Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. O. nivara inhabits swampy areas with a seasonally dry climate, which is an ideal material to discover drought tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1246 lncRNAs were identified, including 1091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes enriched in stress responsive GO terms; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

10.21203/rs.3.rs-280217/v1 ◽

2021 ◽

Author(s):

Yong-Chao Xu ◽

Jie Zhang ◽

Dong-Yan Zhang ◽

Ying-Hui Nan ◽

Song Ge ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Wild Rice ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Antisense Transcripts ◽

High Genetic Diversity ◽

Natural Antisense Transcripts ◽

Form Complex ◽

Oryza Nivara

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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Overexpression of the pitaya phosphoethanolamine N-methyltransferase gene (HpPEAMT) enhanced simulated drought stress in tobacco

Plant Cell Tissue and Organ Culture (PCTOC) ◽

10.1007/s11240-021-02040-3 ◽

2021 ◽

Author(s):

Ai-Hua Wang ◽

Lan Yang ◽

Xin-Zhuan Yao ◽

Xiao-Peng Wen

Keyword(s):

Drought Stress ◽

Stress Response ◽

Transgenic Plants ◽

Drought Tolerance ◽

Transgenic Tobacco ◽

Sequence Similarity ◽

Amino Acid Sequence Similarity ◽

Transgenic Tobacco Plants ◽

Wild Type ◽

Tobacco Plants

AbstractPhosphoethanolamine N-methyltransferase (PEAMTase) catalyzes the methylation of phosphoethanolamine to produce phosphocholine and plays an important role in the abiotic stress response. Although the PEAMT genes has been isolated from many species other than pitaya, its role in the drought stress response has not yet been fully elucidated. In the present study, we isolated a 1485 bp cDNA fragment of HpPEAMT from pitaya (Hylocereus polyrhizus). Phylogenetic analysis showed that, during its evolution, HpPEAMT has shown a high degree of amino acid sequence similarity with the orthologous genes in Chenopodiaceae species. To further investigate the function of HpPEAMT, we generated transgenic tobacco plants overexpressing HpPEAMT, and the transgenic plants accumulated significantly more glycine betaine (GB) than did the wild type (WT). Drought tolerance trials indicated that, compared with those of the wild-type (WT) plants, the roots of the transgenic plants showed higher drought tolerance ability and exhibited improved drought tolerance. Further analysis revealed that overexpression of HpPEAM in Nicotiana tabacum resulted in upregulation of transcript levels of GB biosynthesis-related genes (NiBADH, NiCMO and NiSDC) in the leaves. Furthermore, compared with the wild-type plants, the transgenic tobacco plants displayed a significantly lower malondialdehyde (MDA) accumulation and higher activities of the superoxide dismutase (SOD) and peroxidase (POD) antioxidant enzymes under drought stress. Taken together, our results suggested that HpPEAMT enhanced the drought tolerance of transgenic tobacco.

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The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice

Gene ◽

10.1016/j.gene.2004.06.008 ◽

2004 ◽

Vol 340 (1) ◽

pp. 133-139 ◽

Cited By ~ 59

Author(s):

M. Shahid Masood ◽

Tomotaro Nishikawa ◽

Shu-ichi Fukuoka ◽

Peter K. Njenga ◽

Takahiko Tsudzuki ◽

...

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Chloroplast Genome ◽

Complete Nucleotide Sequence ◽

Wild Rice ◽

Comparative Sequence Analysis ◽

Cultivated Rice ◽

Comparative Sequence ◽

Oryza Nivara ◽

Genome Wide

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Genetic diversity of cultivated rice (Oryza sativa L.) and wild rice (Oryza rufipogon Griff.) in Asia, especially in Myanmar, as revealed by organelle markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-017-0566-5 ◽

2017 ◽

Vol 65 (3) ◽

pp. 713-726

Author(s):

Masako Okoshi ◽

Tomotaro Nishikawa ◽

Hiromori Akagi ◽

Tatsuhito Fujimura

Keyword(s):

Genetic Diversity ◽

Oryza Sativa ◽

Wild Rice ◽

Oryza Sativa L ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Oryza Rufipogon Griff

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Identification of drought stress tolerance in wild species germplasm of rice based on leaf and root morphology

Plant Genetic Resources ◽

10.1017/s1479262117000284 ◽

2017 ◽

Vol 16 (4) ◽

pp. 289-295 ◽

Cited By ~ 1

Author(s):

Kumari Neelam ◽

Gurpreet K. Sahi ◽

Kishor Kumar ◽

Kuldeep Singh

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Stress Tolerance ◽

Root Morphology ◽

Wild Species ◽

Root Length ◽

Wide Spectrum ◽

Abiotic Stress Tolerance ◽

Oryza Rufipogon ◽

Sub Saharan Africa

AbstractDrought is the major abiotic constraint to the rice production in the rain-fed areas across Asia and sub-Saharan Africa. Wild species of Oryza offer a wide spectrum of adaptive traits and can serve as potential donors of biotic and abiotic stress tolerance. At the Punjab Agricultural University, we are maintaining an active collection of 1630 accessions of wild species germplasm (AA, CC, BBCC and CCDD) of rice. These accessions were screened to assess genetic variation for drought tolerance under field conditions. Severe water stress was imposed at the late vegetative stage by withholding water initially for 25 d and then extended further to 35 d during kharif season in the years 2013–14 and 2015–16. The tolerance score for drought stress was based on the extent of leaf rolling and leaf drying. Based on the 2 years’ data, seven accessions from Oryza rufipogon, four from Oryza longistaminata and one each from Oryza officinalis and Oryza latifolia were found tolerant to drought stress. These selected accessions were further phenotype for root morphology. The average root length among the selected accessions ranges between 36 and 80 cm and the number of primary roots vary from 30 to 87 cm. The O. rufipogon accession IRGC 106433, O. longistaminata accession IRGC 92656A, O. officinalis accession IRGC 101152 and O. latifolia accession IRGC 80769 showed approximately 2–2.5 times longer root length and number than the indica rice elite cultivar PR121. The results indicated potentiality of selected wild species germplasm for conferring drought tolerance to the elite cultivars.

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BrEXLB1, a Brassica rapa Expansin-Like B1 Gene Is Associated with Root Development, Drought Stress Response, and Seed Germination

Genes ◽

10.3390/genes11040404 ◽

2020 ◽

Vol 11 (4) ◽

pp. 404 ◽

Cited By ~ 2

Author(s):

Muthusamy Muthusamy ◽

Joo Yeol Kim ◽

Eun Kyung Yoon ◽

Jin A. Kim ◽

Soo In Lee

Keyword(s):

Abiotic Stress ◽

Drought Stress ◽

Stress Response ◽

Seed Germination ◽

Drought Tolerance ◽

Root Growth ◽

Brassica Rapa ◽

Root Development ◽

Clubroot Disease ◽

Qrt Pcr

Expansins are structural proteins prevalent in cell walls, participate in cell growth and stress responses by interacting with internal and external signals perceived by the genetic networks of plants. Herein, we investigated the Brassica rapa expansin-like B1 (BrEXLB1) interaction with phytohormones (IAA, ABA, Ethephon, CK, GA3, SA, and JA), genes (Bra001852, Bra001958, and Bra003006), biotic (Turnip mosaic Virus (TuMV), Pectobacterium carotovorum, clubroot disease), and abiotic stress (salt, oxidative, osmotic, and drought) conditions by either cDNA microarray or qRT-PCR assays. In addition, we also unraveled the potential role of BrEXLB1 in root growth, drought stress response, and seed germination in transgenic Arabidopsis and B. rapa lines. The qRT-PCR results displayed that BrEXLB1 expression was differentially influenced by hormones, and biotic and abiotic stress conditions; upregulated by IAA, ABA, SA, ethylene, drought, salt, osmotic, and oxidative conditions; and downregulated by clubroot disease, P. carotovorum, and TuMV infections. Among the tissues, prominent expression was observed in roots indicating the possible role in root growth. The root phenotyping followed by confocal imaging of root tips in Arabidopsis lines showed that BrEXLB1 overexpression increases the size of the root elongation zone and induce primary root growth. Conversely, it reduced the seed germination rate. Further analyses with transgenic B. rapa lines overexpressing BrEXLB1 sense (OX) and antisense transcripts (OX-AS) confirmed that BrEXLB1 overexpression is positively associated with drought tolerance and photosynthesis during vegetative growth phases of B. rapa plants. Moreover, the altered expression of BrEXLB1 in transgenic lines differentially influenced the expression of predicted BrEXLB1 interacting genes like Bra001852 and Bra003006. Collectively, this study revealed that BrEXLB1 is associated with root development, drought tolerance, photosynthesis, and seed germination.

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Enhancement of Rice Leaf Photosynthesis by Crossing between Cultivated Rice,Oryza sativaand Wild Rice Species,Oryza rufipogon

Plant Production Science ◽

10.1626/pps.7.252 ◽

2004 ◽

Vol 7 (3) ◽

pp. 252-259 ◽

Cited By ~ 13

Author(s):

Chisato Masumoto ◽

Takashige Ishii ◽

Sono Kataoka ◽

Tomoko Hatanaka ◽

Naotsugu Uchida

Keyword(s):

Wild Rice ◽

Oryza Rufipogon ◽

Leaf Photosynthesis ◽

Cultivated Rice ◽

Rice Leaf ◽

Wild Rice Species

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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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