Identification of PtGai (a DELLA protein) in trifoliate orange and expression patterns in response to drought stress

Abstract Background Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. Results In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

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Mycorrhizal symbiosis down-regulates or does not change root aquaporin expression in trifoliate orange under drought stress

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2019.10.001 ◽

2019 ◽

Vol 144 ◽

pp. 292-299 ◽

Cited By ~ 2

Author(s):

Ying-Ning Zou ◽

Hui-Hui Wu ◽

Bhoopander Giri ◽

Qiang-Sheng Wu ◽

Kamil Kuča

Keyword(s):

Drought Stress ◽

Mycorrhizal Symbiosis ◽

Trifoliate Orange

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Effect of Drought on Storage Root Development and Gene Expression Profile of Sweetpotato under Greenhouse and Field Conditions

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.3.317 ◽

2014 ◽

Vol 139 (3) ◽

pp. 317-324 ◽

Cited By ~ 12

Author(s):

Julio Solis ◽

Arthur Villordon ◽

Niranjan Baisakh ◽

Don LaBonte ◽

Nurit Firon

Keyword(s):

Drought Stress ◽

Differential Expression ◽

Root Development ◽

Water Deprivation ◽

Expression Patterns ◽

Storage Root ◽

Altered Expression ◽

Sand Control ◽

Binding Factor ◽

Drought Conditions

Greenhouse and field culture systems were used to study the effect of drought conditions on the storage root (SR) formation in ‘Beauregard’ sweetpotato (Ipomoea batatas). In the greenhouse culture system, drought was simulated by withholding water for 5 and 10 days after transplanting (DAT) cuttings in dry sand. Control plants received water at planting and every 3 days thereafter. In the field studies, natural drought conditions and selective irrigation were used to impose water deprivation during the critical SR formation period. Greenhouse drought for 5 and 10 DAT reduced the number of SRs by 42% and 66%, respectively, compared with the controls. Field drought resulted in a 49% reduction in U.S. #1 SR yield compared with the irrigated condition. Quantitative real-time polymerase chain reaction (PCR) analysis showed differential expression of a set of sweetpotato transcription factors and protein kinases among greenhouse-grown plants subjected to well-watered conditions and water deficit during 5 DAT. A significant enhancement of expression was observed for known drought stress-associated genes such as an abscisic acid-responsive elements-binding factor, dehydration-responsive element-binding factor, and homeo-domain-zip proteins. Members of calcium-binding proteins showed differential expression under drought stress. For the first time it is reported that knotted1-like homeobox and BEL1-like genes showed altered expression in response to drought stress under a greenhouse condition. In summary, the results suggest that water deprivation during the SR formation period influences root development and expression patterns of stress-responsive genes and those previously found associated with SR formation in sweetpotato.

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Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

Canadian Journal of Plant Science ◽

10.1139/cjps-2020-0160 ◽

2021 ◽

Author(s):

Bo Shu ◽

YaChao Xie ◽

Fei Zhang ◽

Dejian Zhang ◽

Chunyan Liu ◽

...

Keyword(s):

Abiotic Stress ◽

Drought Stress ◽

Arbuscular Mycorrhizal Fungi ◽

Stress Responses ◽

Mycorrhizal Fungi ◽

Expression Patterns ◽

Arbuscular Mycorrhizal ◽

Biotic And Abiotic Stress ◽

Genome Wide ◽

A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

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Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

International Journal of Molecular Sciences ◽

10.3390/ijms20215419 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5419 ◽

Cited By ~ 4

Author(s):

Gao-Feng Zhou ◽

Li-Ping Zhang ◽

Bi-Xian Li ◽

Ou Sheng ◽

Qing-Jiang Wei ◽

...

Keyword(s):

Signal Transduction ◽

Plant Hormones ◽

Target Genes ◽

Expression Patterns ◽

Poncirus Trifoliata ◽

Differentially Expressed ◽

Boron Deficiency ◽

Trifoliate Orange ◽

Genome Wide ◽

A Genome

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

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Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21228520 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8520

Author(s):

Ling Qin ◽

Erying Chen ◽

Feifei Li ◽

Xiao Yu ◽

Zhenyu Liu ◽

...

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Drought Stress ◽

Expression Profiles ◽

Expression Patterns ◽

Foxtail Millet ◽

Gene Expression Profiles ◽

Sugar Metabolism ◽

Setaria Italica ◽

Phenylpropanoid Biosynthesis

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

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An ABA-flavonoid relationship contributes to the differences in drought resistance between different sea buckthorn subspecies

Tree Physiology ◽

10.1093/treephys/tpaa155 ◽

2020 ◽

Author(s):

Guori Gao ◽

Zhongrui Lv ◽

Guoyun Zhang ◽

Jiayi Li ◽

Jianguo Zhang ◽

...

Keyword(s):

Drought Stress ◽

Rna Sequencing ◽

Drought Resistance ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Normal Growth ◽

Carotenoid Biosynthesis ◽

Sea Buckthorn ◽

Mutual Regulation ◽

The Difference

Abstract Drought is the most severe abiotic stress and hinders the normal growth and development of plants. Sea buckthorn (Hippophae rhamnoides Linn.) is a typical drought-resistant tree species. In this study, the leaves of the H. rhamnoides ssp. sinensis (“FN”) and H. rhamnoides ssp. mongolica (“XY”) were selected during drought-recovery cycles for RNA sequencing, and physiological and biochemical analyses. The results revealed that drought stress significantly decreased leaf water potential, net photosynthetic rate, and stomatal conductance in both sea buckthorn subspecies. Similarly, the contents of flavone, flavonol, isoflavone and flavanone significantly decreased under drought stress in “XY.” Conversely, in “FN,” the flavone and abscisic acid (ABA) contents were significantly higher under drought stress and recovered after rehydration. Meanwhile, 4,618 and 6,100 differentially expressed genes (DEGs) were identified under drought stress in “FN” and “XY,” respectively. In total, 5,164 DEGs were observed in the comparison between “FN” and “XY” under drought stress. This was more than the 3,821 and 3,387 DEGs found when comparing the subspecies under control and rehydration conditions, respectively. These DEGs were mainly associated with carotenoid biosynthesis, flavonoid biosynthesis, photosynthesis, and plant hormone signal transduction. Six hub DEGs (ABCG5, ABCG22, ABCG32, ABCG36, ABF2 and PYL4) were identified to respond to drought stress based on WGCNA and BLAST analysis using DroughtDB. These six DEGs were annotated to play roles in the ABA-dependent signaling pathway. Sixteen RNA sequencing results involving eight genes and similar expression patterns (12/16) were validated using quantitative real-time PCR. The biochemical and molecular mechanisms underlying the regulation of drought responses by ABA and flavonoids in sea buckthorn were clarified. In this study, gene co-expression networks were constructed, and the results suggested that the mutual regulation of ABA and flavonoid signaling contributed to the difference in drought resistance between the different sea buckthorn subspecies.

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Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

Agronomy ◽

10.3390/agronomy9080435 ◽

2019 ◽

Vol 9 (8) ◽

pp. 435 ◽

Cited By ~ 2

Author(s):

Yaning Bao ◽

Xing Huang ◽

Muzammal Rehman ◽

Yunhe Wang ◽

Bo Wang ◽

...

Keyword(s):

Drought Stress ◽

Auxin Transport ◽

Expression Patterns ◽

Gene Families ◽

Ramie Fiber ◽

Biological Functions ◽

Qrt Pcr ◽

Boehmeria Nivea ◽

Auxin Distribution ◽

Indole 3 Acetic Acid

Auxin regulates diverse aspects of growth and development. Furthermore, polar auxin transport, which is mediated by the PIN-FORMED (PIN) and AUXIN1/LIKE-AUX (AUX/LAX) proteins, plays a crucial role in auxin distribution. In this study, six PIN and four AUX/LAX genes were identified in ramie (Boehmeria nivea L.). We used qRT-PCR to characterize and analyze the two gene families, including phylogenetic relationships, intron/exon structures, cis-elements, subcellular localization, and the expression patterns in different tissues. The expression of these genes in response to indole-3-acetic acid (IAA) treatment and drought stress was also assessed; the results indicate that most of the BnAUX/LAX and BnPIN genes were regulated as a result of IAA treatment and drought stress. Our study provides insights into ramie auxin transporters and lays the foundation for further analysis of their biological functions in ramie fiber development and adaptation to environmental stresses.

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Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

International Journal of Molecular Sciences ◽

10.3390/ijms20061425 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1425 ◽

Cited By ~ 1

Author(s):

Dongli Wang ◽

Sen Meng ◽

Wanlong Su ◽

Yu Bao ◽

Yingying Lu ◽

...

Keyword(s):

Drought Stress ◽

Rna Editing ◽

Functional Divergence ◽

Expression Patterns ◽

Purifying Selection ◽

Structural Features ◽

Specific Expression ◽

Poplar Genome ◽

Physiological Processes ◽

Genome Wide

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I–VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the dN/dS ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation.

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Coordinated Regulation of Arbuscular Mycorrhizal Fungi and Soybean MAPK Pathway Genes Improved Mycorrhizal Soybean Drought Tolerance

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-14-0251-r ◽

2015 ◽

Vol 28 (4) ◽

pp. 408-419 ◽

Cited By ~ 22

Author(s):

Zhilei Liu ◽

Yuanjing Li ◽

Lina Ma ◽

Haichao Wei ◽

Jianfeng Zhang ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Drought Tolerance ◽

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Mapk Pathway ◽

Expression Patterns ◽

Soluble Sugar ◽

Arbuscular Mycorrhizal ◽

Mapk Cascades

Mitogen-activated protein kinase (MAPK) cascades play important roles in the stress response in both plants and microorganisms. The mycorrhizal symbiosis established between arbuscular mycorrhizal fungi (AMF) and plants can enhance plant drought tolerance, which might be closely related to the fungal MAPK response and the molecular dialogue between fungal and soybean MAPK cascades. To verify the above hypothesis, germinal Glomus intraradices (syn. Rhizophagus irregularis) spores and potted experiments were conducted. The results showed that AMF GiMAPKs with high homology with MAPKs from Saccharomyces cerevisiae had different gene expression patterns under different conditions (nitrogen starvation, abscisic acid treatment, and drought). Drought stress upregulated the levels of fungi and soybean MAPK transcripts in mycorrhizal soybean roots, indicating the possibility of a molecular dialogue between the two symbiotic sides of symbiosis and suggesting that they might cooperate to regulate the mycorrhizal soybean drought-stress response. Meanwhile, the changes in hydrogen peroxide, soluble sugar, and proline levels in mycorrhizal soybean as well as in the accelerated exchange of carbon and nitrogen in the symbionts were contributable to drought adaptation of the host plants. Thus, it can be preliminarily inferred that the interactions of MAPK signals on both sides, symbiotic fungus and plant, might regulate the response of symbiosis and, thus, improve the resistance of mycorrhizal soybean to drought stress.

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