Accurate identification of traps and pinch-outs on a stratigraphic reservoir-A case from Hala'alate Mountain in the Junggar Basin, China.

In the investigation of stratigraphic reservoirs, a significant discrepancy frequently exists between the delineation of the formation pinch-out line as traced using the characteristics of seismic wave reflections and the actual location of the formation pinch-out line. This has been the main problem restricting further hydrocarbon exploration and development. In this study, Hala'alate Mountain on the northwestern margin of the Junggar Basin is taken as an example for carrying out the study of stratigraphic reservoirs by integrating logging, drilling, and 3D seismic data. On the one hand, in studies based on the identification of formation pinch-out points using seismic data, the identification error of reservoir pinch-out lines is reduced by the improved included angle extrapolation method by utilizing the half energy attribute. On the other hand, the Poisson's ratio curve is reconstructed using acoustic curves and oil-gas sensitive logging, then the reservoir oil-bearing facies zone is predicted using Poisson's ratio post-stack genetic inversion to comprehensively analyze the controlling factors of stratigraphic reservoirs. The study area mainly features structural lithologic reservoirs, structural stratigraphic reservoirs and stratigraphic overlaps that pinch out reservoirs. The boundary of a stratigraphic reservoir is affected by the dip angle of the unconformity surface, the formation dip angle, and other factors. The improved included angle extrapolation method improves the identification accuracy of stratigraphic overlap pinch-out reservoirs. The reservoir distribution then is calculated according to Poisson's ratio inversion, improving the prediction accuracy for the reservoir. This method improves the predictive effect for stratigraphic reservoirs and provides a new idea for the exploration and development of similar reservoirs.

Twist-Angle-Controlled Nonlinear Circular Dichroism on Gold-Crystal Hybrid Metasurfaces.

Optical chirality, which plays important roles in liquid crystal display and biological and chemical detection, has been attracting scientists' attention due to its potential applications in optical information processing. Usually, the chiral optical response of natural molecules is very weak. However, the emergence of metasurfaces offers a promising solution to solve this issue. By judiciously designing the geometry of meta-atoms, we have realized strong optical circular dichroism (CD) in both linear and nonlinear optical regimes. However, tuning of the CD with a metasurface remains challenging. Here, we propose the twist-angle-controlled nonlinear CD effect by using the second-harmonic generation process on a gold-crystal hybrid metasurface. The CD effect of the second-harmonic waves can be tuned well by controlling the twist angle between the two constituent materials. The proposed hybrid metasurface may open new avenues for developing ultracompact and multifunctional nonlinear optical devices.

Exploiting genomic tools for genetic dissection and improving the resistance to Fusarium stalk rot in tropical maize.

KEY MESSAGE: A stable genomic region conferring FSR resistance at ~250 Mb on chromosome 1 was identified by GWAS. Genomic prediction has the potential to improve FSR resistance. Fusarium stalk rot (FSR) is a global destructive disease in maize; the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools of genome-wide association study (GWAS) and genomic prediction (GP) provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the combinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99 × 10-7 to 8.27 × 10-13, and the phenotypic variance explained (PVE) values ranging from 0.94 to 8.30%. The genetic effects of the 15 favorable alleles ranged from -4.29 to -14.21% of the FSR severity. One stable genomic region at ~ 250 Mb on chromosome 1 was detected across all populations, and the PVE values of the SNPs detected in this region ranged from 2.16 to 5.18%. Prediction accuracies of FSR severity estimated with the genome-wide SNPs were moderate and ranged from 0.29 to 0.51. By incorporating genotype-by-environment interaction, prediction accuracies were improved between 0.36 and 0.55 in different breeding scenarios. Considering both the genome coverage and the threshold of the P-value of SNPs to select a subset of molecular markers further improved the prediction accuracies. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.

ZmADF5, a Maize Actin-Depolymerizing Factor Conferring Enhanced Drought Tolerance in Maize.

Drought stress is seriously affecting the growth and production of crops, especially when agricultural irrigation still remains quantitatively restricted in some arid and semi-arid areas. The identification of drought-tolerant genes is important for improving the adaptability of maize under stress. Here, we found that a new member of the actin-depolymerizing factor (ADF) family; the ZmADF5 gene was tightly linked with a consensus drought-tolerant quantitative trait locus, and the significantly associated signals were detected through genome wide association analysis. ZmADF5 expression could be induced by osmotic stress and the application of exogenous abscisic acid. Its overexpression in Arabidopsis and maize helped plants to keep a higher survival rate after water-deficit stress, which reduced the stomatal aperture and the water-loss rate, as well as improved clearance of reactive oxygen species. Moreover, seventeen differentially expressed genes were identified as regulated by both drought stress and ZmADF5, four of which were involved in the ABA-dependent drought stress response. ZmADF5-overexpressing plants were also identified as sensitive to ABA during the seed germination and seedling stages. These results suggested that ZmADF5 played an important role in the response to drought stress.

All-optical ultrafast polarization switching with nonlinear plasmonic metasurfaces.

Optical switching has important applications in optical information processing, optical computing, and optical communications. The long-term pursuit of optical switch is to achieve short switching time and large modulation depth. Among various mechanisms, all-optical switching based on Kerr effect represents a promising solution. However, it is usually difficult to compromise both switching time and modulation depth of a Kerr-type optical switch. To circumvent this constraint, symmetry selective polarization switching via second-harmonic generation (SHG) in nonlinear crystals has been attracting scientists' attention. Here, we demonstrate SHG-based all-optical ultrafast polarization switching by using geometric phase controlled nonlinear plasmonic metasurfaces. A switching time of hundreds of femtoseconds and a modulation depth of 97% were experimentally demonstrated. The function of dual-channel all-optical switching was also demonstrated on a metasurface, which consists of spatially variant meta-atoms. The nonlinear metasurface proposed here represents an important platform for developing all-optical ultrafast switches and would benefit the area of optical information processing.

Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize.

Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion.

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.

Maize ZmBES1/BZR1-1 transcription factor negatively regulates drought tolerance.

Drought stress is a common abiotic factor and restricts plant growth and development. Exploring maize stress-related genes and their regulatory mechanisms is crucial for ensuring agricultural productivity and food security. The BRI1-EMS1 suppressor (BES1)/brassinazole-resistant 1 (BZR1) transcription factors (TFs) play important roles in plant growth, development, and stress response. However, maize ZmBES1/BZR1s are rarely reported. In the present study, the ZmBES1/BZR1-1 gene was cloned from maize B73 and functionally characterized in transgenic Arabidopsis and rice in drought stress response. The ZmBES1/BZR1-1 protein possessed a conserved bHLH domain characterized by BES1/BZR1 TFs, localized in the nucleus, and showed transcription activation activity. The expression of ZmBES1/BZR1-1 exhibited no tissue specificity but drought-inhibitory expression in maize. Under drought stress, overexpression of ZmBES1/BZR1-1 resulted in the enhancement of drought sensitivity of transgenic Arabidopsis and rice with a lower survival rate, reactive oxygen species (ROS) level and relative water content (RWC) and a higher stomatal aperture and relative electrolyte leakage (REL). The RNA-seq results showed that 56 differentially expressed genes (DEGs) were regulated by ZmBES1/BZR1-1 by binding to E-box elements in their promoters. The GO analysis showed that the DEGs were significantly annotated with response to oxidative stress and oxygen level. The study suggests that the ZmBES1/BZR1-1 gene negatively regulates drought stress, which provides insights into further underlying molecular mechanisms in the drought stress response mediated by BZR1/BES1s.

Sedimentary Characteristics and Hydrocarbon-Generation Potential of the Permian Pingdiquan Formation in Dongdaohaizi Sag, Junggar Basin, Northwest China.

After several years of extensive exploration, a series of oil and gas reservoirs or structures have been discovered in the Dongdaohaizi sag, situated in the hinterland of the Junggar Basin. However, in recent years, some wells around the sag have failed. Herein, sedimentary facies, the plane distribution of dark mudstone, geochemical characteristics of source rocks, and the control of sedimentary facies on the distribution and development of source rocks in the Permian Pingdiquan Formation in the Dongdaohaizi sag were systematically investigated. A combined geological and geochemical method was used to fully understand the distribution law and resource potential of the source rocks in this area. Investigation results indicate that the Pingdiquan Formation primarily inherited continuous deposition, and the sedimentary facies of the sag, such as semideep lake, shore-shallow lake, prefan delta, fan delta front, and fan delta plain, were developed from the center sag to the outside. The fan delta facies, predominantly distributed in the northern margin of the sag, are characterized by lithology mainly composed of sandy conglomerate and coarse sandstone. The sandstone has a coarse particle size and poor sorting ability, while lacustrine mudstone is widely developed in the sag with a large sedimentary thickness, which is the primary source rock of the Dongdaohaizi sag. The source rocks in the Pingdiquan Formation exhibit medium-to-good quality. The organic matter is categorized as types II1-III, and the thermal evolution maturity is in the mature-high mature stage, indicating a high resource potential. The development of the source rock in the Dongdaohaizi sag is closely related to the sedimentary environment. The sedimentation rate of fan delta facies is high and burial is fast, bringing a large amount of terrestrial organic matter to the lake, thereby increasing the nutrition and organic matter quantity of the lake. Due to the stable water of the lake, low energy at the bottom, and medium conditions of strong reduction, a large amount of organic matter accumulated in the deep to semideep lake facies of the study area, resulting in the development of thick dark mudstone with a thickness of over 400 m. The abundance of organic matter has reached a good level, and the maturity and content of organic matter are high, signifying a high hydrocarbon-generation potential.

Integrative transcriptome and metabolome analysis reveals the mechanisms of light-induced pigmentation in purple waxy maize.

Introduction: Waxy maize, mainly consumed at the immature stage, is a staple and vegetable food in Asia. The pigmentation in the kernel of purple waxy maize enhances its nutritional and market values. Light, a critical environmental factor, affects anthocyanin biosynthesis and results in pigmentation in different parts of plants, including in the kernel. SWL502 is a light-sensitive waxy maize inbred line with purple kernel color, but the regulatory mechanism of pigmentation in the kernel resulting in purple color is still unknown. Methods: In this study, cyanidin, peonidin, and pelargonidin were identified as the main anthocyanin components in SWL502, evaluated by the ultra-performance liquid chromatography (UPLC) method. Investigation of pigment accumulation in the kernel of SWL502 was performed at 12, 17, and 22 days after pollination (DAP) under both dark and light treatment conditions via transcriptome and metabolome analyses. Results: Dark treatment affected genes and metabolites associated with metabolic pathways of amino acid, carbohydrate, lipid, and galactose, biosynthesis of phenylpropanoid and terpenoid backbone, and ABC transporters. The expression of anthocyanin biosynthesis genes, such as 4CL2, CHS, F3H, and UGT, was reduced under dark treatment. Dynamic changes were identified in genes and metabolites by time-series analysis. The genes and metabolites involved in photosynthesis and purine metabolism were altered in light treatment, and the expression of genes and metabolites associated with carotenoid biosynthesis, sphingolipid metabolism, MAPK signaling pathway, and plant hormone signal transduction pathway were induced by dark treatment. Light treatment increased the expression level of major transcription factors such as LRL1, myc7, bHLH125, PIF1, BH093, PIL5, MYBS1, and BH074 in purple waxy maize kernels, while dark treatment greatly promoted the expression level of transcription factors RVE6, MYB4, MY1R1, and MYB145. Discussion: This study is the first report to investigate the effects of light on waxy maize kernel pigmentation and the underlying mechanism at both transcriptome and metabolome levels, and the results from this study are valuable for future research to better understand the effects of light on the regulation of plant growth.

Pollen self-elimination CRISPR-Cas genome editing prevents transgenic pollen dispersal in maize.

This study reports the development of a programmed pollen self-elimination CRISPR-Cas (PSEC) system in which the pollen is infertile when PSEC is present in haploid pollen. PSEC can be inherited through the female gametophyte and retains genome editing activity in vivo across generations. This system could greatly alleviate serious concerns about the widespread diffusion of genetically modified (GM) elements into natural and agricultural environments via outcrossing.

Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn.

Sweet corn and waxy corn has a better taste and higher accumulated nutritional value than regular maize, and is widely planted and popularly consumed throughout the world. Plant height (PH), ear height (EH), and tassel branch number (TBN) are key plant architecture traits, which play an important role in improving grain yield in maize. In this study, a genome-wide association study (GWAS) and genomic prediction analysis were conducted on plant architecture traits of PH, EH, and TBN in a fresh edible maize population consisting of 190 sweet corn inbred lines and 287 waxy corn inbred lines. Phenotypic data from two locations showed high heritability for all three traits, with significant differences observed between sweet corn and waxy corn for both PH and EH. The differences between the three subgroups of sweet corn were not obvious for all three traits. Population structure and PCA analysis results divided the whole population into three subgroups, i.e., sweet corn, waxy corn, and the subgroup mixed with sweet and waxy corn. Analysis of GWAS was conducted with 278,592 SNPs obtained from resequencing data; 184, 45, and 68 significantly associated SNPs were detected for PH, EH, and TBN, respectively. The phenotypic variance explained (PVE) values of these significant SNPs ranged from 3.50% to 7.0%. The results of this study lay the foundation for further understanding the genetic basis of plant architecture traits in sweet corn and waxy corn. Genomic selection (GS) is a new approach for improving quantitative traits in large plant breeding populations that uses whole-genome molecular markers. The marker number and marker quality are essential for the application of GS in maize breeding. GWAS can choose the most related markers with the traits, so it can be used to improve the predictive accuracy of GS.

QTL mapping and genomic prediction of resistance to wheat head blight caused by Fusarium verticillioides.

Fusarium head blight (FHB), is one of the destructive fugue diseases of wheat worldwide caused by the Fusarium verticillioides (F.v). In this study, a population consisting of 262 recombinant inbred lines (RILs) derived from Zhongmai 578 and Jimai 22 was used to map Quantitative Trait Locus (QTL) for FHB resistance, with the genotype data using the wheat 50 K single nucleotide polymorphism (SNP) array. The percentage of symptomatic spikelet (PSS) and the weighted average of PSS (PSSW) were collected for each RIL to represent their resistance to wheat head blight caused by F.v. In total, 22 QTL associated with FHB resistance were identified on chromosomes 1D, 2B, 3B, 4A, 5D, 7A, 7B, and 7D, respectively, from which 10 and 12 QTL were detected from PSS and PSSW respectively, explaining 3.82%-10.57% of the phenotypic variances using the inclusive composite interval mapping method. One novel QTL, Qfhb. haust-4A.1, was identified, explaining 10.56% of the phenotypic variation. One stable QTL, Qfhb. haust-1D.1 was detected on chromosome 1D across multiple environments explaining 4.39%-5.70% of the phenotypic variation. Forty-seven candidate genes related to disease resistance were found in the interval of Qfhb. haust-1D.1 and Qfhb. haust-4A.1. Genomic prediction accuracies were estimated from the five-fold cross-validation scheme ranging from 0.34 to 0.40 for PSS, and from 0.34 to 0.39 for PSSW in in-vivo inoculation treatment. This study provided new insight into the genetic analysis of resistance to wheat head blight caused by F.v, and genomic selection (GS) as a potential approach for improving the resistance of wheat head blight.

Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses.

CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally.

Maize ZmBES1/BZR1-3 and -9 Transcription Factors Negatively Regulate Drought Tolerance in Transgenic Arabidopsis.

The BRI1-EMS suppressor 1 (BES1)/brassinazole-resistant 1(BZR1) transcription factors play crucial roles in plant growth, development, and stress response. However, little is known about the function of maize's BES1/BZR1s. In this study, the ZmBES1/BZR1-3 and ZmBES1/BZR1-9 genes were cloned from maize's inbred line, B73, and they were functionally evaluated by analyzing their expression pattern, subcellular localization, transcriptional activation activity, as well as their heterologous expression in Arabidopsis, respectively. The results of the qRT-PCR showed that the ZmBES1/BZR1-3 and ZmBES1/BZR1-9 genes were predominantly expressed in the root, and their expression was significantly down-regulated by drought stress. The ZmBES1/BZR1-3 and ZmBES1/BZR1-9 proteins localized in the nucleus but showed no transcriptional activation activity as a monomer. Subsequently, it was found that the heterologous expression of the ZmBES1/BZR1-3 and ZmBES1/BZR1-9 genes in Arabidopsis decreased drought tolerance, respectively. The transgenic lines showed a more serious wilting phenotype, shorter root length, lower fresh weight, and higher relative electrolyte leakage (REL) and malondialdehyde (MDA) content compared to the control under drought stress. The RNA-sequencing data showed that the 70.67% and 93.27% differentially expressed genes (DEGs) were significantly down-regulated in ZmBES1/BZR1-3 and ZmBES1/BZR1-9 transgenic Arabidopsis, respectively. The DEGs of ZmBES1/BZR1-3 gene's expressing lines were mainly associated with oxidative stress response and amino acid metabolic process and enriched in phenylpropanoid biosynthesis and protein processing in the endoplasmic reticulum. But the DEGs of the ZmBES1/BZR1-9 gene's expressing lines were predominantly annotated with water deprivation, extracellular stimuli, and jasmonic acid and enriched in phenylpropanoid biosynthesis and plant hormone signal transduction. Moreover, ZmBES1/BZR1-9 increased stomatal aperture in transgenic Arabidopsis under drought stress. This study indicates that ZmBES1/BZR1-3 and ZmBES1/BZR1-9 negatively regulate drought tolerance via different pathways in transgenic Arabidopsis, and it provides insights into the underlying the function of BES1/BZR1s in crops.

Nonlinear vectorial holography with quad-atom metasurfaces.

Vectorial optical holography represents a solution to control the polarization and amplitude distribution of light in the Fourier space. While vectorial optical holography has been experimentally demonstrated in the linear optical regime, its nonlinear counterpart, which can provide extra degrees of freedom of light-field manipulation through the frequency conversion processes, remains unexplored. Here, we experimentally demonstrate the nonlinear vectorial holography through the second harmonic generation process on a quad-atom plasmonic metasurface. The quad-atom metasurface consists of gold meta-atoms with threefold rotational symmetry. Based on the concept of nonlinear geometric phase, we can simultaneously manipulate the phase and amplitude of the left and right circularly polarized second harmonic waves generated from the quad-atom metasurface. By superposing the two orthogonal polarization components, the quad-atom metasurface can produce nonlinear holographic images with vectorial polarization distributions. The proposed metasurface platform may have important applications in vectorial polarization nonlinear optical source, high-capacity optical information storage, and optical encryption.

Evaluation and Identification of Resistance Lines and QTLs of Maize to Seedborne Fusarium verticillioides.

Internal fungal contamination in cereal grains may affect plant growth and result in health concerns for humans and animals. Fusarium verticillioides is a seedborne fungus that can systemically infect maize. However, few efforts had been devoted to studying the genetics of maize resistance to seedborne F. verticillioides. In this study, we developed a disease evaluation method to identify resistance to seedborne F. verticillioides in maize, by which a set of 121 diverse maize inbred lines were evaluated. A 160 F10-generation recombinant inbred line (RIL) population derived from a cross of the resistant (BT-1) and susceptible (N6) inbred line was further used to identify major quantitative trait loci (QTLs) for seedborne F. verticillioides resistance. Eighteen inbred lines with a high resistance to seedborne F. verticillioides were characterized and could be used as potential germplasm resources for genetic improvement of maize resistance. Six QTLs with high heritability across multiple environments were detected on chromosomes 3, 4, 6, and 10, among which was a major QTL, qISFR4-1. Located on chromosome 4 at the interval of 12922609-13418025, qISFR4-1 could explain 16.63% of the total phenotypic variance. Distinct expression profiles of eight candidate genes in qISFR4-1 between BT-1 and N6 inbred lines suggested their pivotal regulatory roles in seedborne F. verticillioides resistance. Taken together, these results will improve our understanding of the resistant mechanisms of seedborne F. verticillioides and would provide valuable germplasm resources for disease resistance breeding in maize.

Identification and fine mapping of a major QTL (qRtsc8-1) conferring resistance to maize tar spot complex and validation of production markers in breeding lines.

KEY MESSAGE: A major QTL of qRtsc8-1 conferring TSC resistance was identified and fine mapped to a 721 kb region on chromosome 8 at 81 Mb, and production markers were validated in breeding lines. Tar spot complex (TSC) is a major foliar disease of maize in many Central and Latin American countries and leads to severe yield loss. To dissect the genetic architecture of TSC resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid population were used for GWAS and selective genotyping analysis, respectively. A total of 115 SNPs in bin 8.03 were detected by GWAS and three QTL in bins 6.05, 6.07, and 8.03 were detected by selective genotyping. The major QTL qRtsc8-1 located in bin 8.03 was detected by both analyses, and it explained 14.97% of the phenotypic variance. To fine map qRtsc8-1, the recombinant-derived progeny test was implemented. Recombinations in each generation were backcrossed, and the backcross progenies were genotyped with Kompetitive Allele Specific PCR (KASP) markers and phenotyped for TSC resistance individually. The significant tests for comparing the TSC resistance between the two classes of progenies with and without resistant alleles were used for fine mapping. In BC5 generation, qRtsc8-1 was fine mapped in an interval of ~ 721 kb flanked by markers of KASP81160138 and KASP81881276. In this interval, the candidate genes GRMZM2G063511 and GRMZM2G073884 were identified, which encode an integral membrane protein-like and a leucine-rich repeat receptor-like protein kinase, respectively. Both genes are involved in maize disease resistance responses. Two production markers KASP81160138 and KASP81160155 were verified in 471 breeding lines. This study provides valuable information for cloning the resistance gene, and it will also facilitate the routine implementation of marker-assisted selection in the breeding pipeline for improving TSC resistance.

The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize.

Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is a major threat to maize production worldwide. Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR. Here, we report the molecular cloning and characterization of RppC, which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus. Furthermore, we identified the corresponding avirulence effector, AvrRppC, which is secreted by P. polysora and triggers RppC-mediated resistance. Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance, indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production. Currently, RppC is the most frequently deployed SCR resistance gene in China, and a better understanding of its mode of action is critical for extending its durability.

Genomic Prediction of Resistance to Tar Spot Complex of Maize in Multiple Populations Using Genotyping-by-Sequencing SNPs.

Tar spot complex (TSC) is one of the most important foliar diseases in tropical maize. TSC resistance could be furtherly improved by implementing marker-assisted selection (MAS) and genomic selection (GS) individually, or by implementing them stepwise. Implementation of GS requires a profound understanding of factors affecting genomic prediction accuracy. In the present study, an association-mapping panel and three doubled haploid populations, genotyped with genotyping-by-sequencing, were used to estimate the effectiveness of GS for improving TSC resistance. When the training and prediction sets were independent, moderate-to-high prediction accuracies were achieved across populations by using the training sets with broader genetic diversity, or in pairwise populations having closer genetic relationships. A collection of inbred lines with broader genetic diversity could be used as a permanent training set for TSC improvement, which can be updated by adding more phenotyped lines having closer genetic relationships with the prediction set. The prediction accuracies estimated with a few significantly associated SNPs were moderate-to-high, and continuously increased as more significantly associated SNPs were included. It confirmed that TSC resistance could be furtherly improved by implementing GS for selecting multiple stable genomic regions simultaneously, or by implementing MAS and GS stepwise. The factors of marker density, marker quality, and heterozygosity rate of samples had minor effects on the estimation of the genomic prediction accuracy. The training set size, the genetic relationship between training and prediction sets, phenotypic and genotypic diversity of the training sets, and incorporating known trait-marker associations played more important roles in improving prediction accuracy. The result of the present study provides insight into less complex trait improvement via GS in maize.