Maize Near-isogenic Lines Research Articles

RETRACTION: Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines.

L. Morales, A. C. Repka, K. L. Swarts, W. C. Stafstrom, Y. He, S. M. Sermons, Q. Yang, L. O. Lopez-Zuniga, E.Rucker, W. E. Thomason, R. J. Nelson, P. J. Balint-Kurti. "Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines," The Plant Journal 103, no. 3 (2020): 1246-1255. https://doi.org/10.1111/tpj.14787. The above article, published online on 29 April 2020, in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors; the journal Editor-in-Chief, Katherine Denby; Society for Experimental Biology (SEB); and John Wiley & Sons Ltd. The retraction has been agreed following a report submitted by the authors indicating that the imputation of genotypes outlined in the article caused errors in the reported positions of introgressions in the lines. The authors also declared that some of the pedigree information is inaccurate. As a result, all authors agree that the paper must be retracted. The authors have stated their intention to publish a corrected report with improved analyses of introgression positions.

Management and rhizosphere microbial associations modulate genetic-driven nitrogen fate

The interplay between plant genotype and nutrient management affects rhizodeposition, which in turn modulates the rhizosphere-microbiome and microbe-mediated functions. Substituting mineral nitrogen (N) with an N-fixing inoculant reduces reliance on N fertilizer while supplying N to crops. We evaluated the effectiveness of integrating maize near-isogenic lines (NIL 1 and NIL 2) with the biological nitrification inhibition (BNI) trait into management practices aimed at optimizing N provisioning. Management strategies included mineral N inputs (0 and 67 kg ha⁻¹) with and without an N-fixing inoculant. Our approach synthesized insights from amplicon sequencing data and evaluated nitrification rates, rhizosphere N content, maize N uptake, and N use efficiency (NUE). Genotypes and management structured prokaryotic communities, while the developmental stages of genotypes further refined both fungal and prokaryotic communities. The N-fixing inoculant increased N availability, triggering the BNI capacity without increasing the nitrification rate. This was reflected in lower NO₃⁻ and higher NH₄⁺ levels in BNI-NIL leachate compared to B73, suggesting improved N retention. NIL2, characterized by distinct fungal biomarkers, exhibited higher N content (72.3 kg ha⁻¹) and superior NUE compared to NIL1 (65.0 kg ha⁻¹). NIL2’s enhanced N uptake was associated with a robust microbial network, featuring Archangium (prokaryote) and Trichoderma (eukaryote) as keystone taxa. Notably, Archangium was linked to rhizosphere N dynamics Synergizing BNI with diazotroph inoculants reduces N fertilizer reliance and increases maize N supply for sustainable agroecosystems.

Maize near-isogenic lines with enhanced flavonoids alleviated dextran sodium sulfate-induced murine colitis via modulation of the gut microbiota.

The rising incidence of inflammatory bowel disease (IBD) has necessitated the search for safe and effective novel therapeutic strategies. Dietary flavonoids exhibited antioxidant, antiproliferative, and anticarcinogenic activities in several model systems with proven abilities to reduce inflammation and oxidative stress, thus they could be promising therapeutic agents for IBD prevention/treatment. However, understanding the role of a specific class of compounds in foods that promote health is difficult because of the chemically complex food matrices. This study aimed to utilize four maize near-isogenic lines to determine the anti-colitis effects of specific classes of flavonoids, anthocyanins and/or phlobaphenes, in a whole-food matrix. Results showed that the intake of anthocyanin and phlobaphene-enriched maize diets effectively alleviated dextran sodium sulfate (DSS)-induced colitis in mice via reducing the intestinal permeability and restoring the barrier function. Anthocyanin diets were more effective in maintaining the crypt structure and muc2 protein levels and reducing inflammation. Bacterial communities of mice consuming diets enriched with anthocyanins and phlobaphenes were more similar to the healthy control compared to the DSS control group, suggesting the role of flavonoids in modulating the gut microbiota to retrieve intestinal homeostasis. Microbiota depletion rendered these compounds ineffective against colitis. Lower serum concentrations of several phenolic acids were detected in the microbiota-depleted mice, indicating that gut microbiota plays a role in flavonoid metabolism and bioavailability.

The Unique Seed Protein Composition of Quality Protein Popcorn Promotes Growth of Beneficial Bacteria From the Human Gut Microbiome.

The effects of fiber, complex carbohydrates, lipids, and small molecules from food matrices on the human gut microbiome have been increasingly studied. Much less is known about how dietary protein can influence the composition and function of the gut microbial community. Here, we used near-isogenic maize lines of conventional popcorn and quality-protein popcorn (QPP) to study the effects of the opaque-2 mutation and associated quality-protein modifiers on the human gut microbiome. Opaque-2 blocks the synthesis of major maize seed proteins (α-zeins), resulting in a compensatory synthesis of new seed proteins that are nutritionally beneficial with substantially higher levels of the essential amino acids lysine and tryptophan. We show that QPP lines stimulate greater amounts of butyrate production by human gut microbiomes in in vitro fermentation of popped and digested corn from parental and QPP hybrids. In human gut microbiomes derived from diverse individuals, bacterial taxa belonging to the butyrate-producing family Lachnospiraceae, including the genera Coprococcus and Roseburia were consistently increased when fermenting QPP vs. parental popcorn lines. We conducted molecular complementation to further demonstrate that lysine-enriched seed protein can stimulate growth and butyrate production by microbes through distinct pathways. Our data show that organisms such as Coprococcus can utilize lysine and that other gut microbes, such as Roseburia spp., instead, utilize fructoselysine produced during thermal processing (popping) of popcorn. Thus, the combination of seed composition in QPP and interaction of protein adducts with carbohydrates during thermal processing can stimulate the growth of health-promoting, butyrate-producing organisms in the human gut microbiome through multiple pathways.

Heterogeneous nutrient supply promotes maize growth and phosphorus acquisition: additive and compensatory effects of lateral roots and root hairs.

Root proliferation is a response to a heterogeneous nutrient distribution. However, the growth of root hairs in response to heterogeneous nutrients and the relationship between root hairs and lateral roots remain unclear. This study aims to understand the effects of heterogeneous nutrients on root hair growth and the trade-off between root hairs and lateral roots in phosphorus (P) acquisition. Near-isogenic maize lines, the B73 wild type (WT) and the rth3 root hairless mutant, were grown in rhizoboxes with uniform or localized supply of 40 (low) or 140 (high) mg P kg-1 soil. Both WT and rth3 had nearly two-fold greater shoot biomass and P content under local than uniform treatment at low P. Significant root proliferation was observed in both WT and rth3 in the nutrient patch, with the WT accompanied by an obvious increase (from 0.7 to 1.2 mm) in root hair length. The root response ratio of rth3 was greater than that of WT at low P, but could not completely compensate for the loss of root hairs. This suggests that plants enhanced P acquisition through complementarity between lateral roots and root hairs, and thus regulated nutrient foraging and shoot growth. The disappearance of WT and rth3 root response differences at high P indicated that the P application reduced the dependence of the plants on specific root traits to obtain nutrients. In addition to root proliferation, the root response to a nutrient-rich patch was also accompanied by root hair elongation. The genotypes without root hairs increased their investment in lateral roots in a nutrient-rich patch to compensate for the absence of root hairs, suggesting that plants enhanced nutrient acquisition by regulating the trade-off of complementary root traits.

Raman Spectroscopy as a Robust New Tool for Rapid and Accurate Evaluation of Drought Tolerance Levels in Both Genetically Diverse and Near-Isogenic Maize Lines.

Improving drought tolerance of crops has become crucial due to the current scenario of rapid climate change. In particular, development of new maize germplasm with increased drought tolerance is viewed as a major breeding goal to ensure sustainable food and feed production. Therefore, accurate rapid phenotyping techniques for selection of superior maize genotypes are required. The objectives of this study were to determine whether Raman microscopy technique can be applied for accurate assessment of drought-tolerance levels in both genetically diverse and near-isogenic maize lines that differ in their levels of drought-tolerance. Carotenoid degradation is known to be a direct stress response initiated by reactive oxygen species during osmotic stress such as drought. Using Raman mapping, we observed real-time changes in the rate of carotenoid degradation in chloroplasts that was dependent on the strength of osmotic stress. In addition, we showed that the rate of carotenoid degradation as measured by Raman spectroscopy correlates directly with drought tolerance levels of diverse maize genotypes. We conclude that Raman technique is a robust, biochemically selective and non-invasive phenotyping technique that accurately distinguishes drought tolerance levels in both genetically diverse and near-isogenic maize genotypes. We conclude that this technique can be further developed to render it suitable for field-based early assessment of breeding materials with superior drought-tolerance traits.

Characterization of Maize Near-Isogenic Lines With Enhanced Flavonoid Expression to Be Used as Tools in Diet-Health Complexity

Increasing incidence of chronic diseases in the 21st century has emphasized the importance of developing crops with enhanced nutritional value. Plant-based diets are associated with reduced incidence of many chronic diseases. The growing population and increased food demand have prioritized the development of high-yielding commercial crop varieties at the expense of natural flavors as well as health-benefiting compounds including polyphenols. Flavonoids are a large subfamily of polyphenols abundant in the plant kingdom with known health-promoting effects, making them a promising trait to be re-introduced into elite lines. Given the vast array of flavonoids and the complexity of plant food metabolome interactions, it is difficult to identify with certainty the specific class(es) of flavonoids in the food matrix that are anti-inflammatory. To address this, we have developed four maize near-isogenic lines (NILs); a line that lacked both anthocyanins and phlobaphenes, a second NIL containing phlobaphenes, a third line had anthocyanins, and a fourth line that contained both anthocyanins and phlobaphenes. The phytochemical profiles and the antioxidant potential of the NILs were characterized. The accumulation of anthocyanins and phlobaphenes contributed significantly to antioxidant capacity compared to maize lines that lacked one or both of the compounds (p < 0.05). Pilot study showed that intake of flavonoid-rich maize diets were able to alleviate experimental colitis in mice. These NILs offer novel materials combining anthocyanins and phlobaphenes and can be used as powerful tools to investigate the disease-preventive effects of specific flavonoid compound in diet/feeding experiments.

Maize Flavan-4-ols and Anthocyanins Alleviated Dextran Sulfate Sodium-Induced Colitis in Mice via Intestinal Barrier Function Restoration

Abstract Objectives This study investigated the anti-inflammatory effects of anthocyanins and flavan-4-ols (precursor of phlobaphenes) within a whole-food matrix against dextran sulfate sodium (DSS)-induced colitis using four maize near-isogenic lines (NILs) that differ only in a single class of flavonoids. The four NILs are A (lacks anthocyanins and phlobaphenes), B (phlobaphenes +), C (anthocyanins +) and D (anthocyanins + and phlobaphenes +). Methods Conventional male C57BL6 mice were subjected to control diet 25% A, B, C, and D supplemented corn diet. Germ-free (GF) C57BL6 mice were subjected to either control or 25% D supplemented diet. Colitis was induced in both conventional and GF mice by 3% and 1.25% (w/v) DSS in the drinking water, respectively. Intestinal permeability was measured using FITC-dextran. RT-PCR was used to analyze the gene expression levels and 16S rRNA for bacterial relative abundance. Results In conventional mice, supplementation of A, B, C, and D prevented DSS-induced colon shortening and body weight loss compared to mice on the control diet (P &amp;lt; 0.05). Mice supplemented with B, C, D diets had lower gut permeability than DSS mice (P &amp;lt; 0.05). The mRNA expression level of pro-inflammatory interleukin-6 (IL-6) was suppressed in B, C and D supplemented mice whereas, interleukin 1β (IL-1β) expression was lowered in mice supplemented with C and D diets only. Supplementation of the four NILs decreased the abundance of the genus Pseudomonas in colitic mice (P &amp;lt; 0.05). In GF mice, D diet ameliorated DSS-induced colon shortening and elevated gut permeability. The expression level of IL-6 and IL-1β were downregulated in GF mice fed with D diet (P &amp;lt; 0.05). Conclusions In summary, flavan-4-ols and/or anthocyanins in the whole-food matrix exerted their protective effects against DSS-induced chronic inflammation and concommitantly restored intestinal barrier function. GF mice experiment results demonstrated that above mentioned beneficial effects from bioactive corn compounds were partially independent of gut microbiota. Funding Sources USDA-NIFA awards 2016-67,017-29,285 and 2019-67,017-29,258.

Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines.

Genome-wide association (GWA) studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping (NAM) can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height and resistance to three foliar diseases, and genotyped with genotyping-by-sequencing. Across traits, broad-sense heritability (0.4-0.8) was relatively high. The 896 genotyped nNILs contain 2638 introgressions, which span the entire genome with substantial overlap within and among allele donors. GWA with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize NAM population in a B73 background combined with data on six agronomically important traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions, and could readily be used for future fine mapping studies.

Food/Feed and Environmental Risk Assessment of Insect-Resistant and Herbicide-Tolerant Genetically Modified Maize Bt11 from Syngenta Seeds for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (EFSA/GMO/RX/Bt11)

Food/Feed and Environmental Risk Assessment of Insect-Resistant and Herbicide-Tolerant Genetically Modified Maize Bt11 from Syngenta Seeds for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (EFSA/GMO/RX/Bt11)

Intestinal Mucosal Barrier Function Restoration in Mice by Maize Diet Containing Enriched Flavan-4-Ols.

Inflammatory bowel disease (IBD), a chronic intestinal inflammatory condition, awaits safe and effective preventive strategies. Naturally occurring flavonoid compounds are promising therapeutic candidates against IBD due to their great antioxidant potential and ability to reduce inflammation and improve immune signaling mediators in the gut. In this study, we utilized two maize near-isogenic lines flavan-4-ols-containing P1-rr (F+) and flavan-4-ols-lacking p1-ww (F−) to investigate the anti-inflammatory property of flavan-4-ols against carboxymethylcellulose (CMC)-induced low-grade colonic inflammation. C57BL/6 mice were exposed to either 1% CMC (w/v) or water for a total of 15 weeks. After week six, mice on CMC treatment were divided into four groups. One group continued on the control diet. The second and third groups were supplemented with F+ at 15% or 25% (w/w). The fourth group received diet supplemented with F− at 15%. Here we report that mice consuming F+(15) and F+(25) alleviated CMC-induced increase in epididymal fat-pad, colon histology score, pro-inflammatory cytokine interleukin 6 expression and intestinal permeability compared to mice fed with control diet and F−(15). F+(15) and F+(25) significantly enhanced mucus thickness in CMC exposed mice (p < 0.05). These data collectively demonstrated the protective effect of flavan-4-ol against colonic inflammation by restoring intestinal barrier function and provide a rationale to breed for flavan-4-ols enriched cultivars for better dietary benefits.

De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase.

Gray leaf spot (GLS) disease in maize, caused by the fungus Cercospora zeina, is a threat to maize production globally. Understanding the molecular basis for quantitative resistance to GLS is therefore important for food security. We developed a de novo assembly pipeline to identify candidate maize resistance genes. Near-isogenic maize lines with and without a QTL for GLS resistance on chromosome 10 from inbred CML444 were produced in the inbred B73 background. The B73-QTL line showed a 20% reduction in GLS disease symptoms compared to B73 in the field (p = 0.01). B73-QTL leaf samples from this field experiment conducted under GLS disease pressure were RNA sequenced. The reads that did not map to the B73 or C. zeina genomes were expected to contain novel defense genes and were de novo assembled. A total of 141 protein-coding sequences with B73-like or plant annotations were identified from the B73-QTL plants exposed to C. zeina. To determine whether candidate gene expression was induced by C. zeina, the RNAseq reads from C. zeina-challenged and control leaves were mapped to a master assembly of all of the B73-QTL reads, and differential gene expression analysis was conducted. Combining results from both bioinformatics approaches led to the identification of a likely candidate gene, which was a novel allele of a lectin receptor-like kinase named L-RLK-CML that (i) was induced by C. zeina, (ii) was positioned in the QTL region, and (iii) had functional domains for pathogen perception and defense signal transduction. The 817AA L-RLK-CML protein had 53 amino acid differences from its 818AA counterpart in B73. A second “B73-like” allele of L-RLK was expressed at a low level in B73-QTL. Gene copy-specific RT-qPCR confirmed that the l-rlk-cml transcript was the major product induced four-fold by C. zeina. Several other expressed defense-related candidates were identified, including a wall-associated kinase, two glutathione s-transferases, a chitinase, a glucan beta-glucosidase, a plasmodesmata callose-binding protein, several other receptor-like kinases, and components of calcium signaling, vesicular trafficking, and ethylene biosynthesis. This work presents a bioinformatics protocol for gene discovery from de novo assembled transcriptomes and identifies candidate quantitative resistance genes.

Differential Expression of Signaling Pathway Genes Associated With Aflatoxin Reduction Quantitative Trait Loci in Maize (Zea mays L.).

The roles of signaling pathway genes related to the aflatoxin reduction trait in maize were studied for the improvement of maize resistance to the fungal pathogen Aspergillus flavus (A. flavus). In this study, 55 maize genes in plant–pathogen interaction signaling pathways were investigated among 12 maize near-isogenic lines (NILs) that carry maize quantitative trait loci (QTL) associated with aflatoxin reduction. These maize NILs were developed from maize inbred lines Mp313E (resistant donor parent) and Va35 (susceptible recurrent parent). The quantitative RT-PCR (qRT-PCR) technique was used to study the gene expression patterns. Seven calcium-dependent protein kinases and one respiratory burst oxidase displayed significant differential expression levels among the maize QTL-NILs. In addition, the gene expression profiles of WRKY transcription factors were also examined. Maize WRKY 52, WRKY 71, and WRKY83 genes displayed significantly differential expression levels among the QTL-NILs. The elucidation of differentially expressed signaling pathway genes involving maize resistance to A. flavus can provide insights into maize disease resistance and enhance maize molecular breeding.

Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

BackgroundC-type cytoplasmic male sterility (CMS-C) is one of the three major types of cytoplasmic male sterility (CMS) in maize. Rf4 is a dominant restorer gene for CMS-C and has great value in hybrid maize breeding, but little information concerning its functional mechanism is known.ResultsTo reveal the functional mechanism of Rf4, we developed a pair of maize near-isogenic lines (NILs) for the Rf4 locus, which included a NIL_rf4 male-sterile line and a NIL_Rf4 male fertility-restored line. Genetic analysis and molecular marker detection indicated that the male fertility of NIL_Rf4 was controlled by Rf4. Whole-genome sequencing demonstrated genomic differences between the two NILs was clustered in the Rf4 mapping region. Unmapped reads of NILs were further assembled to uncover Rf4 candidates. RNA-Seq was then performed for the developing anthers of the NILs to identify critical genes and pathways associated with fertility restoration. A total of 7125 differentially expressed genes (DEGs) were identified. These DEGs were significantly enriched in 242 Gene Ontology (GO) categories, wherein 100 DEGs were involved in pollen tube development, pollen tube growth, pollen development, and gametophyte development. Homology analysis revealed 198 male fertility-related DEGs, and pathway enrichment analysis revealed that 58 DEGs were enriched in cell energy metabolism processes involved in glycolysis, the pentose phosphate pathway, and pyruvate metabolism. By querying the Plant Reactome Pathway database, we found that 14 of the DEGs were involved in the mitochondrial tricarboxylic acid (TCA) cycle and that most of them belonged to the isocitrate dehydrogenase (IDH) and oxoglutarate dehydrogenase (OGDH) enzyme complexes. Transcriptome sequencing and real-time quantitative PCR (qPCR) showed that all the above TCA cycle-related genes were up-regulated in NIL_Rf4. The results of our subsequent enzyme-linked immunosorbent assay (ELISA) experiments pointed out that the contents of both the IDH and OGDH enzymes accumulated more in the spikelets of NIL_Rf4 than in those of NIL_rf4.ConclusionThe present research provides valuable genomic resources for deep insight into the molecular mechanism underlying CMS-C male fertility restoration. Importantly, our results indicated that genes involved in energy metabolism, especially some mitochondrial TCA cycle-related genes, were associated with maize CMS-C male fertility restoration.

Genetic Mapping of the Leaf Number above the Primary Ear and Its Relationship with Plant Height and Flowering Time in Maize.

The leaf number above the primary ear (LA) is a major contributing factor to plant architecture in maize. The yield of leafy maize, which has extra LA compared to normal maize, is higher than normal maize in some regions. One major concern is that increasing LA may be accompanied by increased plant height and/or flowering time. Using an F2:3 population comprising 192 families derived from a leafy maize line and a normal maize line, an association population comprising 437 inbred maize lines, and a pair of near-isogenic maize lines, we mapped the quantitative trait loci (QTL) associated with LA and assessed its genetic relationship with flowering time and plant height. Ten QTL with an additive and dominant effect, 18 pairs of interacting QTL in the F2:3 population and seventeen significant SNPs in the association population were detected for LA. Two major QTL, qLA3-4 and qLA7-1, were repeatedly detected and explained a large proportion of the phenotypic variation. The qLA3-4 was centered on lfy1, which is a dominant gene underlying extra leaves above the ear in leafy maize. Four LA QTL were found to overlap with flowering time and/or plant height, which suggested that these QTL might have a pleiotropic effect. The pleiotropy of the lfy1 locus on LA, flowering time and plant height were validated by near-isogenic line analysis. These results enhance our understanding of the genetic architecture affecting maize LA and the development of maize hybrids with increased LA.

Comparative studies on the photosynthetic characteristics of two maize (Zea mays L.) near-isogenic lines differing in their susceptibility to low light intensity

The objective of our study was to quantify the effect of low light intensity on chlorophyll (Chl) content, photosynthetic parameters, chlorophyll fluorescence parameters and growth of two maize (Zea mays L.) near-isogenic lines (NILs) differing in their susceptibility to low light to reveal the cause of the resistance to weak light in maize. A field-experiment was conducted in the central plain of Liaohe river in northeast China (41°49′N, 123°34′E), on a meadow brown soil. Two levels of photosynthetically-active radiation (removal of 0% and 40% of sunlight) were tested on SN98A (shading sensitive) and SN98B (shading tolerant) lines. The results showed that shading lengthened the anthesis-silking interval (ASI), increased the percentage of barren stalk and reduced the percentage of silking, and shading decreased leaf Chl content, net photosynthetic rate (Pn), quantum yield of PS II (Y(II)), electron transport rate (ETR), and photochemical quenching (qP) in the two maize NILs. The shading tolerances differed between different near-isogenic lines. Maximum efficiency of PSII photochemistry under dark-adaption (Fv/Fm) of SN98B was increased under low light intensity, meanwhile relatively more stable contents of Chl, Pn, Y(II), ETR, and qP were able to enhance light-use efficiency and reduce the dissipation of light energy, which relieved the reduction in photosynthetic efficiency which caused reduced production of ear assimilative products, thus resulting in a smaller reduction in percentage of barren stalk in SN98B under shading. These fidings demonstrate that low light intensity depressed photosynthetic activity and growth of SN98A more than that of SN98B. SN98A could be more restricted by limited carbon assimilation, leading to the production of barren stalks in low light intensity than that of SN98B. Therefore, improvements in light-harvesting and -use capability and increasing ear filling under low light intensity stress might be important characteristics for plant breeders. Selection of SN98B as a shade-tolerant germplasm for breeding in maize would alleviate the problem of barren stalk development under low light intensity.

Biosynthesis of 8-O-Methylated Benzoxazinoid Defense Compounds in Maize.

Benzoxazinoids are important defense compounds in grasses. Here, we investigated the biosynthesis and biological roles of the 8-O-methylated benzoxazinoids, DIM2BOA-Glc and HDM2BOA-Glc. Using quantitative trait locus mapping and heterologous expression, we identified a 2-oxoglutarate-dependent dioxygenase (BX13) that catalyzes the conversion of DIMBOA-Glc into a new benzoxazinoid intermediate (TRIMBOA-Glc) by an uncommon reaction involving a hydroxylation and a likely ortho-rearrangement of a methoxy group. TRIMBOA-Glc is then converted to DIM2BOA-Glc by a previously described O-methyltransferase BX7. Furthermore, we identified an O-methyltransferase (BX14) that converts DIM2BOA-Glc to HDM2BOA-Glc. The role of these enzymes in vivo was demonstrated by characterizing recombinant inbred lines, including Oh43, which has a point mutation in the start codon of Bx13 and lacks both DIM2BOA-Glc and HDM2BOA-Glc, and Il14H, which has an inactive Bx14 allele and lacks HDM2BOA-Glc in leaves. Experiments with near-isogenic maize lines derived from crosses between B73 and Oh43 revealed that the absence of DIM2BOA-Glc and HDM2BOA-Glc does not alter the constitutive accumulation or deglucosylation of other benzoxazinoids. The growth of various chewing herbivores was not significantly affected by the absence of BX13-dependent metabolites, while aphid performance increased, suggesting that DIM2BOA-Glc and/or HDM2BOA-Glc provide specific protection against phloem feeding insects.

Transcriptome analysis of near‐isogenic lines provides molecular insights into starch biosynthesis in maize kernel

Starch is the major component in maize kernels, providing a stable carbohydrate source for humans and livestock as well as raw material for the biofuel industry. Increasing maize kernel starch content will help meet industry demands and has the potential to increase overall yields. We developed a pair of maize near-isogenic lines (NILs) with different alleles for a starch quantitative trait locus on chromosome 3 (qHS3), resulting in different kernel starch content. To investigate the candidate genes for qHS3 and elucidate their effects on starch metabolism, RNA-Seq was performed for the developing kernels of the NILs at 14 and 21 d after pollination (DAP). Analysis of genomic and transcriptomic data identified 76 genes with nonsynonymous single nucleotide polymorphisms and 384 differentially expressed genes (DEGs) in the introgressed fragment, including a hexokinase gene, ZmHXK3a, which catalyzes the conversion of glucose to glucose-6-phosphate and may play a key role in starch metabolism. The expression pattern of all DEGs in starch metabolism shows that altered expression of the candidate genes for qHS3 promoted starch synthesis, with positive consequences for kernel starch content. These results expand the current understanding of starch biosynthesis and accumulation in maize kernels and provide potential candidate genes to increase starch content.

Differences in properties and proteomes of the midribs contribute to the size of the leaf angle in two near-isogenic maize lines

The midrib of maize leaves provides the primary support for the blade and is largely associated with leaf angle size. To elucidate the role of the midrib in leaf angle formation, the maize line Shen137 (larger leaf angle) and a near isogenic line (NIL, smaller leaf angle) were used in the present study. The results of the analysis showed that both the puncture forces and proximal collenchyma number of the midribs of the first and second leaves above the ear were higher in NIL than in Shen137. Comparative proteomic analysis was performed to reveal protein profile differences in the midribs of the 5th, 10th and 19th newly expanded leaves between Shen137 and NIL. Quantitative analysis of 24 identified midrib proteins indicated that the maximum changes in abundance of 22 proteins between Shen137 and NIL appeared at the 10th leaf stage, of which phosphoglycerate kinase, adenosine kinase, fructose-bisphosphate aldolase and adenylate kinase were implicated in glycometabolism. Thus, glycometabolism might be associated with leaf angle formation and the physical and mechanical properties of the midribs. These results provide insight into the mechanism underlying maize leaf angle formation.

Comparative transcriptome profiling of two maize near-isogenic lines differing in the allelic state for bacterial brown spot disease resistance

The bacterial brown spot disease (BBS), caused primarily by Pseudomonas syringae pv. syringae van Hall (Pss), reduces plant vigor, yield and quality in maize. To reveal the nature of the defense mechanisms and identify genes involved in the effective host resistance, the dynamic changes of defense transcriptome triggered by the infection of Pss were investigated and compared between two maize near-isogenic lines (NILs). We found that Pss infection resulted in a sophisticated transcriptional reprogramming of several biological processes and the resistant NIL employed much faster defense responses than the susceptible NIL. Numerous genes encoding essential components of plant basal resistance would be able to be activated in the susceptible NIL, such as PEN1, PEN2, PEN3, and EDR1, however, in a basic manner, such resistance might not be sufficient for suppressing Pss pathogenesis. In addition, the expressions of a large number of PTI-, ETI-, PR-, and WRKY-related genes were pronouncedly activated in the resistant NIL, suggesting that maize employ a multitude of defense pathways to defend Pss infection. Six R-gene homologs were identified to have significantly higher expression levels in the resistant NIL at early time point, indicating that a robust surveillance system (gene-to-gene model) might operate in maize during Pss attacks, and these homolog genes are likely to be potential candidate resistance genes involved in BBS disease resistance. Furthermore, a holistic group of novel pathogen-responsive genes were defined, providing the repertoire of candidate genes for further functional characterization and identification of their regulation patterns during pathogen infection.