scholarly journals Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Yanrong Zhang ◽  
Fuchao Jiao ◽  
Jun Li ◽  
Yuhe Pei ◽  
Meiai Zhao ◽  
...  
Keyword(s):  
Grain Size ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Kernel Weight ◽  
Grain Development ◽  
Key Factor ◽  
Length Width ◽  
Maize Grain ◽  
Grain Width ◽  
Transcriptome Level

Abstract Backgrounds Grain size is a key factor in crop yield that gradually develops after pollination. However, few studies have reported gene expression patterns in maize grain development using large-grain mutants. To investigate the developmental mechanisms of grain size, we analyzed a large-grain mutant, named tc19, at the morphological and transcriptome level at five stages corresponding to days after pollination (DAP). Results After maturation, the grain length, width, and thickness in tc19 were greater than that in Chang7-2 (control) and increased by 3.57, 8.80, and 3.88%, respectively. Further analysis showed that grain width and 100-kernel weight in tc19 was lower than in Chang7-2 at 14 and 21 DAP, but greater than that in Chang7-2 at 28 DAP, indicating that 21 to 28 DAP was the critical stage for kernel width and weight development. For all five stages, the concentrations of auxin and brassinosteroids were significantly higher in tc19 than in Chang7-2. Gibberellin was higher at 7, 14, and 21 DAP, and cytokinin was higher at 21 and 35 DAP, in tc19 than in Chang7-2. Through transcriptome analysis at 14, 21, and 28 DAP, we identified 2987, 2647 and 3209 differentially expressed genes (DEGs) between tc19 and Chang7-2. By using KEGG analysis, 556, 500 and 633 DEGs at 14, 21 and 28 DAP were pathway annotated, respectively, 77 of them are related to plant hormone signal transduction pathway. ARF3, AO2, DWF4 and XTH are higher expressed in tc19 than that in Chang7-2. Conclusions We found some DEGs in maize grain development by using Chang7-2 and a large-grain mutant tc19. These DEGs have potential application value in improving maize performance.

scholarly journals Transcriptomic Analysis of the Maize Mutant TC19 Identifies Genes Regulating the Development of Grain Size Through the IAA and BR Pathways

2021 ◽  
Author(s):  
Yanrong Zhang ◽  
Fuchao Jiao ◽  
Jun Li ◽  
Yuhe Pei ◽  
Meiai Zhao ◽  
...  
Keyword(s):  
Grain Size ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Grain Filling ◽  
Maize Breeding ◽  
Key Factor ◽  
Cell Components ◽  
Length Width ◽  
Grain Width ◽  
Grain Filling Stage

Abstract Backgrounds: Grain size is a key factor in crop yield that gradually develops after pollination. However, few studies have reported gene expression patterns in maize grain development using mutants. To investigate the developmental mechanisms of grain size, we analyzed a large-grain mutant, named TC19, at the morphological and transcriptome level at five stages corresponding to days after pollination (DAP).Results: After maturation, the grain length, width, and thickness in TC19 were greater than that in Chang 7-2 (control) and increased by 3.57%, 8.80%, and 3.88%, respectively. Further analysis showed that grain width in TC19 was lower than in Chang 7-2 at 7, 14, and 21 DAP, but greater than that in Chang 7-2 at 28 and 35 DAP, indicating that 21 to 28 DAP was the critical stage for kernel width development. For all five stages, the concentrations of indole-3-acetic acid and brassinosteroids were significantly higher in TC19 than in Chang 7-2. Gibberellin was higher at 7, 14, and 21 DAP, and cytokinin was higher at 21 and 35 DAP, in TC19 than in Chang 7-2. Through transcriptome analysis at 14, 21, and 28 DAP, we identified 2987, 2647, and 3209 differentially expressed genes (DEGs) between TC19 and Chang 7-2. Gene Ontology analysis indicated that most of the grain size–related genes corresponded to three aspects, including cell components, molecular functions, and biological processes. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that 77 DEGs were enriched in the plant hormone signal transduction pathway. We further analyzed several highly expressed candidate genes, including AO2, ARF3, and IAA15, which are involved in the synthesis of IAA; and DWF4 and XTH, which are involved in the synthesis of BR.Conclusions: Our results elucidated the mechanisms of grain size development at the grain-filling stage and have potential application in maize breeding.

scholarly journals The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division

2019 ◽  
Vol 116 (32) ◽  
pp. 16121-16126 ◽  
Author(s):  
Ying Zhang ◽  
Yan Xiong ◽  
Renyi Liu ◽  
Hong-Wei Xue ◽  
Zhenbiao Yang
Keyword(s):  
Grain Size ◽  
Cell Division ◽  
Grain Yield ◽  
Molecular Mechanisms ◽  
Grain Filling ◽  
High Yield ◽  
Rice Grain ◽  
Rop Gtpase ◽  
Key Factor ◽  
Grain Width

Grain size is a key factor for determining grain yield in crops and is a target trait for both domestication and breeding, yet the mechanisms underlying the regulation of grain size are largely unclear. Here we show that the grain size and yield of rice (Oryza sativa) is positively regulated by ROP GTPase (Rho-like GTPase from plants), a versatile molecular switch modulating plant growth, development, and responses to the environment. Overexpression of rice OsRac1ROP not only increases cell numbers, resulting in a larger spikelet hull, but also accelerates grain filling rate, causing greater grain width and weight. As a result, OsRac1 overexpression improves grain yield in O. sativa by nearly 16%. In contrast, down-regulation or deletion of OsRac1 causes the opposite effects. RNA-seq and cell cycle analyses suggest that OsRac1 promotes cell division. Interestingly, OsRac1 interacts with and regulates the phosphorylation level of OsMAPK6, which is known to regulate cell division and grain size in rice. Thus, our findings suggest OsRac1 modulates rice grain size and yield by influencing cell division. This study provides insights into the molecular mechanisms underlying the control of rice grain size and suggests that OsRac1 could serve as a potential target gene for breeding high-yield crops.

scholarly journals Physical Characterisation of Brown and White Fractions of Approved Rice Varieties of Pakistan

2019 ◽  
Vol 62 (3) ◽  
pp. 139-147
Author(s):  
Rebia Ejaz ◽  
Mian Kamran Sharifa ◽  
Imran Pasha ◽  
Muhammad Anjum Zia
Keyword(s):  
Grain Size ◽  
Bulk Density ◽  
Brown Rice ◽  
Kernel Weight ◽  
Width Ratio ◽  
Rice Varieties ◽  
Mean Values ◽  
White Rice ◽  
Foreign Earnings ◽  
Grain Width

 This study was carried out to assess the quality attributes of rice varieties named as Super Kernel, Super Basmati, Basmati-515, PK-386, Kainat and IRRI-9 after milling for the establishment of claimed standards for approved varieties to prohibit rice adulteration. Furthermore, brown and white fractions of selected varieties were evaluated for physical characteristics including grain size (grain length/grain width ratio) thousand kernel weight (TKW) and bulk density. Mean values for grain size (L/W ratio), bulk density and TKW were ranged from 3.86±0.30 to 4.59±0.32, 0.71±0.08 to 0.80±0.10g/mL and 16.74±1.18 to 17.96±0.85g among the rice cultivars. Overall, grain size (4.00±0.21 to 4.48±0.35 and 4.14±0.43 to 4.81±0.37), bulk density (0.66±0.05 to 0.72±0.09g/mL and 0.77±0.05 to 0.82±0.27g/mL) and TKW  (18.00±0.48 to 19.22±0.35g and 15.91±0.84 to 16.78±0.32g) varied significantly in brown and white rice samples. The lowest decrease in length after milling was seen in white rice of Kainat (8.90%) followed by PK-386 (9.86%) and Basmati-515 (10.70%), while the IRRI-9 showed highest decrease (11.84%) as compare to brown rice. Likewise, lowest increase in width was observed in IRRI-9 (10.27%) as compared to Kainat (19.87%) which indicates that IRRI-9 had more width. Conclusively, grain dimensions, kernel weight and bulk density of both brown and white rice fractions were significantly influenced by genetic, environmental and socio-economic factors among locations and cultivars. There is an urgent need to discriminate among premium and local rice varieties of country to boost up the export and foreign earnings.  

scholarly journals Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ting-Ying Wu ◽  
Marlen Müller ◽  
Wilhelm Gruissem ◽  
Navreet K. Bhullar
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Expression Patterns ◽  
Grain Filling ◽  
Aleurone Layer ◽  
Rice Grain ◽  
Sequence Motifs ◽  
Grain Development ◽  
Spatio Temporal ◽  
Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main Text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

scholarly journals Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Lin Zhang ◽  
Bin Ma ◽  
Zhong Bian ◽  
Xiaoyuan Li ◽  
Changquan Zhang ◽  
...  
Keyword(s):  
Grain Size ◽  
Grain Yield ◽  
Rational Design ◽  
Width Ratio ◽  
Functional Markers ◽  
Rice Breeding ◽  
Nucleotide Polymorphisms ◽  
Yield And Quality ◽  
Grain Width ◽  
Grain Yield And Quality

Abstract Background Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. Result In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio. Conclusions The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

Mechanism of anteroposterior axis specification in vertebrates. Lessons from the amphibians

Development ◽  
1992 ◽  
Vol 114 (2) ◽  
pp. 285-302 ◽  
Author(s):  
J.M. Slack ◽  
D. Tannahill
Keyword(s):  
Molecular Markers ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Homeobox Gene ◽  
Neural Induction ◽  
High Sensitivity ◽  
Neural Plate ◽  
Mesoderm Induction ◽  
Inducing Factors ◽  
Almost All

Interest in the problem of anteroposterior specification has quickened because of our near understanding of the mechanism in Drosophila and because of the homology of Antennapedia-like homeobox gene expression patterns in Drosophila and vertebrates. But vertebrates differ from Drosophila because of morphogenetic movements and interactions between tissue layers, both intimately associated with anteroposterior specification. The purpose of this article is to review classical findings and to enquire how far these have been confirmed, refuted or extended by modern work. The “pre-molecular” work suggests that there are several steps to the process: (i) Formation of anteroposterior pattern in mesoderm during gastrulation with posterior dominance. (ii) Regional specific induction of ectoderm to form neural plate. (iii) Reciprocal interactions from neural plate to mesoderm. (iv) Interactions within neural plate with posterior dominance. Unfortunately, almost all the observable markers are in the CNS rather than in the mesoderm where the initial specification is thought to occur. This has meant that the specification of the mesoderm has been assayed indirectly by transplantation methods such as the Einsteckung. New molecular markers now supplement morphological ones but they are still mainly in the CNS and not the mesoderm. A particular interest attaches to the genes of the Antp-like HOX clusters since these may not only be markers but actual coding factors for anteroposterior levels. We have a new understanding of mesoderm induction based on the discovery of activins and fibroblast growth factors (FGFs) as candidate inducing factors. These factors have later consequences for anteroposterior pattern with activin tending to induce anterior, and FGF posterior structures. Recent work on neural induction has implicated cAMP and protein kinase C (PKC) as elements of the signal transduction pathway and has provided new evidence for the importance of tangential neural induction. The regional specificity of neural induction has been reinvestigated using molecular markers and provides conclusions rather similar to the classical work. Defects in the axial pattern may be produced by retinoic acid but it remains unclear whether its effects are truly coordinate ones or are concentrated in certain regions of high sensitivity. In general the molecular studies have supported and reinforced the “pre-molecular ones”. Important questions still remain: (i) How much pattern is there in the mesoderm (how many states?) (ii) How is this pattern generated by the invaginating organizer? (iii) Is there one-to-one transmission of codings to the neural plate? (iv) What is the nature of the interactions within the neural plate? (v) Are the HOX cluster genes really the anteroposterior codings?

Dissection of Closely Linked QTLs Controlling Grain Size in Rice

2021 ◽  
Author(s):  
Pao Xue ◽  
Yu-yu Chen ◽  
Xiao-xia Wen ◽  
Bei-fang Wang ◽  
Qin-qin Yang ◽  
...  
Keyword(s):  
Grain Size ◽  
Genetic Resources ◽  
Candidate Genes ◽  
Cell Expansion ◽  
Grain Weight ◽  
Cytological Observation ◽  
Yield Improvement ◽  
Transcript Levels ◽  
Grain Width ◽  
Successive Generations

Abstract Grain size is a key constituent of grain weight and appearance in rice. However, insufficient attention has been paid to the small-effect QTLs on grain size. In the present study, residual heterozygous populations were developed for mapping two genetically linked small-effect QTLs for grain size. After genotyping and phenotyping of five successive generations, qGS7.1 was dissected into three QTLs and two were selected for further analysis. qTGW7.2a was finally mapped into a 21.10-kb interval containing four annotated candidate genes. Transcript levels assay showed that the expression of candidates LOC_Os07g39490 and LOC_Os07g39500 were significantly reduced in the NIL- qTGW7.2a BG1 . Cytological observation indicated that qTGW7.2a regulated grain width through controlling cell expansion. Use the same strategy, qTGW7.2b was fine mapped into a 52.71-kb interval, showing a significant effect on grain length and width with opposite allelic directions but little on grain weight. Our study provides new genetic resources for yield improvement and fine-tunes of grain size in rice.

scholarly journals Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.)

2019 ◽  
Vol 20 (4) ◽  
pp. 962 ◽  
Author(s):  
Jianxin Bian ◽  
Pingchuan Deng ◽  
Haoshuang Zhan ◽  
Xiaotong Wu ◽  
Mutthanthirige Nishantha ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Rna Editing ◽  
Signal Transduction Pathway ◽  
Sugar Metabolism ◽  
Transcriptome Profiling ◽  
Barley Grain ◽  
Grain Development ◽  
Hordeum Vulgare L ◽  
Functional Studies ◽  
Transcriptional Dynamics

Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts’ activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in “essential” genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a ‘regulator’ to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond.

Dysregulated Prefrontal Cortical RhoA Signal Transduction in Bipolar Disorder with Psychosis: New Implications for Disease Pathophysiology

2019 ◽  
Vol 30 (1) ◽  
pp. 59-71
Author(s):  
Bailey A Kermath ◽  
Amanda M Vanderplow ◽  
Michael E Cahill
Keyword(s):  
Signal Transduction ◽  
Bipolar Disorder ◽  
Signal Transduction Pathway ◽  
Signal Transduction Pathways ◽  
Cellular Functions ◽  
Protein Activity ◽  
Cortical Function ◽  
Prefrontal Cortical ◽  
Dorsolateral Prefrontal ◽  
Key Factor

Abstract While research has identified alterations in dorsolateral prefrontal cortical function as a key factor to the etiology of bipolar disorder, few studies have uncovered robust changes in protein signal transduction pathways in this disorder. Given the direct relevance of protein-based expressional alterations to cellular functions and because many of the key regulatory mechanisms for the disease pathogenesis likely include alterations in protein activity rather than changes in expression alone, the identification of alterations in discrete signal transduction pathways in bipolar disorder would have broad implications for understanding the disease pathophysiology. As prior microarray data point to a previously unrecognized involvement of the RhoA network in bipolar disorder, here we investigate the protein expression and activity of key components of a RhoA signal transduction pathway in dorsolateral prefrontal cortical homogenates from subjects with bipolar disorder. The results of this investigation implicate overactivation of prefrontal cortical RhoA signaling in specific subtypes of bipolar disorder. The specificity of these findings is demonstrated by a lack of comparable changes in schizophrenia; however, our findings do identify convergence between both disorders at the level of activity-mediated actin cytoskeletal regulation. These findings have implications for understanding the altered cortical synaptic connectivity of bipolar disorder.

Sign in / Sign up

Export Citation Format

Share Document