scholarly journals Genome-Wide Small RNA Analysis of Soybean Reveals Auxin-Responsive microRNAs that are Differentially Expressed in Response to Salt Stress in Root Apex

2016 ◽  
Vol 6 ◽  
Author(s):  
Zhengxi Sun ◽  
Youning Wang ◽  
Fupeng Mou ◽  
Yinping Tian ◽  
Liang Chen ◽  
...  
Keyword(s):  
Salt Stress ◽  
Small Rna ◽  
Root Apex ◽  
Differentially Expressed ◽  
Rna Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules

2009 ◽  
Vol 21 (9) ◽  
pp. 2780-2796 ◽  
Author(s):  
Christine Lelandais-Brière ◽  
Loreto Naya ◽  
Erika Sallet ◽  
Fanny Calenge ◽  
Florian Frugier ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Small Rna ◽  
Rna Analysis ◽  
Genome Wide

scholarly journals Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yanchao Yuan ◽  
Huixian Xing ◽  
Wenguan Zeng ◽  
Jialing Xu ◽  
Lili Mao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Upland Cotton ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Salt Tolerant ◽  
Genome Wide ◽  
Germination Stage

Abstract Background Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. Results In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. Conclusions These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.

Combined RNA-seq, small RNA and degradome sequencing approaches insights into salt-stress responses in Beta vulgaris

2019 ◽  
Author(s):  
Junliang Li ◽  
Jie Cui ◽  
Dayou Cheng ◽  
Cuihong Dai ◽  
Tianjiao Liu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Beta Vulgaris ◽  
Small Rna ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Salt Stress Response ◽  
Degradome Sequencing ◽  
A Genome

Abstract Background Salinity is one of the most serious threat to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt. While a genome-wide analysis of genes involved in salt-stress remains largely unknown in B. vulgaris. Results Three high-throughput sequencing approaches, namely, RNA-seq, small RNA and degradome sequencing were used to exploring the molecular basis of salt-resistance in beta vulgaris. A total of 12 230 differentially expressed genes were identified, which were mainly related to transcription factors, protein kinases, and enzymes. The small RNA sequencing resulted in the identification of 476 miRNAs included 219 known and 257 novel miRNAs, of which 130 were differentially expressed under salt-stress. A total of 2534 targets were predicted for 317 miRNAs by bioinformatics and degradome sequencing. Functional analysis of these targets suggested that miRNA-mediated post-transcriptional regulation plays a crucial role in transcriptional reprogramming under stress. The combination analysis of multi-omics revealed 209 negative correlation mRNA-miRNA pairs. All these data were used to construct a hypothetical regulatory network of beta vulgaris in response to salt stress. Conclusion These components and the preliminary network provides better insights into the molecular mechanism of salt-stress response, and also offers candidate genes for beet improvement.

scholarly journals Comparative Profiling of Small RNAs Originated From Two Varieties of Chinese Cabbage (Brassica Rapa) With Distinct Leaf Traits

2021 ◽  
Author(s):  
XU XIN LIU ◽  
XIANG YU ◽  
HAN WANG ◽  
YU KE HE
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Small Rna ◽  
Small Rnas ◽  
Leaf Shape ◽  
Leaf Traits ◽  
Differentially Expressed ◽  
High Yield ◽  
Genome Wide ◽  
A Genome

Abstract The species Brassica rapa includes many important vegetable crops. For a genome-wide survey of small RNAs in B. rapa, we performed massively parallel small RNA deep sequencing by using two representative varieties of non-heading Chinese cabbage (B. rapa ssp. chinensis) that are distinct in leaf shape, size, color and curvature. In total, 13.30 million small RNA reads were generated from Huaq, a variety with up-curved blades and wide petioles, and 14.69 million for Wut, a variety with down-curved blades and narrow petioles. After normalization, about half of small RNA reads in each variety were mapped to the published reference genome of B. rapa. In Huaq seedlings, unique small RNAs were much more than in Wut seedlings. Among them, 45 miRNAs were up-regulated or down-regulated in one variety, compared with those in another variety. Numbers of ta-siRNAs (trans-acting siRNAs) and ra-siRNAs (repeat-associated siRNAs) in Huaq seedlings were more than those detected in Wut seedlings, while gene-derived siRNAs (siRNAs derived from the sense and antisense strands of annotated genes regeion) in Huaq seedlings were less than in Wut seedlings. Especially, bra-miR156, bra-miR166 and bra-miR319 and one of ta-siRNAs that play important role in leaf shape, leaf size, leaf curvature and phase transition were differentially expressed between two varieties. In addition, total number of small RNAs derived from chloroplast genome of Wut was more than that of Huaq. The differentially-expressed small RNAs on genome-wide level provides the clue for the study of small-RNA-mediated morphology of leaves and is useful for developing of small RNA markers for leaf traits desirable for high yield and quality.

scholarly journals Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samina Shabbir ◽  
Prerona Boruah ◽  
Lingli Xie ◽  
Muhammad Fakhar-e-Alam Kulyar ◽  
Mohsin Nawaz ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Ovarian Follicle ◽  
Follicular Development ◽  
Differentially Expressed ◽  
Ovary Development ◽  
Estrogen Metabolism ◽  
Genome Wide ◽  
Micro Rnas ◽  
Hu Sheep

AbstractOvary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

scholarly journals Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 232
Author(s):  
Weiran Zheng ◽  
Haichao Hu ◽  
Qisen Lu ◽  
Peng Jin ◽  
Linna Cai ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

scholarly journals Transcriptomic Analysis of Rice Plants Overexpressing PsGAPDH in Response to Salinity Stress

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 641
Author(s):  
Hyemin Lim ◽  
Hyunju Hwang ◽  
Taelim Kim ◽  
Soyoung Kim ◽  
Hoyong Chung ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salinity Stress ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Rice Plants ◽  
Significant Difference

In plants, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a main enzyme in the glycolytic pathway. It plays an essential role in glycerolipid metabolism and response to various stresses. To examine the function of PsGAPDH (Pleurotus sajor-caju GAPDH) in response to abiotic stress, we generated transgenic rice plants with single-copy/intergenic/homozygous overexpression PsGAPDH (PsGAPDH-OX) and investigated their responses to salinity stress. Seedling growth and germination rates of PsGAPDH-OX were significantly increased under salt stress conditions compared to those of the wild type. To elucidate the role of PsGAPDH-OX in salt stress tolerance of rice, an Illumina HiSeq 2000 platform was used to analyze transcriptome profiles of leaves under salt stress. Analysis results of sequencing data showed that 1124 transcripts were differentially expressed. Using the list of differentially expressed genes (DEGs), functional enrichment analyses of DEGs such as Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed. KEGG pathway enrichment analysis revealed that unigenes exhibiting differential expression were involved in starch and sucrose metabolism. Interestingly, trehalose-6-phosphate synthase (TPS) genes, of which expression was enhanced by abiotic stress, showed a significant difference in PsGAPDH-OX. Findings of this study suggest that PsGAPDH plays a role in the adaptation of rice plants to salt stress.

scholarly journals Microtubule Dynamics Plays a Vital Role in Plant Adaptation and Tolerance to Salt Stress

2021 ◽  
Vol 22 (11) ◽  
pp. 5957
Author(s):  
Hyun Jin Chun ◽  
Dongwon Baek ◽  
Byung Jun Jin ◽  
Hyun Min Cho ◽  
Mi Suk Park ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Salt Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Related Gene ◽  
Plant Adaptation ◽  
Salt Stress Response ◽  
Network Analyses ◽  
Cell Wall Biogenesis

Although recent studies suggest that the plant cytoskeleton is associated with plant stress responses, such as salt, cold, and drought, the molecular mechanism underlying microtubule function in plant salt stress response remains unclear. We performed a comparative proteomic analysis between control suspension-cultured cells (A0) and salt-adapted cells (A120) established from Arabidopsis root callus to investigate plant adaptation mechanisms to long-term salt stress. We identified 50 differentially expressed proteins (45 up- and 5 down-regulated proteins) in A120 cells compared with A0 cells. Gene ontology enrichment and protein network analyses indicated that differentially expressed proteins in A120 cells were strongly associated with cell structure-associated clusters, including cytoskeleton and cell wall biogenesis. Gene expression analysis revealed that expressions of cytoskeleton-related genes, such as FBA8, TUB3, TUB4, TUB7, TUB9, and ACT7, and a cell wall biogenesis-related gene, CCoAOMT1, were induced in salt-adapted A120 cells. Moreover, the loss-of-function mutant of Arabidopsis TUB9 gene, tub9, showed a hypersensitive phenotype to salt stress. Consistent overexpression of Arabidopsis TUB9 gene in rice transgenic plants enhanced tolerance to salt stress. Our results suggest that microtubules play crucial roles in plant adaptation and tolerance to salt stress. The modulation of microtubule-related gene expression can be an effective strategy for developing salt-tolerant crops.

scholarly journals Genome-wide identification of the GATA transcription factor family and their expression patterns under temperature and salt stress in Aspergillus oryzae

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunmiao Jiang ◽  
Gongbo Lv ◽  
Jinxin Ge ◽  
Bin He ◽  
Zhe Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Gata Transcription Factor ◽  
Starting Point ◽  
Evolutionary Features ◽  
First Time

AbstractGATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X2-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.

scholarly journals Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peng Xu ◽  
Qi Guo ◽  
Shan Meng ◽  
Xianggui Zhang ◽  
Zhenzhen Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Fresh Matter ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

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