flow (MD = 0.84, 95%CI: 0.37-1.31), forced expiratory volume in 1 s (MD = 0.40, 95%CI: 0.08-0.72). CONCLUSIONS: This study provides good-quality evidence that respiratory muscle training is effective in improving respiratory muscle strength, pulmonary function, and functional capacity for patients with early stroke. Inspiratory muscle training combined with expiratory muscle training seems to promote functional recovery in patients with early stroke more than inspiratory muscle training alone. TRIAL REGISTRATION: Prospero registration number: CRD42021291918.

Deletion of the sugar importer gene OsSWEET1b accelerates sugar starvation-promoted leaf senescence in rice.

Leaf senescence is a combined response of plant cells stimulated by internal and external signals. Sugars acting as signaling molecules or energy metabolites can influence the progression of leaf senescence. Both sugar starvation and accumulation can promote leaf senescence with diverse mechanisms that are reported in different species. Sugars Will Eventually be Exported Transporters (SWEETs) are proposed to play essential roles in sugar transport, but whether they have roles in senescence and the corresponding mechanism are unclear. Here, we functionally characterized a sugar transporter, OsSWEET1b, which transports sugar and promotes senescence in rice (Oryza sativa L.). OsSWEET1b could import glucose and galactose when heterologously expressed in Xenopus oocytes and translocate glucose and galactose from the extracellular apoplast into intracellular cytosol in rice. Loss of function of OsSWEET1b decreased glucose and galactose accumulation in leaves. ossweet1b mutants showed accelerated leaf senescence under natural and dark-induced conditions. Exogenous application of glucose and galactose complemented the defect of OsSWEET1b deletion-promoted senescence. Moreover, the senescence-activated transcription factor OsWRKY53, acting as a transcriptional repressor, genetically functions upstream of OsSWEET1b to suppress its expression. OsWRKY53-overexpressing plants had attenuated sugar accumulation, exhibiting a similar phenotype as the ossweet1b mutants. Our findings demonstrate that OsWRKY53 downregulates OsSWEET1b to impair its influx transport activity, leading to compromised sugar accumulation in the cytosol of rice leaves where sugar starvation promotes leaf senescence.

Spontaneous movement of a retrotransposon generated genic dominant male sterility providing a useful tool for rice breeding.

Male sterility in plants provides valuable breeding tools in germplasm innovation and hybrid crop production. However, genetic resources for dominant genic male sterility, which hold great promise to facilitate breeding processes, are extremely rare in natural germplasm. Here we characterized the Sanming Dominant Genic Male Sterility in rice and identified the gene SDGMS using a map-based cloning approach. We found that spontaneous movement of a 1978-bp long terminal repeat (LTR) retrotransposon into the promoter region of the SDGMS gene activates its expression in anther tapetum, which causes abnormal programmed cell death of tapetal cells resulting in dominant male sterility. SDGMS encodes a ribosome inactivating protein showing N-glycosidase activity. The activation of SDGMS triggers transcription reprogramming of genes responsive to biotic stress leading to a hypersensitive response which causes sterility. The results demonstrate that an ectopic gene activation by transposon movement can give birth to a novel trait which enriches phenotypic diversity with practical utility.

Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice.

One-step and two-step pathways are proposed to synthesize cytokinin in plants. The one-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for the two-step pathway remains to be identified. Here, we show that quantitative trait locus GY3 may boost grain yield by more than 20% through manipulating a two-step pathway. Locus GY3 encodes a LOG protein that acts as a 5'-ribonucleotide phosphohydrolase by excessively consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP to produce iPR. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds, which demonstrates the great value of GY302428 in indica rice production.

Investigation on the influence of heterogeneous synergy in contagion processes on complex networks.

Synergistic contagion in a networked system occurs in various forms in nature and human society. While the influence of network's structural heterogeneity on synergistic contagion has been well studied, the impact of individual-based heterogeneity on synergistic contagion remains unclear. In this work, we introduce individual-based heterogeneity with a power-law form into the synergistic susceptible-infected-susceptible model by assuming the synergistic strength as a function of individuals' degree and investigate this synergistic contagion process on complex networks. By employing the heterogeneous mean-field (HMF) approximation, we analytically show that the heterogeneous synergy significantly changes the critical threshold of synergistic strength σc that is required for the occurrence of discontinuous phase transitions of contagion processes. Comparing to the synergy without individual-based heterogeneity, the value of σc decreases with degree-enhanced synergy and increases with degree-suppressed synergy, which agrees well with Monte Carlo prediction. Next, we compare our heterogeneous synergistic contagion model with the simplicial contagion model [Iacopini et al., Nat. Commun. 10, 2485 (2019)], in which high-order interactions are introduced to describe complex contagion. Similarity of these two models are shown both analytically and numerically, confirming the ability of our model to statistically describe the simplest high-order interaction within HMF approximation.

Inferring synchronizability of networked heterogeneous oscillators with machine learning.

In the study of network synchronization, an outstanding question of both theoretical and practical significance is how to allocate a given set of heterogeneous oscillators on a complex network in order to improve the synchronization performance. Whereas methods have been proposed to address this question in the literature, the methods are all based on accurate models describing the system dynamics, which, however, are normally unavailable in realistic situations. Here, we show that this question can be addressed by the model-free technique of a feed-forward neural network (FNN) in machine learning. Specifically, we measure the synchronization performance of a number of allocation schemes and use the measured data to train a machine. It is found that the trained machine is able to not only infer the synchronization performance of any new allocation scheme, but also find from a huge amount of candidates the optimal allocation scheme for synchronization.

A minimal genome design to maximally guarantee fertile inter-subspecific hybrid rice.

Hybrid rice has made considerable contributions to achieve the ambitious goal of food security for the world's population. Hybrid rice from indica/xian and japonica/geng subspecies shows much higher heterosis and is thereby an important innovation in promoting rice production in the next decade. However, such inter-subspecific hybrid rice has long suffered from serious hybrid sterility, which is a major challenge that needs to be addressed. In this study, we performed a genome design strategy to produce fertile inter-subspecific hybrid by creation of wide compatibility varieties that are able to overcome hybrid sterility. Based on combined genetic analyses in two indica-japonica crosses, we determined that four hybrid sterility loci, S5, f5, pf12 and Sc, are the major QTLs controlling inter-subspecific hybrid sterility and thus the minimal targets that can be manipulated for breeding sub-specific hybrid rice. We then cloned the pf12 locus, one of the most effective loci for hybrid male sterility, by map-based cloning, and showed that artificial disruption of pf12A gene at this locus could successfully rescue hybrid fertility. We further dissected the genetic basis of wide compatibility using three pairwise crosses from a wide-compatibility variety Dular and representative indica and japonica varieties. On this basis, we constructed and assembled different combinations of naturally compatible alleles of four loci, S5, Sc, pf12, and f5, and found that the improved lines could fully recover pollen and embryo sac fertility in test-crossed F1s, thereby completely fulfilling the demands of inter-subspecific hybrid spikelet fertility in agricultural production. This breeding scheme would facilitate redesign of future inter-subspecific hybrid rice with a higher yield potential.

Seasonal Fluctuations in Nitrate Levels Can Trigger Lead Solder Corrosion Problems in Drinking Water.

After a utility switched its source water from ground to surface water in 2017, first draw water lead levels spiked due to increased lead solder corrosion that could not be explained by existing knowledge. When lead release was not adequately reduced with a 90:10 orthophosphate/polyphosphate corrosion inhibitor blend or even high levels of 100% orthophosphate, an in-depth investigation of possible causes revealed a strong correlation between 90th percentile lead and seasonal fluctuations in surface water nitrate levels. Complementary bench-scale studies that tested new copper coupons with lead solder and harvested pipes from a worst case home verified a strong relationship between nitrate and elevated lead. Lead release in the presence of nitrate became increasingly erratic with time, resulting in the spalling of large lead solder particulates up to 7 mm in length into the water. Lead levels were occasionally >1000 ppb in homes and >100000 ppb in the bench experiments with harvested pipe. Orthophosphate was unable to sufficiently reduce lead levels below the action level during periods with high nitrate levels in the bench studies. Water utilities and regulators should proactively consider possible unintended consequences of higher nitrate levels on lead release when changing source waters or during seasonal runoff events.

GLW7.1, a Strong Functional Allele of Ghd7, Enhances Grain Size in Rice.

Grain size is a key determinant of both grain weight and grain quality. Here, we report the map-based cloning of a novel quantitative trait locus (QTL), GLW7.1 (Grain Length, Width and Weight 7.1), which encodes the CCT motif family protein, GHD7. The QTL is located in a 53 kb deletion fragment in the cultivar Jin23B, compared with the cultivar CR071. Scanning electron microscopy analysis and expression analysis revealed that GLW7.1 promotes the transcription of several cell division and expansion genes, further resulting in a larger cell size and increased cell number, and finally enhancing the grain size as well as grain weight. GLW7.1 could also increase endogenous GA content by up-regulating the expression of GA biosynthesis genes. Yeast two-hybrid assays and split firefly luciferase complementation assays revealed the interactions of GHD7 with seven grain-size-related proteins and the rice DELLA protein SLR1. Haplotype analysis and transcription activation assay revealed the effect of six amino acid substitutions on GHD7 activation activity. Additionally, the NIL with GLW7.1 showed reduced chalkiness and improved cooking and eating quality. These findings provide a new insight into the role of Ghd7 and confirm the great potential of the GLW7.1 allele in simultaneously improving grain yield and quality.

A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid.

Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F2 s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.

Fujian cytoplasmic male sterility and the fertility restorer gene OsRf19 provide a promising breeding system for hybrid rice.

Cytoplasmic male sterility (CMS) determined by mitochondrial genes and restorer of fertility (Rf) controlled by nuclear-encoded genes provide the breeding systems of many hybrid crops for the utilization of heterosis. Although several CMS/Rf systems have been widely exploited in rice, hybrid breeding using these systems has encountered difficulties due to either fertility instability or complications of two-locus inheritance or both. In this work, we characterized a type of CMS, Fujian Abortive cytoplasmic male sterility (CMS-FA), with stable sporophytic male sterility and a nuclear restorer gene that completely restores hybrid fertility. CMS is caused by the chimeric open reading frame FA182 that specifically occurs in the mitochondrial genome of CMS-FA rice. The restorer gene OsRf19 encodes a pentatricopeptide repeat (PPR) protein targeted to mitochondria, where it mediates the cleavage of FA182 transcripts, thus restoring male fertility. Comparative sequence analysis revealed that OsRf19 originated through a recent duplication in wild rice relatives, sharing a common ancestor with OsRf1a/OsRf5, a fertility restorer gene for Boro II and Hong-Lian CMS. We developed six restorer lines by introgressing OsRf19 into parental lines of elite CMS-WA hybrids; hybrids produced from these lines showed equivalent or better agronomic performance relative to their counterparts based on the CMS-WA system. These results demonstrate that CMS-FA/OsRf19 provides a highly promising system for future hybrid rice breeding.

Criticality in reservoir computer of coupled phase oscillators.

Accumulating evidence shows that the cerebral cortex is operating near a critical state featured by power-law size distribution of neural avalanche activities, yet evidence of this critical state in artificial neural networks mimicking the cerebral cortex is still lacking. Here we design an artificial neural network of coupled phase oscillators and, by the technique of reservoir computing in machine learning, train it for predicting chaos. It is found that when the machine is properly trained, oscillators in the reservoir are synchronized into clusters whose sizes follow a power-law distribution. This feature, however, is absent when the machine is poorly trained. Additionally, it is found that despite the synchronization degree of the original network, once properly trained, the reservoir network is always developed to the same critical state, exemplifying the "attractor" nature of this state in machine learning. The generality of the results is verified in different reservoir models and by different target systems, and it is found that the scaling exponent of the distribution is independent of the reservoir details and the bifurcation parameters of the target system, but is modified when the dynamics of the target system is changed to a different type. The findings shed light on the nature of machine learning, and are helpful to the design of high-performance machines in physical systems.

qFC6, a major gene for crude fat content and quality in rice.

KEY MESSAGE: qFC6, a major quantitative trait locus for rice crude fat content, was fine mapped to be identical with Wx. FC6 negatively regulates crude fat content and rice quality. Starch, protein and lipids are the three major components in rice endosperm. The lipids content in rice influences both storage and quality. In this study, we identified a quantitative trait locus (QTL), qFC6, for crude fat (free lipids) content through association analysis and linkage analysis. Gene-based association analysis revealed that LOC_Os06g04200, also known as Wx, was the candidate gene for qFC6. Complementation and knockout transgenic lines revealed that Wx negatively regulates crude fat content. Lipid composition and content analysis by gas chromatography and taste evaluation analysis showed that FC6 positively influenced bound lipids content and negatively affected both free lipids content and taste. Besides, higher free lipids content rice varieties exhibit more lustrous appearance after cooking and by adding extra oil during cooking could improve rice luster and taste score, indicating that higher free lipids content may make rice more lustrous and delicious. Together, we cloned a QTL coordinating rice crude fat content and eating quality and assisted in uncovering the genetic basis of rice lipid content and in the improvement of rice eating quality.

Optimizing synchrony with a minimal coupling strength of coupled phase oscillators on complex networks based on desynchronous clustering.

Finding the globally optimal network is an unsolved problem in synchrony optimization. In this paper, an efficient edge-adding optimization method based on global information is proposed. The edge-adding scheme is obtained through the eigenvector corresponding to the maximum eigenvalue of the system's Jacobian matrix. With different frequency distributions, we find that the optimized networks have similar features, concluded as three conditions: (i) The deviations of nodes' frequencies from the mean value are linear with the nodes' degrees, (ii) the oscillators form a bipartite network divided according to the frequencies of the oscillators, and (iii) oscillators are only connected to those with sufficiently large frequency differences. An optimal network can be constructed directly based on these three conditions for a given distribution of natural frequencies. We show that the critical coupling strengths of these constructed networks approach the theoretical lower bound. The constructed networks are or at least close to the globally optimal ones for synchrony.

The rice heavy-metal transporter OsNRAMP1 regulates disease resistance by modulating ROS homoeostasis.

Crop diseases threaten food security and sustainable agriculture. Consumption of crops containing nonessential toxic metals leads to health risks for humans. Therefore, cultivation of disease-resistant and toxic metal-safe crops is a double-gain strategy that can contribute to food security. Here, we show that rice heavy-metal transporter OsNRAMP1 plays an important role in plant immunity by modulating metal ion and reactive oxygen species (ROS) homoeostasis. OsNRAMP1 expression was induced after pathogenic bacteria and fungi infections. The osnramp1 mutants had an increased content of H2 O2 and activity of superoxide dismutase, but decreased activity of catalase, showing enhanced broad-spectrum resistance against bacterial and fungal pathogens. RNA-seq analysis identified a number of differentially expressed genes that were involved in metal ion and ROS homoeostasis. Altered expression of metal ion-dependent ROS-scavenging enzymes genes and lower accumulation of cations such as Mn together induced compromised metal ion-dependent enzyme-catalysing activity and modulated ROS homoeostasis, which together contributed towards disease resistance in osnramp1 mutants. Furthermore, the osnramp1 mutants contained lower levels of toxic heavy metals Cd and Pb and micronutrients Ni and Mn in leaves and grains. Taken together, a proof of concept was achieved that broad-spectrum disease-resistant and toxic heavy-metal-safe rice was engineered by removal of the OsNRAMP1 gene.

Heterogeneity induced splay state of amplitude envelope in globally coupled oscillators.

Splay states of the amplitude envelope are stably observed as a heterogenous node is introduced into the globally coupled identical oscillators with repulsive coupling. With the increment of the frequency mismatches between the heterogenous nodes and the rest identical globally coupled oscillators, the formal stable splay state based on the time series becomes unstable, while a splay state based on the new-born amplitude envelopes of time series is stably observed among the rest identical oscillators. The characteristics of the splay state based on the amplitude envelope are numerically and theoretically presented for different parameters of the coupling strength ϵ and the frequency mismatches Δω for small coupling strength and large frequency mismatches. We expect that all these results could reveal the generality of splay states in coupled nonidentical oscillators and help to understand the rich dynamics of amplitude envelopes in multidisciplinary fields.

From Green Super Rice to green agriculture: Reaping the promise of functional genomics research.

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.