scholarly journals Transcriptome Analysis of Anther Wall Reveals Novel Insights Into the Regulatory Mechanisms Underlying Anther Wall Development in Rice

2021 ◽  
Author(s):  
Woo-Jong Hong ◽  
Su Kyoung Lee ◽  
Seok-Hui Kim ◽  
Yu-Jin Kim ◽  
Sunok Moon ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Male Fertility ◽  
Regulatory Mechanism ◽  
Future Research ◽  
Anther Wall ◽  
Regulatory Sequences ◽  
Hybrid Seed Production ◽  
Anther Dehiscence ◽  
Splicing Variants ◽  
Anther Wall Development

Abstract Rice is an important food staple that is consumed by half of the human population. Therefore, understanding the regulatory mechanism of male fertility in rice can improve production by enhancing the efficiency of hybrid seed production. However, information on the control mechanism of male fertility by anther dehiscence or wall development in rice is very limited. To further understand the regulatory mechanism for anther dehiscence in rice, we carried out transcriptome analysis for two tissues: the anther wall and pollen at the anthesis stage. With the anatomical meta-expression data, in addition to these tissues, the differentially expressed genes (DEGs) between the two tissues were further refined to identify 1,717 pollen-preferred genes and 534 anther wall-preferred genes. A GUS transgenic line and RT-qPCR analysis for anther wall-preferred genes supported the fidelity of our gene candidates for further analysis. The refined DEGs were functionally classified through Gene Ontology (GO) enrichment and MapMan analyses. Through the analysis of cis-acting elements and alternative splicing variants, we also suggest the feature of regulatory sequences in promoter regions for anther wall-preferred expression and provide information of the unique splicing variants in anther walls. Subsequently, it was found that hormone signaling and the resulting transcriptional regulation pathways may play an important role in anther dehiscence and anther wall development. Our result could provide useful insight for future research to broaden the molecular mechanism of anther dehiscence or anther wall development in rice.

Anther wall development and structure in wild tomatoes (Solanum sect. Lycopersicon): functional inferences

2006 ◽  
Vol 54 (1) ◽  
pp. 83 ◽  
Author(s):  
Carolina Carrizo García ◽  
Gloria E. Barboza
Keyword(s):  
Anther Wall ◽  
Mechanical Support ◽  
Anther Dehiscence ◽  
Buzz Pollination ◽  
Dorsal Wall ◽  
Pollination Mechanism ◽  
Number Of Layers ◽  
Solanum Sect ◽  
Anther Wall Development ◽  
Number Of Cells

Development of the anther wall and its structure at maturity in wild tomatoes (Solanum sect. Lycopersicon) are described, and the features are discussed in relation to anther dehiscence and the buzz-pollination mechanism. The anther wall formation follows two different patterns in the same microsporangia and a high number of cells divisions may occur. The number of layers formed varies across the ventral, dorsal and lateral surfaces of each theca. Large epidermal cells develop, lining the stomium, and they could possibly be involved in stomium opening. Cells with thickenings are formed in the apical fifth of the anther, where the tissues seem to degenerate after the stomium opening, forming a wider aperture through which the pollen can be shed. The multilayered dorsal wall remains swollen and could act as an attractant to pollinators and as mechanical support. The apparently disordered anther wall development sets up different structures across and along the anther, which can be interpreted as histological adaptations to the buzz-pollination mechanism.

scholarly journals Plant Hormone Metabolome and Transcriptome Analysis of Dwarf and Wild-type Banana

2021 ◽  
Author(s):  
Biao Deng ◽  
Xuan Wang ◽  
Xing Long ◽  
Ren Fang ◽  
Shuangyun Zhou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
Feedback Regulation ◽  
Wild Type ◽  
Hormone Levels ◽  
Transporter Protein ◽  
Repressor Proteins ◽  
Differential Gene ◽  
The Relationship

AbstractGibberellin (GA), auxin (IAA) and brassinosteroid (BR) are indispensable in the process of plant growth and development. Currently, research on the regulatory mechanism of phytohormones in banana dwarfism is mainly focused on GA, and few studies are focused on IAA and BR. In this study, we measured the contents of endogenous GA, IAA and BR and compared the transcriptomes of wild-type Williams banana and its dwarf mutant across five successive growth periods. We investigated the relationship between hormones and banana dwarfism and explored differential gene expression through transcriptome analysis, thus revealing the possible metabolic regulatory mechanism. We inferred a complex regulatory network of banana dwarfing. In terms of endogenous hormone levels, GA and IAA had significant effects on banana dwarfing, while BR had little effect. The key gene in GA biosynthesis of is GA2ox, and the key genes in IAA biosynthesis are TDC and YUCCA. The differential expression of these genes might be the main factor affecting hormone levels and plant height. In terms of hormone signal transduction, DELLA and AUX/IAA repressor proteins were the core regulators of GA and IAA, respectively. They inhibited the process of signal transduction and had feedback regulation on hormone levels. Finally, the transporter protein PIN, AUX1/LAX protein family and ABCB subfamily played supplementary roles in the transport of IAA. These results provide new insights into GA and IAA regulation of banana growth and a reliable foundation for the improvement of dwarf varieties.

scholarly journals De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Liu ◽  
Xiaoting Liu ◽  
Rangrang Zhou ◽  
Hong Chen ◽  
Huaigang Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Processing Technique ◽  
Sodium Selenate ◽  
Control Group ◽  
Primary Mechanism ◽  
High Selenium

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.

scholarly journals The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Lili Ma ◽  
Qing Wang ◽  
Jianlou Mu ◽  
Anzhen Fu ◽  
Changlong Wen ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Transcriptome Analysis ◽  
Fruit Development ◽  
Repetitive Sequences ◽  
Genetic Research ◽  
Future Research ◽  
Comparative Genomic ◽  
Crop Species ◽  
Total Size ◽  
Fruit Development And Ripening

AbstractSnake gourd (Trichosanthes anguina L.), which belongs to the Cucurbitaceae family, is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world. Although progress has been made in its genetic improvement, the organization, composition, and evolution of the snake gourd genome remain largely unknown. Here, we report a high-quality genome assembly for snake gourd, comprising 202 contigs, with a total size of 919.8 Mb and an N50 size of 20.1 Mb. These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date. The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0% of the genome consists of repetitive sequences. Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor ~33–47 million years ago. The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species. In addition, fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.

scholarly journals Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response

2020 ◽  
Vol 21 (24) ◽  
pp. 9556
Author(s):  
Viktor Hlaváč ◽  
Radka Václavíková ◽  
Veronika Brynychová ◽  
Renata Koževnikovová ◽  
Katerina Kopečková ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Genetic Variation ◽  
Abc Transporters ◽  
Statistical Significance ◽  
Strong Support ◽  
Disease Free Survival ◽  
Cancer Prognosis ◽  
Future Research ◽  
Regulatory Sequences

Breast cancer is the most common cancer in women in the world. The role of germline genetic variability in ATP-binding cassette (ABC) transporters in cancer chemoresistance and prognosis still needs to be elucidated. We used next-generation sequencing to assess associations of germline variants in coding and regulatory sequences of all human ABC genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). A total of 43 prioritized variants associating with response or survival in the above testing phase were then analyzed by allelic discrimination in the large validation set (n = 802). Variants in ABCA4, ABCA9, ABCA12, ABCB5, ABCC5, ABCC8, ABCC11, and ABCD4 associated with response and variants in ABCA7, ABCA13, ABCC4, and ABCG8 with survival of the patients. No association passed a false discovery rate test, however, the rs17822931 (Gly180Arg) in ABCC11, associating with response, and the synonymous rs17548783 in ABCA13 (survival) have a strong support in the literature and are, thus, interesting for further research. Although replicated associations have not reached robust statistical significance, the role of ABC transporters in breast cancer should not be ruled out. Future research and careful validation of findings will be essential for assessment of genetic variation which was not in the focus of this study, e.g., non-coding sequences, copy numbers, and structural variations together with somatic mutations.

scholarly journals Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Mao-Sheng Chen ◽  
Mei-Li Zhao ◽  
Gui-Juan Wang ◽  
Hui-Ying He ◽  
Xue Bai ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Metabolic Pathway ◽  
Jatropha Curcas ◽  
Woody Plant ◽  
Regulatory Mechanism ◽  
Adenosine Kinase ◽  
Inflorescence Architecture ◽  
Inflorescence Development ◽  
Order Branch ◽  
Important Regulator

Abstract Background In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. Results Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence buds between dxh and g mutants and WT plants, indicating that they may participate in inflorescence development in Jatropha. The expression of JcTFL1 was downregulated, while the expression of JcLFY and JcAP1 were upregulated in inflorescences in low-branch g mutant. Conclusions Cytokinin is an important regulator in controlling inflorescence branching in Jatropha. The regulation of inflorescence architecture by the genes involved in floral development, including TFL1, LFY and AP1, may be conservative in Jatropha and Arabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture in Jatropha.

scholarly journals Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat

2017 ◽  
Vol 114 (47) ◽  
pp. 12614-12619 ◽  
Author(s):  
Zheng Wang ◽  
Jian Li ◽  
Shaoxia Chen ◽  
Yanfang Heng ◽  
Zhuo Chen ◽  
...  
Keyword(s):  
Male Sterility ◽  
Bread Wheat ◽  
Male Fertility ◽  
Binding Activity ◽  
Hybrid Seed Production ◽  
Hybrid Wheat ◽  
Phospholipid Binding ◽  
Allohexaploid Wheat ◽  
Molecular Nature

Male sterility is an essential trait in hybrid seed production for monoclinous crops, including rice and wheat. However, compared with the high percentage of hybrid rice planted in the world, little commercial hybrid wheat is planted globally as a result of the lack of a suitable system for male sterility. Therefore, understanding the molecular nature of male fertility in wheat is critical for commercially viable hybrid wheat. Here, we report the cloning and characterization of Male Sterility 1 (Ms1) in bread wheat by using a combination of advanced genomic approaches. MS1 is a newly evolved gene in the Poaceae that is specifically expressed in microsporocytes, and is essential for microgametogenesis. Orthologs of Ms1 are expressed in diploid and allotetraploid ancestral species. Orthologs of Ms1 are epigenetically silenced in the A and D subgenomes of allohexaploid wheat; only Ms1 from the B subgenome is expressed. The encoded protein, Ms1, is localized to plastid and mitochondrial membranes, where it exhibits phospholipid-binding activity. These findings provide a foundation for the development of commercially viable hybrid wheat.

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