Multiomics Combined Analysis of Low-Phosphorus and Drought Stresses in Lotus Japonicus

Abstract BackgroundLotus japonicus is a perennial herb in Leguminosae. It is a good feed source and improves soil. It is also an excellent honey source and medicinal plant. Low-phosphorus and drought stresses are among the main abiotic stress factors limiting the production of pulse roots. MethodsIn this experiment, the effects of low-phosphorus and drought stresses on Baimai roots were analyzed under three treatments: control (zl1), low-phosphorus stress (zl2) and drought stress (zl3). Results A total of 2176, 3026 and 2980 differentially expressed genes were screened in zl1 vs. zl2, zl1 vs. zl3 and zl2 vs. zl3, respectively. The differentially expressed genes were enriched in functions related to cells, membranes, ion binding, enzyme activity and resistance to low-phosphorus and drought stresses. The enriched KEGG pathways included the MAPK signaling pathway-plant, flavor biosynthesis, starch and sucrose metabolism and plant hormone signal transmission. In particular, a large number of differentially expressed genes were enriched in the response to plant hormone signal transmission pathways among different treatments, and gene expression changes were analyzed. In addition, the differentially expressed genes identified under drought stress and the phase response genes identified under osmotic stress were upregulated. Differential metabolites were mainly enriched in the important metabolic pathways of flavonoid biosynthesis, arginine and proline metabolism and starch and sucrose metabolism. Differentially expressed proteins were mainly enriched in GO terms related to cell, membrane, ion binding and enzyme activity functions, and the main enriched KEGG pathways included the ribosome, starch and sucrose metabolism and plant hormone signal transmission pathways. ConclusionIn conclusion, these results of transcriptome, metabolome and proteome sequencing are helpful for understanding the response mechanisms, gene changes, metabolite changes and protein changes in Baimai roots under low-phosphorus and drought stress conditions to lay a foundation for future research on Lotus japonicus.

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Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat

10.21203/rs.3.rs-45684/v1 ◽

2020 ◽

Author(s):

Xiangchi Zhang ◽

Weidan Lu ◽

Xiaoli Wang ◽

Bin Ma ◽

Kaiyong Fu ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Winter Wheat ◽

Differentially Expressed Genes ◽

Stress Responses ◽

Differentially Expressed ◽

Phosphorus Level ◽

Root Tips ◽

Percentage Content ◽

Low Phosphorus

Abstract Phosphorus stress and drought stress are common abiotic stresses. In this study, two winter wheat “Xindong20” and “Xindong23” were solution cultured and then treated with drought stress under conventional phosphorus level (CP: 1.0 mmol/L) and low phosphorus level (LP: 0.05 mmol /L), respectively. The results showed that with the increase of drought stress, the LP application was more conducive to the growth of root tips, length, forks, surfarea and root vitality of wheat. Under the LP treatment, the total phosphorus content of root at rewatered 3d was increased by 94.2% in Xindong20 wheat and decreased by 48.9% in Xindong23 wheat, compared with their respective samples at drought 0d. The LP treatment increased the percentage content of K and decreased the P and Ca percentage content. However, under CP treatment, the percentage content of Zn after rewatered 3 days were increased, compared with drought 7d. Based on the GeneChip analysis of root samples from drought 7d, the microarray results showed that 4577 and 202 differentially expressed genes were detected from Xindong20 and Xindong23, respectively. Among them, 89.9% of differentially expressed genes were involved in organelles and vesicles in Xindong20, and 69.8% were involved in genes encoding root anatomical structure, respiratory chain, electron transport chain, ion transport and enzyme activity in Xindong23. Therefore, the supply of low phosphorus has more effects on the drought tolerance of wheat, and the wheat with different drought tolerance has different regulatory genes. The higher drought-tolerant wheat has more genes up-regulation in response to drought stress.

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Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

International Journal of Genomics ◽

10.1155/2018/3057272 ◽

2018 ◽

Vol 2018 ◽

pp. 1-13 ◽

Cited By ~ 6

Author(s):

Chunsheng Gao ◽

Chaohua Cheng ◽

Lining Zhao ◽

Yongting Yu ◽

Qing Tang ◽

...

Keyword(s):

Drought Stress ◽

Differentially Expressed Genes ◽

Cannabis Sativa ◽

Expression Profiles ◽

Expression Patterns ◽

Signal Transduction Pathway ◽

Differentially Expressed ◽

Growth And Yield ◽

Rna Seq ◽

Kegg Pathways

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

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

Scientific Reports ◽

10.1038/s41598-021-88055-4 ◽

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.

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Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

BioMed Research International ◽

10.1155/2018/9150723 ◽

2018 ◽

Vol 2018 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Songbai Yang ◽

Xiaolong Zhou ◽

Yue Pei ◽

Han Wang ◽

Ke He ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Hormone Secretion ◽

Differentially Expressed ◽

Receptor Interaction ◽

The Novel ◽

Kegg Pathways ◽

Go Enrichment ◽

Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2 Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

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