BSA-Seq and Transcriptomic Analysis Provide Candidate Genes Associated with Inflorescence Architecture and Kernel Orientation by Phytohormone Homeostasis in Maize.

The developmental plasticity of the maize inflorescence depends on meristems, which directly affect reproductive potential and yield. However, the molecular roles of upper floral meristem (UFM) and lower floral meristem (LFM) in inflorescence and kernel development have not been fully elucidated. In this study, we characterized the reversed kernel1 (rk1) novel mutant, which contains kernels with giant embryos but shows normal vegetative growth like the wild type (WT). Total RNA was extracted from the inflorescence at three stages for transcriptomic analysis. A total of 250.16-Gb clean reads were generated, and 26,248 unigenes were assembled and annotated. Gene ontology analyses of differentially expressed genes (DEGs) detected in the sexual organ formation stage revealed that cell differentiation, organ development, phytohormonal responses and carbohydrate metabolism were enriched. The DEGs associated with the regulation of phytohormone levels and signaling were mainly expressed, including auxin (IAA), jasmonic acid (JA), gibberellins (GA), and abscisic acid (ABA). The transcriptome, hormone evaluation and immunohistochemistry observation revealed that phytohormone homeostasis were affected in rk1. BSA-Seq and transcriptomic analysis also provide candidate genes to regulate UFM and LFM development. These results provide novel insights for understanding the regulatory mechanism of UFM and LFM development in maize and other plants.

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.

Early infection response of fungal biotroph Ustilago maydis in maize.

Common smut, caused by Ustilago maydis (DC.) Corda, is a destructive fungal disease of maize worldwide; it forms large tumors, reducing corn yield and quality. However, the molecular defense mechanism to common smut in maize remains unclear. The present study aimed to use a leading maize inbred line Ye478 to analyze the response to U. maydis inoculation. The histological and cytological analyses demonstrated that U. maydis grew gradually to the host cells 6 h post-inoculation (hpi). The samples collected at 0, 3, 6, and 12 hpi were analyzed to assess the maize transcriptomic changes in response to U. maydis. The results revealed differences in hormone signaling, glycometabolism, and photosynthesis after U. maydis infection; specific changes were detected in jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and abscisic acid (ABA) signaling pathways, glycolysis/gluconeogenesis, and photosystems I and II, probably related to defense response. MapMan analysis demonstrated that the differentially expressed genes between the treatment and control groups were clustered into light reaction and photorespiration pathways. In addition, U. maydis inoculation induced chloroplast swelling and damage, suggesting a significant effect on the chloroplast activity and subsequent metabolic process, especially hexose metabolism. A further genetic study using wild-type and galactinol-sucrose galactosyltransferase (gsg) and yellow-green leaf-1 (ygl-1) mutants identified that these two U. maydis-induced genes negatively regulated defense against common smut in maize. Our measurements showed the pathogen early-invasion process, and the key pathways of both chlorophyll biosynthesis and sugar transportation were critical modified in the infected maize line, thereby throwing a light on the molecular mechanisms in the maize-U. maydis interaction.

Photosynthetic and physiological responses to acetochlor in paired near-isogenic lines of waxy maize (Zea mays L.).

Acetochlor is always used in maize (Zea mays L.) fields as a common pre-emergence herbicide. In this field study, we investigated the effects of acetochlor on the photosynthetic characteristics, chlorophyll fluorescence parameters, and antioxidant enzyme activities in acetochlor-resistant (BWC95) and acetochlor-sensitive (BWC12) near-isogenic lines. We sprayed acetochlor after sowing, using water treatment as the control. After spraying acetochlor, the net photosynthetic rate, stomatal conductance, transpiration rate, and the function of chloroplasts were significantly lower in BWC12 than BWC95, whereas the intercellular CO2 concentrations and stomatal limitation values were higher. In addition to nonphotochemical quenching, chlorophyll fluorescence measurements obtained using leaves showed that the maximum photochemical efficiency of photosystem II (PSII), actual photochemical efficiency of PSII, photochemical quenching of chlorophyll fluorescence, and electron transport rate were higher in BWC95 than BWC12 after acetochlor treatment. H2O2 and O2˙- levels were higher in BWC12 than BWC95, which resulted in severe membrane lipid peroxidation due to sustained oxidative stress. Thus, the malondialdehyde content increased significantly with the exposure time in BWC12, and the antioxidant enzyme activities were lower in BWC12 than BWC95. The results show that acetochlor resistance is directly related to a high photosynthetic rate and a protective antioxidant enzyme system.

Reactive oxygen species, antioxidant enzyme activity, and gene expression patterns in a pair of nearly isogenic lines of nicosulfuron-exposed waxy maize (Zea mays L.).

Nicosulfuron is a post-emergence herbicide used for weed control in maize fields (Zea mays L.). Here, the pair of nearly isogenic inbred lines SN509-R (nicosulfuron resistant) and SN509-S (nicosulfuron sensitive) was used to study the effect of nicosulfuron on growth, oxidative stress, and the activity and gene expression of antioxidant enzymes in waxy maize seedlings. Nicosulfuron treatment was applied at the five-leaf stage and water treatment was used as control. After nicosulfuron treatment, the death of SN509-S might be associated with increased oxidative stress. Compared with SN509-R, higher O2·- and H2O2 accumulations were observed in SN509-S, which can severely damage lipids and proteins, thus reducing membrane stability. The effects were exacerbated with extended exposure time. Both O2·- and H2O2 detoxification is regulated by enzymes. After nicosulfuron treatment, superoxide dismutase (SOD), catalase, ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione reductase (GR), and glutathione-S-transferase (GST) of SN509-S were significantly lower than those of SN509-R. Compared to SN509-R, ascorbate content (AA), glutathione (GSH) content, GSH to glutathione disulfide ratios, and AA to dehydroascorbate ratios significantly declined with increasing exposure time in SN509-S. Compared to SN509-S, nicosulfuron treatment increased the transcript levels of most of the APX genes except for APX1, and in contrast to Gst1, upregulated the transcription of sod9, MDHAR, DHAR, and GR genes in SN509-R. These results suggest that on a transcription level and in accordance with their responses, detoxifying enzymes play a vital role in the O2·- and H2O2 detoxification of maize seedlings under nicosulfuron exposure.

[Comparative QTL mapping of resistance to sugarcane mosaic virus in maize based on bioinformatics].

The development of genomics and bioinformatics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for Sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available with the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them was clustered on chromosome 3 and 6. By using meta- analysis method, we identified one and two "consensus QTLs" on chromosomes 3 and 6, respectively. These three QTLs cover the genetic distances of 6.44 cM, 6.16 cM and 27.48 cM on the genetic map IBM2 2005 Neighbors, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via comparative genomics strategy. These results suggested that application of the combined meta-analysis within a species with sequence homologous comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provided useful information for identifying and cloning of the major gene(s) conferring resistance to SCMV in maize.