scholarly journals Transcriptome analysis identifies differentially expressed genes involved in the metabolic regulatory network of progenies from the cross of low phytic acid GmMIPS1 and GmIPK1 soybean mutants

2020 ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Fengjie Yuan ◽  
Xujun Fu
Keyword(s):  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Low Phytic Acid ◽  
Advanced Generation ◽  
High Sucrose

Abstract Lowering the phytic acid (PA) content of crop seeds will be beneficial for improving their nutritional traits. Low phytic acid (lpa) crop lines carrying more than one independent mutated gene have been shown to exhibit more pronounced reductions of PA content than mutants with a single lpa mutated gene. But little is known about the link between PA pathway intermediates and downstream regulation following mutation of these genes in soybean. Here, we performed a comparative transcriptome analysis using an advanced-generation recombinant inbred line [2mlpa (mips1/ipk1)] with low PA and a sibling line with homozygous non-mutant alleles and normal PA [2MWT (MIPS1/IPK1)]. RNA sequencing revealed differential expression levels of numerous genes between seeds of 2mlpa and 2MWT at five developmental stages. A total of 7,945 differentially expressed genes were identified. 3316 DEGs were in 128 metabolic and signal transduction pathways and 4980 DEGs were classified into 345 function terms associated with biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were related to low PA in 2mlpa soybean line. Among these, 36 genes were up/down-regulated in PA metabolic processes, with 22 possibly contributing to the low PA phenotype of 2mlpa. Most of the genes (81 of 117) associated with photosynthesis were down-regulated in 2mlpa at the late seed stage. Three genes involved in sucrose metabolism were up-regulated at the late seed stage, which might explain the high sucrose content of 2mlpa soybeans. Additionally, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this research, the soybean mutant 2mlpa was found to not only exhibit low PA but also have changes in multiple metabolites and secondary metabolites. The results delineate the regulation of these metabolic events by 2mlpa. Many genes associated with PA metabolism would contribute to the drastic reduction of PA and moderate accumulation of InsP3-InsP5 in 2mlpa mutant. And other regulated genes found in photosynthesis, starch and sucrose metabolism, and defense mechanisms would give us more insight into the nutritional and agronomic performance of 2mlpa.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

Transcriptome analysis reveals differentially expressed genes associated with the mantled homeotic flowering abnormality in oil palm (Elaeis guineensis)

2010 ◽  
Vol 7 (1) ◽  
pp. 169-182 ◽  
Author(s):  
Thierry Beulé ◽  
Céline Camps ◽  
Ségolène Debiesse ◽  
Christine Tranchant ◽  
Stéphane Dussert ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Differentially Expressed

scholarly journals Profiling of BABA-induced differentially expressed genes of Zea mays using suppression subtractive hybridization

RSC Advances ◽  
2017 ◽  
Vol 7 (69) ◽  
pp. 43849-43865 ◽  
Author(s):  
Arun K. Shaw ◽  
Pardeep K. Bhardwaj ◽  
Supriya Ghosh ◽  
Ikbal Azahar ◽  
Sinchan Adhikari ◽  
...  
Keyword(s):  
Zea Mays ◽  
Differentially Expressed Genes ◽  
Suppression Subtractive Hybridization ◽  
Defense Mechanisms ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Maize Leaves

This study aims to identify differentially expressed transcripts in BABA-primed maize leaves using suppression subtractive hybridization (SSH) strategy. Findings shed new light on the BABA potentiated defense mechanisms in plants.

scholarly journals Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia

2019 ◽  
Author(s):  
Leah J Radeke ◽  
Michael Herman
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Stenotrophomonas Maltophilia ◽  
Defense Mechanisms ◽  
Virulent Strain ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Transcriptomic Response ◽  
C Elegans ◽  
Realistic Interaction

Abstract Background: Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans , being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans . Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results: Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions: Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.

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