Metabolic remodeling maintains a reducing environment for rapid activation of the yeast DNA replication checkpoint.

Nucleotide metabolism fuels normal DNA replication and is also primarily targeted by the DNA replication checkpoint when replication stalls. To reveal a comprehensive interconnection between genome maintenance and metabolism, we analyzed the metabolomic changes upon replication stress in the budding yeast S. cerevisiae. We found that upon treatment of cells with hydroxyurea, glucose is rapidly diverted to the oxidative pentose phosphate pathway (PPP). This effect is mediated by the AMP-dependent kinase, SNF1, which phosphorylates the transcription factor Mig1, thereby relieving repression of the gene encoding the rate-limiting enzyme of the PPP. Surprisingly, NADPH produced by the PPP is required for efficient recruitment of replication protein A (RPA) to single-stranded DNA, providing the signal for the activation of the Mec1/ATR-Rad53/CHK1 checkpoint signaling kinase cascade. Thus, SNF1, best known as a central energy controller, determines a fast mode of replication checkpoint activation through a redox mechanism. These findings establish that SNF1 provides a hub with direct links to cellular metabolism, redox, and surveillance of DNA replication in eukaryotes.

MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize.

Fertile pollen is critical for the survival, fitness, and dispersal of flowering plants, and directly contributes to crop productivity. Extensive mutational screening studies have been carried out to dissect the genetic regulatory network determining pollen fertility, but we still lack fundamental knowledge about whether and how pollen fertility is controlled in natural populations. We used a genome-wide association study (GWAS) to show that ZmGEN1A and ZmMSH7, two DNA repair-related genes, confer natural variation in maize pollen fertility. Mutants defective in these genes exhibited abnormalities in meiotic or post-meiotic DNA repair, leading to reduced pollen fertility. More importantly, ZmMSH7 showed evidence of selection during maize domestication, and its disruption resulted in a substantial increase in grain yield for both inbred and hybrid. Overall, our study describes the first systematic examination of natural genetic effects on pollen fertility in plants, providing valuable genetic resources for optimizing male fertility. In addition, we find that ZmMSH7 represents a candidate for improvement of grain yield.

ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize.

The number of pollen grains is a critical determinant of reproductive success in seed plants and varies among species and individuals. However, in contrast with many mutant-screening studies relevant to anther and pollen development, the natural genetic basis for variations in pollen number remains largely unexplored. To address this issue, we carried out a genome-wide association study in maize, ultimately revealing that a large presence/absence variation in the promoter region of ZmRPN1 alters its expression level and thereby contributes to pollen number variation. Molecular analyses showed that ZmRPN1 interacts with ZmMSP1, which is known as a germline cell number regulator, and facilitates ZmMSP1 localization to the plasma membrane. Importantly, ZmRPN1 dysfunction resulted in a substantial increase in pollen number, consequently boosting seed production by increasing female-male planting ratio. Together, our findings uncover a key gene controlling pollen number, and therefore, modulation of ZmRPN1 expression could be efficiently used to develop elite pollinators for modern hybrid maize breeding.

Genome-wide association study reveals the genetic architecture of root hair length in maize.

BACKGROUND: Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored. RESULTS: Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways. CONCLUSIONS: These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.

A natural single-nucleotide polymorphism variant in sulfite reductase influences sulfur assimilation in maize.

Plants absorb sulfur from the environment and assimilate it into suitable forms for the biosynthesis of a broad range of molecules. Although the biochemical pathway of sulfur assimilation is known, how genetic differences contribute to natural variation in sulfur assimilation remains poorly understood. Here, using a genome-wide association study, we uncovered a single-nucleotide polymorphism (SNP) variant in the sulfite reductase (SiR) gene that was significantly associated with SiR protein abundance in a maize natural association population. We also demonstrated that the synonymous C to G base change at SNP69 may repress translational activity by altering messenger RNA secondary structure, which leads to reduction in ZmSiR protein abundance and sulfur assimilation activity. Population genetic analyses showed that the SNP69C allele was likely a variant occurring after the initial maize domestication and accumulated with the spread of maize cultivation from tropical to temperate regions. This study provides the first evidence that genetic polymorphisms in the exon of ZmSiR could influence the protein abundance through a posttranscriptional mechanism and in part contribute to natural variation in sulfur assimilation. These findings provide a prospective target to improve maize varieties with proper sulfur nutrient levels assisted by molecular breeding and engineering.

The Number of Meiotic Double-Strand Breaks Influences Crossover Distribution in Arabidopsis.

Meiotic recombination generates genetic diversity and ensures proper chromosome segregation. Recombination is initiated by the programmed formation of double-strand breaks (DSBs) in chromosomal DNA by DNA Topoisomerase VI-A Subunit (SPO11), a topoisomerase-like enzyme. Repair of some DSBs leads to the formation of crossovers (COs). In most organisms, including plants, the number of DSBs greatly exceeds the number of COs and which DSBs become CO sites is tightly controlled. The CO landscape is affected by DNA sequence and epigenome features of chromosomes as well as by global mechanisms controlling recombination dynamics. The latter are poorly understood and their effects on CO distribution are not well elucidated. To study how recombination dynamics affects CO distribution, we engineered Arabidopsis thaliana plants to carry hypomorphic alleles of SPO11-1 Two independent transgenic lines showed ∼30% and 40% reductions in DSB numbers, which were commensurate with the dosage of the SPO11-1 transcript. The reduction in DSB number resulted in proportional, although smaller, reductions of the number of COs. Most interestingly, CO distribution along the chromosomes was dramatically altered, with substantially fewer COs forming in pericentromeric chromosome regions. These results indicate that SPO11 activity, and the resulting DSB numbers are major factors shaping the CO landscape.

Characterization of Proteome Variation During Modern Maize Breeding.

The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel. The minimum extent of correlation between protein and RNA levels suggests that variation in mRNA expression is often not indicative of protein expression at a population scale. This is corroborated by the observation that mRNA- and protein-based coexpression networks are relatively independent of each other, and many pQTLs arise without the presence of corresponding eQTLs. Importantly, compared with transcriptome, the subtypes categorized by the proteome show a markedly high accuracy to resemble the genomic subpopulation. These findings suggest that proteome evolved under a greater evolutionary constraint than transcriptome during maize adaptation from tropical to temperate regions. Overall, the integrated multi-omics analysis provides a functional context to interpret gene expression variation during modern maize breeding.

Dihydroxyacid dehydratase is important for gametophyte development and disruption causes increased susceptibility to salinity stress in Arabidopsis.

Dihydroxyacid dehydratase (DHAD) catalyses a key step in the branched-chain amino acid (BCAA) biosynthetic pathway that exists in numerous organisms, including bacteria, fungi, and plants, but not humans. In Arabidopsis thaliana, DHAD is encoded by a single gene (AT3G23940), but its biological function in controlling plant development remains uncharacterized. In this study, we showed that DHAD is highly expressed in most vegetative and reproductive tissues. It is an essential gene, and complete disruption caused partial sterility in both male and female gametophyte phases. In addition, reduced expression of DHAD in knockdown mutants resulted in a reduction in the accumulation of all three BCAAs in roots and, as a consequence, led to a shorter root phenotype, which could be restored by an exogenous supplement of free BCAAs. Interestingly, the knockdown mutants became hypersensitive to salt stress, not to heavy metal stress, implying that BCAAs may act as osmolytes in salt tolerance. This would be the second amino acid shown to confer such a function in addition to the well-documented proline. Our results provide evidence that BCAA biosynthesis plays important roles in gametophyte and root development, and BCAA homeostasis contributes to the adaptation of Arabidopsis to salinity stress.

Spatiotemporal Dynamics of COVID-19 Pandemic City Lockdown: Insights From Nighttime Light Remote Sensing.

The global COVID-19 outbreak severely hampered the growth of the global economy, prompting the implementation of the strictest prevention policies in China. Establishing a significant relationship between changes in nighttime light and COVID-19 lockdowns from a geospatial perspective is essential. In light of nighttime light remote sensing, we evaluated the spatiotemporal dynamic effects of COVID-19 city lockdowns on human activity intensity in the Zhengzhou region. Prior to the COVID-19 outbreak, nighttime light in the Zhengzhou region maintained a significant growth trend, even under regular control measures. However, following the October 2022 COVID-19 lockdown, nighttime light experienced a substantial decrease. In the central area of Zhengzhou, nighttime light decreased by at least 18% compared to pre-lockdown levels, while in the sub-center, the decrease was around 14%. The areas where nighttime light decreased the most in the central region were primarily within a 15 km radius, while in the sub-center, the decrease was concentrated within a 5 km radius. These changes in both statistical data and nighttime light underscored the significant impact of the COVID-19 lockdown on economic activities in the Zhengzhou region.

Grain security assessment in Bangladesh based on supply-demand balance analysis.

Ensuring the grain supply-demand balance and achieving grain security had been the main tasks for the government of Bangladesh. On the supply side, Bangladesh's supply of grain products has increased substantially, with an average annual growth rate of 1.99 million tons in 1998-2018. Domestic grain production, especially rice production, accounted for the largest proportion in its structure. However, under the constraints of resources and environment, imports and international aid were needed to ensure a stable and sustainable grain supply. On the demand side, Bangladesh's demand for grain products continued to grow at an average annual rate of 2.09 million tons and its structure was constantly diversified. In recent years, domestic grain production has fully met the grain demand for food use, but the overall grain supply dependence on foreign gradually increased. From the analysis of the influencing factors, the grain supply, especially the domestic production of rice and maize, had the greatest impact on the balance of grain supply-demand in Bangladesh. Moreover, multiple cropping index, chemical fertilizer application per hectare and irrigation rate were the three main factors affecting grain production. As a typical agricultural country, Bangladesh's grain security was faced with challenges, such as high population density, insufficient cultivated land resources, international grain trade and frequent natural disasters. It is suggested that its government should strengthen scientific and technological research, adjust agricultural structure, improve the efficient utilization of agricultural resources and grain circulation systems, and balance the grain demand between food use and indirect use, so as to achieve complete grain self-sufficiency and overall grain security.

ZmCom1 Is Required for Both Mitotic and Meiotic Recombination in Maize.

CtIP/Ctp1/Sae2/Com1, a highly conserved protein from yeast to higher eukaryotes, is required for DNA double-strand break repair through homologous recombination (HR). In this study, we identified and characterized the COM1 homolog in maize. The ZmCom1 gene is abundantly expressed in reproductive tissues at meiosis stages. In ZmCom1-deficient plants, meiotic chromosomes are constantly entangled as a formation of multivalents and accompanied with chromosome fragmentation at anaphase I. In addition, the formation of telomere bouquet, homologous pairing and synapsis were disturbed. The immunostaining assay showed that the localization of ASY1 and DSY2 was normal, while ZYP1 signals were severely disrupted in Zmcom1 meiocytes, indicating that ZmCom1 is critically required for the proper SC assembly. Moreover, RAD51 signals were almost completely absent in Zmcom1 meiocytes, implying that COM1 is required for RAD51 loading. Surprisingly, in contrast to the Atcom1 and Oscom1 mutants, Zmcom1 mutant plants exhibited a number of vegetative phenotypes under normal growth condition, which may be partly attributed to mitotic aberrations including chromosomal fragmentation and anaphase bridges. Taken together, our results suggest that although the roles of COM1 in HR process seem to be primarily conserved, the COM1 dysfunction can result in the marked dissimilarity in mitotic and meiotic outcomes in maize compared to Arabidopsis and rice. We suggest that this character may be related to the discrete genome context.

Abrupt drainage basin reorganization following a Pleistocene river capture.

River capture is a dramatic natural process of internal competition through which mountainous landscapes evolve and respond to perturbations in tectonics and climate. River capture may occur when one river network grows at the expense of another, resulting in a victor that steals the neighboring headwaters. While river capture occurs regularly in numerical models, field observations are rare. Here we document a late Pleistocene river capture in the Yimeng Mountains, China that abruptly shifted 25 km2 of drainage area from one catchment to another. River terraces and imbricated cobbles indicate that the main channel incised 27 m into granitic bedrock within 80 kyr, following the capture event, and upstream propagating knickpoints and waterfalls reversed the flow direction of a major river. Topographic analysis shows that the capture shifted the river basins far from topographic equilibrium, and active divide migration is propagating the effects of the capture throughout the landscape.

[Research advances in vulnerability assessment of natural ecosystem response to climate change].

Climate change with global warming as the sign has been caught great attention by the governments, international organizations, and scientists in the world. Human society and natural ecosystem are both exposed to climate change, and more and more people are waked up by its increasing harm. Vulnerability analysis and assessment are the key and basis for adapting and mitigating climate change, being the highlight in the research fields of climate change and ecology in recent years. The vulnerability assessment of climate change is being carried out in various research fields and on different scales, and much progress has been made. This paper introduced the concept of vulnerability, and summarized the research progress in vulnerability assessment of climate change, with the focus on the frame and methodology of vulnerability assessment of natural ecosystem response to climate change. The existed problems and future prospects in this research area were also discussed.