Dataset Information

Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process.

ABSTRACT: In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.

SUBMITTER: Xiong CY

PROVIDER: S-EPMC8268914 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process.

Xiong Cai-Yun CY Gong Qing-You QY Pei Hu H Liao Chang-Jian CJ Yang Rui-Chun RC Li Gao-Ke GK Huang Jun J

International journal of molecular sciences 20210629 13

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq wa ...[more]

PMID: 34209973

Similar Datasets

Project description:BackgroundStalk strength is a critical trait in maize that influences plant architecture, lodging resistance and grain yield. The developmental stage of maize, spanning from the vegetative stage to the reproductive stage, is critical for determining stalk strength. However, the dynamics of the genetic control of this trait remains unclear.ResultsHere, we report a temporal resolution study of the maize stalk transcriptome in one tropical line and one non-stiff-stalk line using 53 transcriptomes collected covering V7 (seventh leaf stage) through silking stage. The time-course transcriptomes were categorized into four phases corresponding to stalk early development, stalk early elongation, stalk late elongation, and stalk maturation. Fuzzy c-means clustering and Gene Ontology (GO) analyses elucidated the chronological sequence of events that occur at four phases of stalk development. Gene Ontology analysis suggests that active cell division occurs in the stalk during Phase I. During Phase II, processes such as cell wall extension, lignin deposition, and vascular cell development are active. In Phase III, lignin metabolic process, secondary cell wall biogenesis, xylan biosynthesis process, cell wall biogenesis, and polysaccharide biosynthetic process contribute to cell wall strengthening. Defense responses, abiotic stresses, and transport of necessary nutrients or substances are active engaged during Phase IV. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the two maize lines presented significant gene expression differences in the phenylpropanoid biosynthesis pathway and the flavonoid biosynthesis pathway. Certain differentially expressed genes (DEGs) encoding transcription factors, especially those in the NAC and MYB families, may be involved in stalk development. In addition, six potential regulatory genes associated with stalk strength were identified through weighted gene co-expression network analysis (WGCNA).ConclusionThe data set provides a high temporal-resolution atlas of gene expression during maize stalk development. These phase-specific genes, differentially expressed genes, and potential regulatory genes reported in this study provide important resources for further studies to elucidate the genetic control of stalk development and stalk strength formation in maize.

Project description:Background/Objectives: Maize (Zea mays L.), a crop of worldwide importance, owes its adaptability to diverse environments to its genetic variation. However, tropical maize exhibits intrinsic photoperiod sensitivity, limiting its adaptability to temperate regions. Photoperiod sensitivity significantly affects the flowering time and other agronomic traits, but the underlying molecular mechanisms remain poorly understood. In this study, the aim is to elucidate the transcriptional regulatory networks mediating photoperiod responses in tropical maize inbred line Su65, providing insights into improving photoperiod adaptability. Methods: RNA-seq analysis was carried out to investigate photoperiod-responsive genes and pathways in tropical line Su65 exposed to varying photoperiod conditions. Differential expression analysis, functional enrichment, and the construction of protein-protein interaction (PPI) networks were carried out to investigate transcriptional dynamics. Additionally, qRT-PCR was employed to confirm the expression patterns of key candidate genes and generate detailed temporal expression profiles. Results: A total of 1728 differentially expressed genes (DEGs) were identified, with significant enrichment in pathways such as stress responses, redox homeostasis, and secondary metabolite biosynthesis. A set of new key hub genes (such as Zm00001d048531, Zm00001d018821, Zm00001d034892, etc.) were identified through PPI network analysis. Temporal expression profiling of ZmPHYB1, ZmPHYC1, ZmFKF2, ZmGI2, and ZmPRR37a, the key genes involved in circadian rhythms, revealed distinct regulatory patterns of photoperiod-sensitive genes at different time points, highlighting their roles in flowering time regulation and developmental transitions. Conclusions: In this study, critical molecular networks underlying photoperiod sensitivity in tropical maize are uncovered and a foundation is provided for improving photoperiod adaptability through genetic improvement. By integrating RNA-seq and qRT-PCR, the research offers valuable insights into transcriptional dynamics and their role in maize development under photoperiodic regulation.

Project description:BackgroundSapium sebiferum, whose seeds contain high level of fatty acids, has been considered as one of the most important oil plants. However, the high male to female flower ratio limited the seed yield improvement and its industrial potentials. Thus, the study of the sex determination in S. sebiferum is of significant importance in increasing the seed yield.ResultsIn this study, we demonstrated that in S. sebiferum, cytokinin (CK) had strong feminization effects on the floral development. Exogenous application with 6-benzylaminopurine (6-BA) or thidiazuron (TDZ) significantly induced the development of female flowers and increased the fruit number. Interestingly, the feminization effects of cytokinin were also detected on the androecious genotype of S. sebiferum which only produce male flowers. To further investigate the mechanism underlying the role of cytokinin in the flower development and sex differentiation, we performed the comparative transcriptome analysis of the floral buds of the androecious plants subjected to 6-BA. The results showed that there were separately 129, 352 and 642 genes differentially expressed at 6 h, 12 h and 24 h after 6-BA treatment. Functional analysis of the differentially expressed genes (DEGs) showed that many genes are related to the hormonal biosynthesis and signaling, nutrients translocation and cell cycle. Moreover, there were twenty one flowering-related genes identified to be differentially regulated by 6-BA treatment. Specifically, the gynoecium development-related genes SPATULA (SPT), KANADI 2 (KAN2), JAGGED (JAG) and Cytochrome P450 78A9 (CYP79A9) were significantly up-regulated, whereas the expression of PISTILLATA (PI), TATA Box Associated Factor II 59 (TAFII59) and MYB Domain Protein 108 (MYB108) that were important for male organ development was down-regulated in response to 6-BA treatment, demonstrating that cytokinin could directly target the floral organ identity genes to regulate the flower sex.ConclusionsOur work demonstrated that cytokinin is a potential regulator in female flower development in S. sebiferum. The transcriptome analysis of the floral sex transition from androecious to monoecious in response to cytokinin treatment on the androecious S. sebiferum provided valuable information related to the mechanism of sex determination in the perennial woody plants.

Project description:Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, stands as one of the most economically burdensome and pervasive diseases affecting maize worldwide. Its impact on food security is particularly pronounced due to the production of fumonisins, toxic secondary metabolites that pose serious health risks, especially for livestock. FER disease severity is complex and polygenic, with few resistance (R) genes being identified for use in breeding resistant varieties. While FER is the subject of several breeding programs, only a few studies have investigated entire populations of F. verticillioides with corresponding virulence data to better understand and characterize the pathogenomics. Here, we sequenced and compared the genomes of 50 Fusarium isolates (43 F. verticillioides and 7 other Fusarium spp.) that were used to inoculate a diverse maize population. Our objectives were to elucidate the genome size and composition of F. verticillioides, explore the variable relationship between fumonisin production and visual disease severity, and shed light on the phylogenetic relationships among the isolates. Additionally, we conducted a comparative analysis of the nucleotide variants (SNPs) and the isolates' effectoromes to uncover potential genetic determinants of pathogenicity. Our findings revealed several promising leads, notably the association of certain gene groups, such as pectate lyase, with disease severity. These genes should be investigated further as putative alleles for breeding resistant maize varieties. We suggest that, beyond validation of the alleles identified in this study, researchers validate each phenotypic dataset on an individual basis, particularly if considering fumonisin concentrations and when using diverse populations. Our study underscores the importance of genomic analysis in tackling FER and offers insights that could inform the development of resilient maize cultivars. By leveraging advances in genomics and incorporating pathogen populations into breeding programs, resistance to FER can be advanced.

Dataset Information

Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process.

Publications

Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets