Comparative regulatory network of transcripts behind radicle emergence and seedling stage of maize (Zea mays L.)
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ABSTRACT:
SUBMITTER: Byregowda R
PROVIDER: S-EPMC10869873 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
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Project description:In underdeveloped nations where low-input agriculture is practiced, low phosphorus (LP) in the soil reduces the production of maize. In the present study, a total of 550 inbred maize lines were assessed for seedling traits under LP (2.5 × 10-6 mol L-1 of KH2PO4) and NP (2.5 × 10-4 mol L-1 of KH2PO4) hydroponic conditions. The purpose of this study was to quantify the amount of variation present in the measured traits, estimate the genetic involvement of these characteristics, examine the phenotypic correlation coefficients between traits, and to integrate this information to prepare a multi-trait selection index for LP tolerance in maize. A great deal of variability in the maize genotype panel was confirmed by descriptive statistics and analysis of variance (ANOVA). Estimated broad-sense heritability (h2) ranged from 0.7 to 0.91, indicating intermediate to high heritability values for the measured traits. A substantial connection between MSL and other root traits suggested that the direct selection of MSL (maximum shoot length) could be beneficial for the enhancement of other traits. The principal component analysis (PCA) of the first two main component axes explained approximately 81.27% of the variation between lines for the eight maize seedling variables. TDM (total dry matter), SDW (shoot dry weight), RDW (root dry weight), SFW (shoot fresh weight), RFW (root fresh weight), MRL (maximum root length), and MSL measurements accounted for the majority of the first principal component (59.35%). The multi-trait indices were calculated based on PCA using all the measured traits, and 30 genotypes were selected. These selected lines might be considered as the potential source for the improvement of LP tolerance in maize.
| S-EPMC10346422 | biostudies-literature
Project description:Abiotic stresses, including drought, salinity, heat, and cold, negatively affect maize (Zea mays L.) development and productivity. To elucidate the molecular mechanisms of resistance to abiotic stresses in maize, RNA-seq was used for global transcriptome profiling of B73 seedling leaves exposed to drought, salinity, heat, and cold stress. A total of 5,330 differentially expressed genes (DEGs) were detected in differential comparisons between the control and each stressed sample, with 1,661, 2,019, 2,346, and 1,841 DEGs being identified in comparisons of the control with salinity, drought, heat, and cold stress, respectively. Functional annotations of DEGs suggested that the stress response was mediated by pathways involving hormone metabolism and signaling, transcription factors (TFs), very-long-chain fatty acid biosynthesis and lipid signaling, among others. Of the obtained DEGs (5,330), 167 genes are common to these four abiotic stresses, including 10 up-regulated TFs (five ERFs, two NACs, one ARF, one MYB, and one HD-ZIP) and two down-regulated TFs (one b-ZIP and one MYB-related), which suggested that common mechanisms may be initiated in response to different abiotic stresses in maize. This study contributes to a better understanding of the molecular mechanisms of maize leaf responses to abiotic stresses and could be useful for developing maize cultivars resistant to abiotic stresses.
| S-EPMC5331654 | biostudies-literature
Project description:BackgroundZhengdan 958 (Zheng 58 × Chang 7-2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear.ResultOur objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7-2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism.ConclusionsThe potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.
| S-EPMC7708177 | biostudies-literature
Project description:Water shortage caused by long-term drought is one of the most serious abiotic stress factors in maize. Different drought conditions lead to differences in growth, development, and metabolism of maize. In previous studies, proteomics and genomics methods have been widely used to explain the response mechanism of maize to long-term drought, but there are only a few articles related to metabolomics. In this study, we used transcriptome and metabolomics analysis to characterize the differential effects of drought stress imposed at seedling or flowering stages on maize. Through the association analysis of genes and metabolites, we found that maize leaves had 61 and 54 enriched pathways under seedling drought and flowering drought, respectively, of which 13 and 11 were significant key pathways, mostly related to the biosynthesis of flavonoids and phenylpropanes, glutathione metabolism and purine metabolism. Interestingly, we found that the α-linolenic acid metabolic pathway differed significantly between the two treatments, and a total of 10 differentially expressed genes and five differentially abundant metabolites have been identified in this pathway. Some differential accumulation of metabolites (DAMs) was related to synthesis of jasmonic acid, which may be one of the key pathways underpinning maize response to different types of long-term drought. In general, metabolomics provides a new method for the study of water stress in maize and lays a theoretical foundation for drought-resistant cultivation of silage maize.
| S-EPMC8839722 | biostudies-literature
Project description:Maize is known to be susceptible to drought stress, which negatively affects vegetative growth and biomass production, as well as the formation of reproductive organs and yield parameters. In this study, 27 responsive traits of germination (G) and seedlings growth were evaluated for 40 accessions of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) germplasm collection, under no stress and simulated drought stress treatments by 10%, 15%, and 20% of polyethylene glycol (PEG). The three treatments significantly reduced G% and retarded seedlings growth, particularly the 15% and 20% PEG treatments; these two treatments also resulted in a significant increase of abnormal seedlings (AS). The heritability (H2) and correlations of the traits were estimated, and drought tolerance indices (DTIs) were calculated for traits and accessions. The H2 of G% values were reduced, and H2 for AS% increased as the PEG stress increased. Positive correlations were found between most trait pairs, particularly shoot and root traits, with 48 highly significant correlations under no stress and 25 highly significant correlations under the 10% PEG treatments, particularly for shoot and root traits. The medium to high heritability of shoot and root seedling traits provides a sound basis for further genetic analyses. PCA analysis clearly grouped accessions with high DTIs together and the accessions with low DTIs together, indicating that the DTI indicates the stress tolerance level of maize germplasm. However, the resemblance in DTI values does not clearly reflect the origin or taxonomic assignments to subspecies and varieties of the examined accessions.
| S-EPMC7284379 | biostudies-literature
Project description:The maize root system is crucial for plant establishment as well as water and nutrient uptake. There is substantial genetic and phenotypic variation for root architecture, which gives opportunity for selection. Root traits, however, have not been used as selection criterion mainly due to the difficulty in measuring them, as well as their quantitative mode of inheritance. Seedling root traits offer an opportunity to study multiple individuals and to enable repeated measurements per year as compared to adult root phenotyping. We developed a new software framework to capture various traits from a single image of seedling roots. This framework is based on the mathematical notion of converting images of roots into an equivalent graph. This allows automated querying of multiple traits simply as graph operations. This framework is furthermore extendable to 3D tomography image data. In order to evaluate this tool, a subset of the 384 inbred lines from the Ames panel, for which extensive genotype by sequencing data are available, was investigated. A genome wide association study was applied to this panel for two traits, Total Root Length and Total Surface Area, captured from seedling root images from WinRhizo Pro 9.0 and the current framework (called ARIA) for comparison using 135,311 single nucleotide polymorphism markers. The trait Total Root Length was found to have significant SNPs in similar regions of the genome when analyzed by both programs. This high-throughput trait capture software system allows for large phenotyping experiments and can help to establish relationships between developmental stages between seedling and adult traits in the future.
| S-EPMC4176968 | biostudies-literature
Project description:The ever-increasing human population is a major concern for food security. Maize is the third largest most important food crop. The major problems of cultivation arise from urbanization and land pollution. This reduces the amount of land available for agriculture. The use of chemicals in agriculture is not environmentally friendly. Thus, plant growth-promoting bacteria (PGPB) have been proposed as alternatives. This study aims to test the growth-promoting effect of maize inoculated with six indigenous PGPB isolates. These isolates were assayed for various biochemical and plant growth-promoting activities. They were also assayed for biocontrol activities. Based on the results, six isolates viz A1, A18, A29, NWU4, NWU14, and NWU198 were used to inoculate maize seeds. The inoculated seeds were tried out on the field. A randomized block design was used. PGPB used were in single, consortia of two, and three organisms. The length of the leaves, roots, and stem, plant height, numbers of leaves, and weight of 100 seeds were taken at the fourth and eighth weeks after planting. Microbial consortia increased growth parameters compared to single inoculant treatments. Thus, they can be of advantage in the eradication of low yield. They can also serve as reliable alternatives to chemical fertilizers.
| S-EPMC6920993 | biostudies-literature
Project description:Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C2H2, were strongly altered by cold stress. Moreover, the tolerant lines' 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines' 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress.
| S-EPMC8535276 | biostudies-literature
Project description:Transcriptional profiling of 4 maize varieties comparing genetic root response under control temperature conditions with genetic root response under low temperature conditions
2016-05-24 | GSE72508 | GEO
Project description:Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10-8 ~3.87 × 10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.
| S-EPMC5707364 | biostudies-literature