Identification of the coexisting virus-derived siRNA in maize and rice infected by rice black-streaked dwarf virus

Rice black-streaked dwarf virus is transmitted by small brown planthoppers, which causes maize rough dwarf disease and rice black-streaked dwarf disease. This virus leads to slow growth or death of the host plants. During the co-evolutionary arms race between viruses and plants, virus-derived small interfering RNAs challenge the plant's defense response and inhibit host immunity through the RNA silencing system. However, it is currently unknown if rice black-streaked dwarf virus can produce the same small interfering RNAs to mediate the RNA silencing in different infected species. In this study, four small RNA libraries and four degradome libraries were constructed by extracting total RNAs from the leaves of the maize (Zea mays) inbred line B73 and japonica rice (Oryza sativa) variety Nipponbare exposed to feeding by viruliferous and non-viruliferous small brown planthoppers. We analyzed the characteristics of small RNAs and explored virus-derived small interfering RNAs in small RNA libraries through high-throughput sequencing. On analyzing the characteristics of small RNA, we noted that the size distributions of small RNAs were mainly 24-nt (19.74%-62.00%), whereas those of virus-derived small interfering RNAs were mostly 21-nt (41.06%-41.87%) and 22-nt (39.72%-42.26%). The 5'-terminal nucleotides of virus-derived small interfering RNAs tended to be adenine or uracil. Exploring the distribution of virus-derived small interfering RNAs hot spots on the viral genome segments revealed that the frequency of hot spots in B73 was higher than those in Nipponbare. Meanwhile, hotspots in the S9 and S10 virus genome segments were distributed similarly in both hosts. In addition, the target genes of small RNA were explored by degradome sequencing. Analyses of the regulatory pathway of these target genes unveiled that viral infection affected the ribosome-related target genes in maize and target genes in metabolism and biosynthesis pathways in rice. Here, 562 and 703 virus-derived small interfering RNAs were separately obtained in maize and rice, and 73 virus-derived small interfering RNAs named as co-vsiRNAs were detected in both hosts. Stem-loop PCR and RT-qPCR confirmed that co-vsiRNA 3.1 and co-vsiRNA 3.5 derived from genome segment S3 simultaneously play a role in maize and rice and inhibited host gene expression. The study revealed that rice black-streaked dwarf virus can produce the same small interfering RNAs in different species and provides a new direction for developing the new antiviral strategies.

Convolutional LSTM model for cine image prediction of abdominal motion

Objective.In this study, we tackle the challenge of latency in magnetic resonance linear accelerator (MR-Linac) systems, which compromises target coverage accuracy in gated real-time radiotherapy. Our focus is on enhancing motion prediction precision in abdominal organs to address this issue. We developed a convolutional long short-term memory (convLSTM) model, utilizing 2D cine magnetic resonance (cine-MR) imaging for this purpose.Approach.Our model, featuring a sequence-to-one architecture with six input frames and one output frame, employs structural similarity index measure (SSIM) as loss function. Data was gathered from 17 cine-MRI datasets using the Philips Ingenia MR-sim system and an Elekta Unity MR-Linac equivalent sequence, focusing on regions of interest (ROIs) like the stomach, liver, pancreas, and kidney. The datasets varied in duration from 1 to 10 min.Main results.The study comprised three main phases: hyperparameter optimization, individual training, and transfer learning with or without fine-tuning. Hyperparameters were initially optimized to construct the most effective model. Then, the model was individually applied to each dataset to predict images four frames ahead (1.24-3.28 s). We evaluated the model's performance using metrics such as SSIM, normalized mean square error, normalized correlation coefficient, and peak signal-to-noise ratio, specifically for ROIs with target motion. The average SSIM values achieved were 0.54, 0.64, 0.77, and 0.66 for the stomach, liver, kidney, and pancreas, respectively. In the transfer learning phase with fine-tuning, the model showed improved SSIM values of 0.69 for the liver and 0.78 for the kidney, compared to 0.64 and 0.37 without fine-tuning.Significance. The study's significant contribution is demonstrating the convLSTM model's ability to accurately predict motion for multiple abdominal organs using a Unity-equivalent MR sequence. This advancement is key in mitigating latency issues in MR-Linac radiotherapy, potentially improving the precision and effectiveness of real-time treatment for abdominal cancers.

Gene pyramiding of ZmGLK36 and ZmGDIα-hel for rough dwarf disease resistance in maize

Maize rough dwarf disease (MRDD) caused by pathogenic viruses in the genus Fijivirus in the family Reoviridae is one of the most destructive diseases in maize. The pyramiding of effective resistance genes into maize varieties is a potential approach to reduce the damage resulting from the disease. Two major quantitative trait loci (QTLs) (qMrdd2 and qMrdd8) have been previously identified. The resistance genes ZmGLK36 and ZmGDIα-hel have also been cloned with the functional markers Indel-26 and IDP25K, respectively. In this study, ZmGLK36 and ZmGDIα-hel were introgressed to improve MRDD resistance of maize lines (Zheng58, Chang7-2, B73, Mo17, and their derived hybrids Zhengdan958 and B73 × Mo17) via marker-assisted selection (MAS). The converted lines and their derived hybrids, carrying one or two genes, were evaluated for MRDD resistance using artificial inoculation methods. The double-gene pyramiding lines and their derived hybrids exhibited increased resistance to MRDD compared to the monogenic lines and the respective hybrids. The genetic backgrounds of the converted lines were highly similar (90.85-98.58%) to the recurrent parents. In addition, agronomic trait evaluation demonstrated that pyramiding lines with one or two genes and their derived hybrids were not significantly different from the recurrent parents and their hybrids under nonpathogenic stress, including period traits (tasseling, pollen shedding, and silking), yield traits (ear length, grain weight per ear and 100-kernel weight) and quality traits (protein and starch content). There were differences in plant architecture traits between the improved lines and their hybrids. This study illustrated the successful development of gene pyramiding for improving MRDD resistance by advancing the breeding process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01466-9.

The maize PLASTID TERMINAL OXIDASE (PTOX) locus controls the carotenoid content of kernels

Carotenoids perform a broad range of important functions in humans; therefore, carotenoid biofortification of maize (Zea mays L.), one of the most highly produced cereal crops worldwide, would have a global impact on human health. PLASTID TERMINAL OXIDASE (PTOX) genes play an important role in carotenoid metabolism; however, the possible function of PTOX in carotenoid biosynthesis in maize has not yet been explored. In this study, we characterized the maize PTOX locus by forward- and reverse-genetic analyses. While most higher plant species possess a single copy of the PTOX gene, maize carries two tandemly duplicated copies. Characterization of mutants revealed that disruption of either copy resulted in a carotenoid-deficient phenotype. We identified mutations in the PTOX genes as being causal of the classic maize mutant, albescent1. Remarkably, overexpression of ZmPTOX1 significantly improved the content of carotenoids, especially β-carotene (provitamin A), which was increased by ~threefold, in maize kernels. Overall, our study shows that maize PTOX locus plays an important role in carotenoid biosynthesis in maize kernels and suggests that fine-tuning the expression of this gene could improve the nutritional value of cereal grains.

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.

Systematic Review of Psychiatric Observation Units and Their Impact on Emergency Department Boarding

Objective: To investigate the effectiveness of acute short-stay hospital admissions in psychiatric observation units for improving the flow of patients with mental health presentations through the emergency department (ED).

Data Sources: CINAHL, MEDLINE, OVID, PsycINFO, PubMed, Web of Science, and Google Scholar were systematically searched for English-language studies from 1990 onward. Descriptors used to describe psychiatric observation units were identified, and in databases with MESH term availability, the terms "mental disorder" and "emergency services, psychiatric" were also utilized to further enhance the search.

Study Selection: A total of 6,571 studies were screened. The PICOS framework was used to determine the inclusion and exclusion criteria, and the process of study selection followed PRISMA guidelines. Articles were included if the unit studied had a length of stay (LOS) < 72 hours and if patients suffered from a mental health condition and were treated as hospital inpatients.

Data Extraction: Reviewers performed data extraction and quality assessment of the included studies following the review protocol.

Results: A total of 14 psychiatric observation unit studies were included in the review: 5 in North America and 9 in Australia. Most of these units were in large urban general hospitals. There appears to be some improvement in ED LOS for patients with mainly crisis mental health presentations. Seven of the 14 studies specifically discussed ED LOS, and 6 of these studies showed mild to moderate improvement in ED LOS, ranging from 17 minutes to > 11 hours.

Conclusions: Psychiatric observation units were mainly located in North American and Australian settings. These units may reduce ED LOS based on limited, poor-quality evidence. Further research is required to determine whether psychiatric observation units have ongoing effects on ED LOS and alleviate access block.

Prim Care Companion CNS Disord 2023;25(6):22r03468.

Author affiliations are listed at the end of this article.

Genome-Wide Characterization of the Maize (Zea mays L.) WRKY Transcription Factor Family and Their Responses to Ustilago maydis

Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens.

Dose Constraints and Planning Considerations for Thoracic Radiation Therapy: Delphi Consensus from a National Survey of Experts

PURPOSE/OBJECTIVE(S)

Many physicians refer to trial protocols or published guidelines (NCCN, QUANTEC, HyTEC) for dose-volume histogram (DVH) metrics. However, there may be variation in implementing these metrics during plan optimization. Some studies have suggested better outcomes for patients treated at high-volume, high-expertise centers. These differences may in part be due to greater standardization or center-specific treatment planning processes. We surveyed radiation oncologists with stated thoracic-specific expertise using the Delphi method to formulate consensus DVH metrics that would be considered ideal for high-quality radiation treatment plans.

MATERIALS/METHODS

Thoracic radiation oncology experts were identified using departmental websites of ACGME-accredited radiation oncology programs. After confirming their expertise, panelists were invited to submit their institutional templates and complete three rounds of questions related to normal organ dose constraints, target coverage metrics, prescribing practices, and other planning considerations. Queried radiation schemes included conventional fractionation, twice-daily fractionation, and stereotactic body radiation therapy (3 and 5 fractions). Preliminary consensus statements were generated using median values for DVH metrics and were iteratively refined in subsequent surveys. Consensus was pre-defined as ≥75% agreement among panelists.

RESULTS

A total of 194 experts were invited, and 100 agreed to participate. The panel was 28% female and included experts from 29 states with a median of 11 years of clinical experience (IQR 6-19). 89% specialized in 1-2 disease sites. Response rates for the Demographics, round 1, 2, and 3 surveys were 83%, 78%, 57%, and 55%, respectively. 93% of panelists believed that DVH metrics should provide thresholds for both optimal and acceptable criteria for treatment planning. 49 of the 96 proposed normal tissue dose constraint statements were iterated to consensus (Table 1), and 5 of 7 proposed target coverage metric statements achieved consensus.

CONCLUSION

This study highlights the heterogeneity in metrics used by thoracic radiation oncologists and provides levels of consensus on ideal and acceptable dose constraints as guidance for treatment planning. Future directions include using these statements to develop prescription templates and acceptance criteria for treatment planning systems for widespread use as well as extending this Delphi approach to additional disease sites.

A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops

Maize rough dwarf disease (MRDD), caused by maize rough dwarf virus (MRDV) or rice black-streaked dwarf virus (RBSDV), seriously threatens worldwide production of all major cereal crops, including maize, rice, wheat and barley. Here we report fine mapping and cloning of a previously reported major quantitative trait locus (QTL) (qMrdd2) for RBSDV resistance in maize. Subsequently, we show that qMrdd2 encodes a G2-like transcription factor named ZmGLK36 that promotes resistance to RBSDV by enhancing jasmonic acid (JA) biosynthesis and JA-mediated defence response. We identify a 26-bp indel located in the 5' UTR of ZmGLK36 that contributes to differential expression and resistance to RBSDV in maize inbred lines. Moreover, we show that ZmDBF2, an AP2/EREBP family transcription factor, directly binds to the 26-bp indel and represses ZmGLK36 expression. We further demonstrate that ZmGLK36 plays a conserved role in conferring resistance to RBSDV in rice and wheat using transgenic or marker-assisted breeding approaches. Our results provide insights into the molecular mechanisms of RBSDV resistance and effective strategies to breed RBSDV-resistant cereal crops.

Evolutionary Analysis of Respiratory Burst Oxidase Homolog (RBOH) Genes in Plants and Characterization of ZmRBOHs

The respiratory burst oxidase homolog (RBOH), as the key producer of reactive oxygen species (ROS), plays an essential role in plant development. In this study, a bioinformatic analysis was performed on 22 plant species, and 181 RBOH homologues were identified. A typical RBOH family was identified only in terrestrial plants, and the number of RBOHs increased from non-angiosperms to angiosperms. Whole genome duplication (WGD)/segmental duplication played a key role in RBOH gene family expansion. Amino acid numbers of 181 RBOHs ranged from 98 to 1461, and the encoded proteins had molecular weights from 11.1 to 163.6 kDa, respectively. All plant RBOHs contained a conserved NADPH_Ox domain, while some of them lacked the FAD_binding_8 domain. Plant RBOHs were classified into five main subgroups by phylogenetic analysis. Most RBOH members in the same subgroup showed conservation in both motif distribution and gene structure composition. Fifteen ZmRBOHs were identified in maize genome and were positioned in eight maize chromosomes. A total of three pairs of orthologous genes were found in maize, including ZmRBOH6/ZmRBOH8, ZmRBOH4/ZmRBOH10 and ZmRBOH15/ZmRBOH2. A Ka/Ks calculation confirmed that purifying selection was the main driving force in their evolution. ZmRBOHs had typical conserved domains and similar protein structures. cis-element analyses together with the expression profiles of the ZmRBOH genes in various tissues and stages of development suggested that ZmRBOH was involved in distinct biological processes and stress responses. Based on the RNA-Seq data and qRT-PCR analysis, the transcriptional response of ZmRBOH genes was examined under various abiotic stresses, and most of ZmRBOH genes were up-regulated by cold stress. These findings provide valuable information for further revealing the biological roles of ZmRBOH genes in plant development and abiotic stress responses.

Artificial Intelligence-Assisted Evaluation of the Spatial Relationship between Brain Arteriovenous Malformations and the Corticospinal Tract to Predict Postsurgical Motor Defects

BACKGROUND AND PURPOSE

Preoperative evaluation of brain AVMs is crucial for the selection of surgical candidates. Our goal was to use artificial intelligence to predict postsurgical motor defects in patients with brain AVMs involving motor-related areas.

MATERIALS AND METHODS

Eighty-three patients who underwent microsurgical resection of brain AVMs involving motor-related areas were retrospectively reviewed. Four artificial intelligence-based indicators were calculated with artificial intelligence on TOF-MRA and DTI, including FN5mm/50mm (the proportion of fiber numbers within 5-50mm from the lesion border), FN10mm/50mm (the same but within 10-50mm), FP5mm/50mm (the proportion of fiber voxel points within 5-50mm from the lesion border), and FP10mm/50mm (the same but within 10-50mm). The association between the variables and long-term postsurgical motor defects was analyzed using univariate and multivariate analyses. Least absolute shrinkage and selection operator regression with the Pearson correlation coefficient was used to select the optimal features to develop the machine learning model to predict postsurgical motor defects. The area under the curve was calculated to evaluate the predictive performance.

RESULTS

In patients with and without postsurgical motor defects, the mean FN5mm/50mm, FN10mm/50mm, FP5mm/50mm, and FP10mm/50mm were 0.24 (SD, 0.24) and 0.03 (SD, 0.06), 0.37 (SD, 0.27) and 0.06 (SD, 0.08), 0.06 (SD, 0.10) and 0.01 (SD, 0.02), and 0.10 (SD, 0.12) and 0.02 (SD, 0.05), respectively. Univariate and multivariate logistic analyses identified FN10mm/50mm as an independent risk factor for long-term postsurgical motor defects (P = .002). FN10mm/50mm achieved a mean area under the curve of 0.86 (SD, 0.08). The mean area under the curve of the machine learning model consisting of FN10mm/50mm, diffuseness, and the Spetzler-Martin score was 0.88 (SD, 0.07).

CONCLUSIONS

The artificial intelligence-based indicator, FN10mm/50mm, can reflect the lesion-fiber spatial relationship and act as a dominant predictor for postsurgical motor defects in patients with brain AVMs involving motor-related areas.

Pathogenicity Variation in Two Genomes of Cercospora Species Causing Gray Leaf Spot in Maize

The gray leaf spots caused by Cercospora spp. severely affect the yield and quality of maize. However, the evolutionary relation and pathogenicity variation between species of the Cercospora genus is largely unknown. In this study, we constructed high-quality reference genomes by nanopore sequencing two Cercospora species, namely, C. zeae-maydis and C. zeina, with differing pathogenicity, collected from northeast (Liaoning [LN]) and southeast (Yunnan [YN]) China, respectively. The genome size of C. zeae-maydis-LN is 45.08 Mb, containing 10,839 annotated genes, whereas that of Cercospora zeina-YN is 42.18 Mb, containing 10,867 annotated genes, of which approximately 86.58% are common in the two species. The difference in their genome size is largely attributed to increased long terminal repeat retrotransposons of 3.8 Mb in total length in C. zeae-maydis-LN. There are 41 and 30 carbohydrate-binding gene subfamilies identified in C. zeae-maydis-LN and C. zeina-YN, respectively. A higher number of carbohydrate-binding families found in C. zeae-maydis-LN, and its unique CBM4, CBM37, and CBM66, in particular, may contribute to variation in pathogenicity between the two species, as the carbohydrate-binding genes are known to encode cell wall-degrading enzymes. Moreover, there are 114 and 107 effectors predicted, with 47 and 46 having unique potential pathogenicity in C. zeae-maydis-LN and C. zeina-YN, respectively. Of eight effectors randomly selected for pathogenic testing, five were found to inhibit cell apoptosis induced by Bcl-2-associated X. Taken together, our results provide genomic insights into variation in pathogenicity between C. zeae-maydis and C. zeina. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genetic basis of maize kernel protein content revealed by high-density bin mapping using recombinant inbred lines

Maize with a high kernel protein content (PC) is desirable for human food and livestock fodder. However, improvements in its PC have been hampered by a lack of desirable molecular markers. To identify quantitative trait loci (QTL) and candidate genes for kernel PC, we employed a genotyping-by-sequencing strategy to construct a high-resolution linkage map with 6,433 bin markers for 275 recombinant inbred lines (RILs) derived from a high-PC female Ji846 and low-PC male Ye3189. The total genetic distance covered by the linkage map was 2180.93 cM, and the average distance between adjacent markers was 0.32 cM, with a physical distance of approximately 0.37 Mb. Using this linkage map, 11 QTLs affecting kernel PC were identified, including qPC7 and qPC2-2, which were identified in at least two environments. For the qPC2-2 locus, a marker named IndelPC2-2 was developed with closely linked polymorphisms in both parents, and when tested in 30 high and 30 low PC inbred lines, it showed significant differences (P = 1.9E-03). To identify the candidate genes for this locus, transcriptome sequencing data and PC best linear unbiased estimates (BLUE) for 348 inbred lines were combined, and the expression levels of the four genes were correlated with PC. Among the four genes, Zm00001d002625, which encodes an S-adenosyl-L-methionine-dependent methyltransferase superfamily protein, showed significantly different expression levels between two RIL parents in the endosperm and is speculated to be a potential candidate gene for qPC2-2. This study will contribute to further research on the mechanisms underlying the regulation of maize PC, while also providing a genetic basis for marker-assisted selection in the future.

Radiation Therapy Decision Making Process and Operations for COVID-19 Positive Patients

Purpose/Objective(s)

A challenging clinical dilemma during the COVID-19 pandemic is management of cancer patients who test positive for COVID. Given the need to balance the risk of disease progression with the risk of transmission to other patients and staff, radiation therapy for these patients requires careful consideration and modification of standard workflows. It is also critical to develop processes to mitigate radiation treatment interruption, which can affect patient outcomes. The objective of this study was to report the clinical operations and outcomes for COVID positive patients receiving radiation therapy during the pandemic at a tertiary cancer center including 2 network locations.

Materials/Methods

During March 2020 to March 2022, the Radiation Oncology COVID committee (RO COVID) developed an integrated process to triage patients, provide treatment recommendations, and implement infection control procedures to safely deliver radiation therapy to COVID positive patients. Policies were created for each center with multidisciplinary input from infectious disease, radiation oncology, radiation therapy, and nursing. All COVID positive patients were presented to the RO COVID group and evaluated for clinical urgency, benefit with radiation, and life expectancy. If deemed necessary, a limited planned break or hypofractionated regimen was recommended to minimize staff exposure. We conducted a retrospective review of COVID positive patients with different primary malignancies treated through the COVID positive pathway.

Results

A total of 68 COVID positive patients were treated with the COVID positive pathway (HN 15, Breast 9, CNS 8, GU 8, GYN, 7, Thoracic 6, GI 5, HEME 5, PED 3, SARC 2). The median age was 57.1 years (IQR 45.8-63.4) and 47% were female. There were 39 patients (57%) who were asymptomatic and were tested for routine pre-radiation screening or due to concerns of COVID exposure. Twenty-three (34%) patients were treated with palliative intent and 8 (12%) were treated for an emergent indication (i.e., spinal cord compression, bleeding). Thirteen (19%) patients were receiving radiation treatment, had a treatment break (7-21 days), and then resumed their radiation course. All treatments were successfully completed without known nosocomial spread of COVID to staff or other patients. Among this heterogenous group of patients, 58 (85%) were alive with a median follow up of 2 months (IQR 0.5-7.5). COVID infection may have contributed to 3 out of 10 deaths (4% of total cohort). The remaining deaths were due to progression of disease or other non-COVID causes.

Conclusion

In this study, COVID positive patients were safely treated with radiation therapy through a comprehensive decision making and clinical operations pathway taking into account evolving COVID guidelines for three different variant surges. Although limited in follow up, patient outcomes are promising with few COVID-related deaths and low overall mortality rates, even with hypofractionated regimens.

Using the dominant mutation gene Ae1-5180 (amylose extender) to develop high-amylose maize

Maize amylose is a type of high value-added starch used for medical, food, and chemical applications. Mutations in the starch branching enzyme (SBEIIb), with recessive ae (amylose extender) and dominant Ae1-5180 alleles, are the primary way to improve maize endosperm amylose content (AC). However, studies on Ae1-5180 mutation are scarce, and its roles in starch synthesis and breeding potential are unclear. We found that the AC of the Ae1-5180 mutant was 47.23%, and its kernels were tarnished and glassy and are easily distinguished from those of the wild type (WT), indicating that the dominant mutant has the classical characteristics of the ae mutant. Starch granules of Ae1-5180 became smaller, and higher in amount with irregular shape. The degree of amylopectin polymerisation changed to induce an increase in starch thermal stability. Compared with WT, the activity of granule-bound starch synthase and starch synthase was higher in early stages and lower in later stages, and other starch synthesis enzymes decreased during kernel development in the Ae1-5180 mutant. We successfully developed a marker (mu406) for the assisted selection of 17 Ae1-5180 near isogenic lines (NILs) according to the position of insertion of the Mu1 transposon in the SBEIIb promoter of Ae1-5180. JH214/Ae1-5180, CANS-1/Ae1-5180, CA240/Ae1-5180, and Z1698/Ae1-5180 have high breeding application potential with their higher AC (> 40%) and their 100-kernel weight decreased to < 25% compared to respective recurrent parents. Therefore, using the dominant Ae1-5180 mutant as a donor can detect the kernel phenotype and AC of Ae1-5180-NILs in advance, thereby accelerating the high-amylose breeding process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01323-7.

Identification of a Fusarium ear rot resistance gene in maize by QTL mapping and RNA sequencing

Fusarium ear rot (FER) caused by Fusarium verticillioides is a prevalent maize disease. To comprehensively characterize the genetic basis of the natural variation in FER resistance, a recombinant inbred line (RIL) population was used to map quantitative trait loci (QTL) for FER resistance. A total of 17 QTL were identified by linkage mapping in eight environments. These QTL were located on six chromosomes and explained 3.88-15.62% of the total phenotypic variation. Moreover, qFER1.03 had the strongest effect and accounted for 4.98-15.62% of the phenotypic variation according to analyses of multiple environments involving best linear unbiased predictions. The chromosome segment substitution lines (CSSLs) derived from a cross between Qi319 (donor parent) and Ye478 (recurrent parent) were used to verify the contribution of qFER1.03 to FER resistance. The line CL171, which harbored an introgressed qFER1.03, was significantly resistant to FER. Further fine mapping of qFER1.03 revealed that the resistance QTL was linked to insertion/deletion markers InDel 8 and InDel 2, with physical distances of 43.55 Mb and 43.76 Mb, respectively. Additionally, qFER1.03 differed from the previous resistance QTL on chromosome 1. There were three annotated genes in this region. On the basis of the RNA-seq data, which revealed the genes differentially expressed between the FER-resistant Qi319 and susceptible Ye478, GRMZM2G017792 (MPK3) was preliminarily identified as a candidate gene in the qFER1.03 region. The Pr-CMV-VIGS system was used to decrease the GRMZM2G017792 expression level in CL171 by 34-57%, which led to a significant decrease in FER resistance. Using RIL and CSSL populations combined with RNA-seq and Pr-CMV-VIGS, the candidate gene can be dissected effectively, which provided important gene resource for breeding FER-resistant varieties.

Using a high density bin map to analyze quantitative trait locis of germination ability of maize at low temperatures

Low temperatures in the spring often lead to a decline in the emergence rate and uniformity of maize, which can affect yield in northern regions. This study used 365 recombinant inbred lines (RILs), which arose from crossing Qi319 and Ye478, to identify low-temperature resistance during the germination stage by measuring eight low-temperature-related traits. The quantitative trait locis (QTLs) were mapped using R/qtl software by combining phenotypic data, and the genotyping by sequencing (GBS) method to produce a high-density genetic linkage map. Twenty QTLs were detected during QTL mapping, of which seven QTLs simultaneously detected a consistent 197.10-202.30 Mb segment on chromosome 1. The primary segment was named cQTL1-2, with a phenotypic variation of 5.18-25.96% and a physical distance of 5.2 Mb. This combines the phenotype and genotype with the identification of seven chromosome segment substitution lines (CSSLs), which were derived from Ye478*Qi319 and related to cQTL1-2. The physical distance of cQTL1-2 was reduced to approximately 1.9 Mb. The consistent meta-QTL mQTL1 was located at 619.06 cM on chromosome 1, had a genetic distance of 7.27 cM, and overlapped with cQTL1-2. This was identified by combining the results of previous QTL studies assessing maize tolerance to low temperatures at the germination stage. An assessment of the results of the RIL population, CSSLs, and mQTL1 found the consistent QTL to be LtQTL1-1. It was identified in bin1.06-1.07 at a confidence interval of between 200,400,148 and 201,775,619 bp. In this interval, qRT-PCR found that relative expression of the candidate genes GRMZM2G082630 and GRMZM2G115730 were both up-regulated in low-temperature tolerant lines and down-regulated in sensitive lines (P < 0.01).

Redefining the N-Terminal Regulatory Region of the Ca2+/H+ Antiporter CAX1 in Tomato

Calcium (Ca²⁺) is an essential plant nutrient, and Ca²⁺/H⁺ exchangers (CAXs) regulate Ca²⁺ partitioning between subcellular compartments. AtCAX1 activity is inhibited by its N-terminal regulatory region (NRR), which was initially defined as the sequence between the first two methionines. However, the accuracy of this NRR definition and the NRR regulatory mechanism remain unclear. Here, using tomato SlCAX1 as a model, we redefined the NRR of CAXs and demonstrated that our new definition is also applicable to Arabidopsis AtCAX1 and AtCAX3. The N-terminal-truncated SlCAX1 (SlCAX1^Δ39) but not the full-length SlCAX1 was active in yeast, similar to Arabidopsis AtCAX1. Characterization of slcax1 mutants generated by CRISPR-Cas9 confirmed the calcium transport ability of SlCAX1. Sequence alignment between SlCAX1, AtCAX1, AtCAX3, and the Bacillus subtilis Ca²⁺/H⁺ antiporter protein YfkE revealed that SlCAX1 does not have the 2nd methionine and YfkE does not have any amino acid residues in front of the first transmembrane domain. Truncating the amino acid residues up to the first transmembrane of SlCAX1 (SlCAX1^Δ66) further increased its activity. The same truncation had a similar effect on Arabidopsis AtCAX1 and AtCAX3. Expression of full-length SlCAX1 and SlCAX1^Δ66 in tomato plants confirmed the results. Our results suggest that SlCAX1 is critical for Ca²⁺ homeostasis and all the amino acid residues in front of the first transmembrane domain inhibit the activity of CAXs. Our redefinition of the NRR will facilitate fine-tuning of Ca²⁺ partitioning to reduce the incidence of Ca²⁺-related physiological disorders in crops.

Fine-tuning shoot meristem size to feed the world

In order to maintain food security for the world's growing population, crop yields need to be significantly improved. Domestication and crop improvement involve modification of traits such as fruit size and seed number to optimize productivity. Although these traits are selected at the mature stage, they are determined during the development of shoot meristem, a tissue that forms successive meristems and reproductive organs that make edible fruits or seeds. Therefore, the architecture of reproductive organs and yield-related traits are determined during the maturation of shoot meristem. Here, we highlight recent progress in understanding how shoot meristem size affects yield-related traits and outline the strategies to fine-tune meristem regulatory genes to meet the demands of a growing population and promote sustainable agriculture.