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Southern corn rust (SCR) caused by Puccinia polysora Underw is a major disease leading to severe yield losses in China Summer Corn Belt. Using six multi-locus GWAS methods, we identified a set of SCR resistance QTNs from a diversity panel of 140 inbred lines collected from China Summer Corn Belt. Thirteen QTNs on chromosomes 1, 2, 4, 5, 6, and 8 were grouped into three types of allele effects and their associations with SCR phenotypes were verified by post-GWAS case-control sampling, allele/haplotype effect analysis. Relative resistance (RRR) and relative susceptibility (RRs) catering to its inbred carrier were estimated from single QTN and QTN-QTN combos and epistatitic effects were estimated for QTN-QTN combos. By transcriptomic annotation, a set of candidate genes were predicted to be involved in transcriptional regulation (S5_145, Zm00001d01613, transcription factor GTE4), phosphorylation (S8_123, Zm00001d010672, Pgk2- phosphoglycerate kinase 2), and temperature stress response (S6_164a/S6_164b, Zm00001d038806, hsp101, and S5_211, Zm00001d017978, cellulase25). The breeding implications of the above findings were discussed.

Immunoscenescence plays a key role in the initiation and development of tumors. Furthermore, immunoscenescence also impacts drug delivery and cancer therapeutic efficacy. To reduce the impact of immunosenescence on anti-tumor therapy, this experimental plan aimed to use neutrophils with tumor tropism properties to deliver sialic acid (SA)-modified liposomes into the tumor, kill tumor cells via SA-mediated photochemotherapy, enhance infiltration of neutrophils into the tumor, induce immunogenic death of tumor cells with chemotherapy, enhance infiltration of CD8+ T cells into the tumor-draining lymph nodes and tumors of immunosenescent mice, and achieve SA-mediated photochemotherapy. We found that CD8+ T cell and neutrophil levels in 16-month-old mice were significantly lower than those in 2- and 8-month-old mice; 16-month-old mice exhibited immunosenescence. The anti-tumor efficacy of SA-mediated non-photochemotherapy declined in 16-month-old mice, and tumors recurred after scabbing. SA-mediated photochemotherapy enhanced tumor infiltration by CD8+ T cells and neutrophils, induced crusting and regression of tumors in 8-month-old mice, inhibited metastasis and recurrence of tumors and eliminated the immunosenescence-induced decline in antitumor therapeutic efficacy in 16-month-old mice via the light-heat-chemical-immunity conversion.

Abstract Lysine-ε-acetylation (Kac) is a reversible post-translational modification that plays important roles during plant-pathogen interactions. Some pathogens can deliver secreted effectors encoding acetyltransferases or deacetylases into host cell to directly modify acetylation of host proteins. However, the function of these acetylated host proteins in plant-pathogen defense remains to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein abundance and lysine acetylation changes in maize infected with Puccinia polysora (P. polysora) at 0 h, 12 h, 24 h, 48 h and 72 h. A total of 7412 Kac sites from 4697 proteins were identified, and 1732 Kac sites from 1006 proteins were quantified. Analyzed the features of lysine acetylation, we found that Kac is ubiquitous in cellular compartments and preferentially targets lysine residues in the -F/W/Y-X-X-K (ac)-N/S/T/P/Y/G- motif of the protein, this Kac motif contained proteins enriched in basic metabolism and defense-associated pathways during fungal infection. Further analysis of acetylproteomics data indicated that maize regulates cellular processes in response to P. polysora infection by altering Kac levels of histones and non-histones. In addition, acetylation of pathogen defense-related proteins presented converse patterns in signaling transduction, defense response, cell wall fortification, ROS scavenging, redox reaction and proteostasis. Our results provide informative resources for studying protein acetylation in plant-pathogen interactions, not only greatly extending the understanding on the roles of acetylation in vivo, but also providing a comprehensive dynamic pattern of Kac modifications in the process of plant immune response.

Abstract Background The aim of our study was to evaluate the curative effect and safety of stereotactic body radiation therapy (SBRT) in treating hepatocellular carcinoma (HCC) patients with inferior vena cava (IVCTT) and right atrial tumor thrombus (RATT). Methods This retrospective study included fifteen advanced HCC patients with IVCTT and RATT who were treated with SBRT between 2013 and 2020. The prescribed dose delivered to the tumor was 45–50 Gy/7–10 fx. We report their treatment responses according to survival time and toxicities. Results For these patients, the median follow-up time was 15 months (2–52 months). Local tumor control rates of the treated area were 80% at the time of death or at the last follow-up. The 6-month, 12-month, 18-month and 24-month OS rates were 80.0%, 60.0%, 33.3% and 26.7%, respectively. None of these patients died from the toxicity outcomes and complications of SBRT. Conclusion SBRT is an effective option for advanced HCC patients with IVCTT and RATT.

Abstract Background Maize kernel row number (KRN) is one of the most important yield traits and has changed greatly during maize domestication and selection. Elucidating the genetic basis of KRN will be helpful to improve grain yield in maize. Results Here, we measured KRN in four environments using a nested association mapping (NAM) population named HNAU-NAM1 with 1,617 recombinant inbred lines (RILs) that were derived from 12 maize inbred lines with a common parent, GEMS41. Then, five consensus quantitative trait loci (QTLs) distributing on four chromosomes were identified in at least three environments along with the best linear unbiased prediction (BLUP) values by the joint linkage mapping (JLM) method. These QTLs were further validated by the separate linkage mapping (SLM) and genome-wide association study (GWAS) methods. Three KRN genes cloned through the QTL assay were found in three of the five consensus QTLs, including qKRN1.1, qKRN2.1 and qKRN4.1. Two new QTLs of KRN, qKRN4.2 and qKRN9.1, were also identified. On the basis of public RNA-seq and genome annotation data, five genes highly expressed in ear tissue were considered candidate genes contributing to KRN. Conclusions This study carried out a comprehensive analysis of the genetic architecture of KRN by using a new NAM population under multiple environments. The present results provide solid information for understanding the genetic components underlying KRN and candidate genes in qKRN4.2 and qKRN9.1. Single-nucleotide polymorphisms (SNPs) closely linked to qKRN4.2 and qKRN9.1 could be used to improve inbred yield during molecular breeding in maize.

Southern corn rust (SCR) caused by Puccinia polysora is a major maize disease that can result in major yield loss. Here, the authors report the expression of a CC-NB-LRR type of R gene RppK results in SCR resistance in susceptible maize lines and it can recognize the effector AvrRppK produced by P. polysora.

Customised bus (CB) is a cutting-edge mean of transportation and has been implemented worldwide. To support the spread of the CB system, methodologies for CB network design have been conducted. However, a majority of them cannot be adopted directly for multi-modal transportation environment. In this paper, we proposed a bi-level programming model to fill this gap. The upper-level problem is to maximise the usage of the CB system with the limitation of operation constraints. Meanwhile, the lower-level problem is to capture the traveller’s choice by minimising traveller’s generalised cost during travel. A solving procedure via genetic algorithm is further proposed and validated via the metro data at Shanghai. The results indicated that the proposed CB route network would attract nearly 5,000 users during morning peak period under the given metro transaction data. We further studied the features of the selected routes and found that the CB network mainly served residence to commercial or industrial parks travellers and would provide travel service with fewer stops, and higher travel efficiency by travelling through expressway.

Didymella leaf blight (DLB) caused by Didymella glomerata is a new fungal disease of maize (Zea mays), first detected in 2021 in Panjin, Liaoning province of China. Here we report the reference genome assembly of D. glomerata to unravel how the fungal pathogen controls its virulence on maize at the molecular level. A maize-infecting strain Pj-2 of the pathogen was sequenced on the Illumina NovaSeq 6000 and PacBio Sequel II platforms at a 575-fold genomic coverage. The 33.17 Mb gapless genome assembly comprises 32 scaffolds with L/N50 of 11/1.36 Mb, four of which represent full-length chromosomes. The Pj-2 genome is predicted to contain 10,334 protein-coding genes, of which 211, 12 and 134 encode effector candidates, secondary metabolite backbone-forming enzymes and CAZymes, respectively. Some of these genes are potentially implicated in niche adaptation and expansion, such as colonizing new hosts like maize. Phylogenomic analysis of eight strains of six Didymella spp., including three sequenced strains of D. glomerata, reveals that the maize (Pj-2)- and Chrysanthemum (CBS 528.66)-infecting strains of D. glomerata are genetically similar (sharing 92.37% genome with 98.89% identity), whereas Pj-2 shows truncated collinearity with extensive chromosomal rearrangements with the Malus-infecting strain M27-16 of D. glomerata (sharing only 55.01% genome with 88.20% identity). Pj-2 and CBS 528.66 carry four major reciprocal translocations in their genomes, which may enable them to colonize the different hosts. Furthermore, germplasm screening against Pj-2 led to the identification of three sources of DLB resistance in maize, including a tropical inbred line CML496. DLB resistance in the line is attributed to the accumulation of ROS H2O2 in the apoplastic space of the infected cells, which likely restricts the fungal growth and proliferation.

Abstract The leaf angle (LA), plant height (PH), and ear height (EH) are key plant architectural traits influencing maize (Zea mays L.) yield. However, their genetic determinants have not yet been well‐characterized. Here, we developed a maize advanced backcross‐nested association mapping population in Henan Agricultural University (HNAU‐NAM1) comprised of 1,625 BC1F4/BC2F4 lines. These were obtained by crossing a diverse set of 12 representative inbred lines with the common GEMS41 line, which were then genotyped using the MaizeSNP9.4K array. Genetic diversity and phenotypic distribution analyses showed considerable levels of genetic variation. We obtained 18–88 quantitative trait loci (QTLs) associated with LA, PH, and EH by using three complementary mapping methods, named as separate linkage mapping, joint linkage mapping, and genome‐wide association studies. Our analyses enabled the identification of ten QTL hot‐spot regions associated with the three traits, which were distributed on nine different chromosomes. We further selected 13 major QTLs that were simultaneously detected by three methods and deduced the candidate genes, of which eight were not reported before. The newly constructed HNAU‐NAM1 population in this study will further broaden our insights into understanding of genetic regulation of plant architecture, thus will help to improve maize yield and provide an invaluable resource for maize functional genomics and breeding research.

Abstract Background Next generation sequencing (NGS) has been widely used in biological research, due to its rapid decrease in cost and increasing ability to generate data. However, while the sequence generation step has seen many improvements over time, the library preparation step has not, resulting in low-efficiency library preparation methods, especially for the most time-consuming and labor-intensive steps: size-selection and quantification. Consequently, there can be bottlenecks in projects with large sample cohorts. Results We have described the all-in-one sequencing (AIO-seq) method, where instead of performing size-selection and quantification for samples individually, one sample one tube, up to 116 samples are pooled and analyzed in a single tube, ‘All-In-One’. The AIO-seq method pools libraries based on the samples’ expected data yields and the calculated concentrations of the size selected regions (target region), which can easily be obtained with the Agilent 2100 Bioanalyzer and Qubit Fluorometer. AIO-seq was applied to whole genome sequencing and RNA-seq libraries successfully, and it is envisaged that it could be applied to any type of NGS library, such as chromatin immunoprecipitation coupled with massively parallel sequencing, assays for transposase-accessible chromatin with high-throughput sequencing, and high-throughput chromosome conformation capture. We also demonstrated that for genetic population samples with low coverage sequences, like recombinant inbred lines (RIL), AIO-seq could be further simplified, by mixing the libraries immediately after PCR, without calculating the target region concentrations. Conclusions The AIO-seq method is thus labor saving and cost effective, and suitable for projects with large sample cohorts, like those used in plant breeding or population genetics research.

Abstract Background Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned. Result To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. As a result, a total of 10 QTL were identified by linkage mapping under four environments, which were located on six chromosomes and explained 1.0–7.1% of the phenotypic variation. Epistatic mapping detected four pairs of QTL that showed significant epistasis effects, explaining 2.1–3.0% of the phenotypic variation. Additionally, 18 single nucleotide polymorphisms (SNPs) were identified across the whole genome by genome-wide association study (GWAS) under five environments. Compared linkage and association mapping revealed five common intervals located on chromosomes 3, 4, and 5 associated with FER resistance, four of which were verified in different near-isogenic lines (NILs) populations. GWAS identified three candidate genes in these consistent intervals, which belonged to the Glutaredoxin protein family, actin-depolymerizing factors (ADFs), and AMP-binding proteins. In addition, two verified FER QTL regions were found consistent with Fusarium cob rot (FCR) and Fusarium seed rot (FSR). Conclusions These results revealed that multi pathways were involved in FER resistance, which was a complex trait that was controlled by multiple genes with minor effects, and provided important QTL and genes, which could be used in molecular breeding for resistance.

Abstract Background To explore the association between biologically effective dose (BED) and survival rates in Child-Pugh A classification (CP-A) small hepatocellular carcinoma (HCC) patients treated with stereotactic body radiation therapy (SBRT). Methods This retrospective study included 108 small HCC patients who were treated with SBRT between 2011 and 2014. The prescribed dose delivered to the tumor were 48Gy/8f, 49Gy/7f, 50Gy/5f and 54Gy/6f. The median biologically effective dose (BED10) of the total prescribed dose was 100Gy (76.8–102.6Gy). Factors associated with the survival rate were examined using the Cox proportion hazards model, and the factors associated with radiation-induced liver injury (RILD) were examined by logistic regression analysis. Results For these patients, the median follow-up time was 42 months (6–77 months), and the 1-, 2- and 3-year overall survival (OS) rates were 96.3, 89.8 and 80.6%, respectively. The 1-, 2- and 3-year progression-free survival (PFS) rates were 85.2, 70.1 and 60.6%, respectively. The 1-, 2- and 3-year local control (LC) rates were 98.1, 96.2 and 95.1%, respectively. The 1-, 2- and 3-year distant metastasis- free survival (DMFS) rates were 86.1, 72.8 and 61.2%. The OS, PFS and DMFS were significantly higher in the BED10 ≥ 100Gy group than in the BED10

Abstract Southern corn rust (SCR), which is caused by the fungal pathogen Puccinia polysora Underw, is a prevalent foliar disease in maize. Breeding for resistant cultivars is a desirable way for the efficient control of this disease. To identify quantitative trait loci (QTL) for conferring resistance to SCR, a recombinant inbred population including 138 lines (RILs) derived from the SCR‐resistant line CML496 and susceptible line Lx9801 was evaluated for phenotypic reaction to SCR in three trials in two locations over 2 years. The population was genotyped with the maize 9.4K SNP Genotyping Array marker platform. A total of 3 QTL were mapped on chromosomes 6, 9 and 10, respectively. One major QTL on chromosome 10 (bin 10.00/10.01), RppCML496, was consistently detected across environments, which explained 43–78% of the total phenotypic variation. Using a fine mapping strategy, we delimited RppCML496 to an interval of 128 Kb. Genome mining of this region suggests two candidate genes, and a NBS‐LRR gene is the promising one for RppCML496 against SCR. The tightly linked molecular markers developed in this study can be used for molecular breeding of resistance to SCR in maize.

Maize (Zea mays), also called corn, is one of the top three staple food crops worldwide and is also utilized as feed (e.g., feed grain and silage) and a source of biofuel (e.g., bioethanol). Maize production is hampered by a myriad of factors, including although not limited to fungal diseases, which reduce grain yield and downgrade kernel quality. One such disease is anthracnose leaf blight and stalk rot (ALB and ASR) caused by the hemibiotrophic fungal pathogen Colletotrichum graminicola. The pathogen deploys a biphasic infection strategy to colonize susceptible maize genotypes, comprising latent (symptomless) biotrophic and destructive (symptomatic) necrotrophic phases. However, the resistant maize genotypes restrict the C. graminicola infection and in planta fungal proliferation during the biotrophic phase of the infection. Some studies on the inheritance of ASR resistance in the populations derived from biparental resistant and susceptible genotypes reveal that anthracnose is likely a gene-for-gene disease in which the resistant maize genotypes and C. graminicola recognize each other by their matching pairs of nucleotide-binding leucine-rich repeat resistance (NLR) proteins (whose coding genes are localized in disease QTL) and effectors (1–2 effectors/NLR) during the biotrophic phase of infection. The Z. mays genome encodes approximately 144 NLRs, two of which, RCg1 and RCg1b, located on chromosome 4, were cloned and functionally validated for their role in ASR resistance. Here, we discuss the genetic architecture of anthracnose resistance in the resistant maize genotypes, i.e., disease QTL and underlying resistance genes. In addition, this review also highlights the disease cycle of C. graminicola and molecular factors (e.g., virulence/pathogenicity factors such as effectors and secondary metabolites) that contribute to the pathogen’s virulence on maize. A detailed understanding of molecular genetics underlying the maize—C. graminicola interaction will help devise effective management strategies against ALB and ASR.

In preclinical studies of young mice, nanoparticles showed excellent anti-tumor therapeutic effects by harnessing Peripheral Blood Monocytes (PBMs) and evading the immune system. However, the changes of age will inevitably affect PBMs and the immune system, and there is a serious lack of relevant research. Sialic acid (SA)-octadecylamine (ODA) was synthesized, and SA- or polyethylene glycol (PEG)-modified epirubicin (EPI) liposomes (EPI-SL and EPI-PL, respectively) were prepared to explore differences in antitumor treatment using 8-month-old and 8-week-old Kunming mice. Based on presented data, 8-month-old mice had more PBMs in peripheral blood than 8-week-old mice, and age differences resulted in different anti-tumor treatment effects following EPI-SL and EPI-PL treatment. Following EPI-PL administration, the tumor volume was significantly smaller in 8-week-old mice than in 8-month-old mice (* p < 0.05). Eight-month-old mice treated with EPI-SL (8M-SL) presented no damage to healthy tissue, with a 100% survival rate, and 50% mice in 8M-SL showed ‘shedding’ of tumor tissues from the growth site. Accordingly, 8-month-old mice treated with EPI-SL achieved the best therapeutic effect at different ages and with different liposomes. EPI-SL could improve the antitumor effect of 8-week-old and 8-month-old mice.

Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.

Ear length (EL) is an important trait in maize ( L.) because it is positively correlated with grain yield. To understand the genetic basis of natural EL variation, a F, a four-way cross and a genome-wide association study (GWAS) population were used to identify the quantitative trait loci (QTLs) and candidate EL genes. Linkage mapping identified 14 QTLs in two types of populations from multiple environments. Six of them were located in three common genomic regions considered “stable QTLs”. Candidate genes for the three stable QTLs were identified by the GWAS results. These were related to auxin transport, cell proliferation, and developmental regulation. These results confirm that maize EL is under strong genetic control by many small-effect genes. They also improve our understanding of the genetic basis of maize EL.

Barren tip on corn ear is an important agronomic trait in maize, which is highly associated with grain yield. Understanding the genetic basis of tip-barrenness may help to reduce the ear tip-barrenness in breeding programs. In this study, ear tip-barrenness was evaluated in two environments in a F2:3 population, and it showed significant genotypic variation for ear tip-barrenness in both environments. Using mixed-model composite interval mapping method, three additive effects quantitative trait loci (QTL) for ear tip-barrenness were mapped on chromosomes 2, 3 and 6, respectively. They explained 16.6% of the phenotypic variation, and no significant QTL × Environment interactions and digenic interactions were detected. The results indicated that additive effect was the main genetic basis for ear tip-barrenness in maize. This is the first report of QTL mapped for ear tip-barrenness in maize.

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed.

Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20-30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R2 = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.