scholarly journals Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiaofang Xie ◽  
Zhiwei Chen ◽  
Binghui Zhang ◽  
Huazhong Guan ◽  
Yan Zheng ◽  
...  
Keyword(s):  
Cell Death ◽  
Molecular Mechanism ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Rna Seq ◽  
Bacterial Leaf Streak ◽  
Wild Type ◽  
Cell Death Pathways ◽  
Rnai Line ◽  
Transgenic Lines

Abstract Bacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation as control. We found that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways. The results suggest that xa5 is the cause of BLS-resistance of QTL qBlsr5a and it displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.

scholarly journals Transcriptome Analysis of xa5-mediated Resistance to Bacterial Leaf Streak in Rice (Oryza sativa L.)

2019 ◽  
Author(s):  
Xiaofang Xie ◽  
Zhiwei Chen ◽  
Huazhong Guan ◽  
Yan Zheng ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Cell Death ◽  
Molecular Mechanism ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Rna Seq ◽  
Bacterial Leaf Streak ◽  
Wild Type ◽  
Cell Death Pathways ◽  
Rnai Line ◽  
Transgenic Lines

AbstractBacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation with water as control. The results showed that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways, suggesting that xa5 displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.

scholarly journals Overexpression of OsABCG48 Lowers Cadmium in Rice (Oryza sativa L.)

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 918
Author(s):  
Xingzhe Cai ◽  
Meng Wang ◽  
Yucong Jiang ◽  
Changhu Wang ◽  
David W. Ow
Keyword(s):  
Oryza Sativa L ◽  
Cost Effective ◽  
Health Issues ◽  
Rna Seq ◽  
Wild Type ◽  
Genetic Changes ◽  
Cd Accumulation ◽  
Lateral Root Development ◽  
Atp Binding Cassette Transporter ◽  
Cost Effective Approach

Cadmium pollution threatens food safety and security by causing health issues and reducing farmland availability. Engineering genetic changes in crop plants to lower Cd accumulation can be a cost-effective approach to address this problem. Previously, we reported that a rice line, 2B, which expresses a truncated version of OsO3L2 had reduced Cd accumulation throughout the plant, including in seed. However, downstream events caused by expression of this gene were not known. In this study, RNA-seq was used to identify differentially expressed genes between the wild type and 2B rice with or without Cd treatment, leading to the study of an ABC transporter gene, OsABCG48 (ATP-Binding Cassette transporter G family member 48). Heterologous expression of OsABCG48 conferred tolerance to Cd in Schizosaccharomyces pombe, Arabidopsis and rice. Moreover, overexpressing OsABCG48 in rice lowered root Cd accumulation that was associated with more extensive lateral root development. These data suggest that OsABCG48 might have applications for engineering low-Cd rice.

scholarly journals Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection

2020 ◽  
Vol 21 (3) ◽  
pp. 848
Author(s):  
Yuan Zhou ◽  
Di Zhao ◽  
Li Shuang ◽  
Dongxue Xiao ◽  
Yuanhu Xuan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Gene Annotation ◽  
Oryza Sativa L ◽  
Development Stage ◽  
Post Inoculation ◽  
Rna Seq ◽  
Wild Type ◽  
Root Knot Nematode ◽  
Rice Roots ◽  
Invasion Stage

Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.

Functional characterisation of OsAMT1.1 overexpression lines of rice, Oryza sativa

2006 ◽  
Vol 33 (4) ◽  
pp. 339 ◽  
Author(s):  
Anshuman Kumar ◽  
Brent N. Kaiser ◽  
M. Yaeesh Siddiqi ◽  
Anthony D. M. Glass
Keyword(s):  
Oryza Sativa ◽  
Plant Biomass ◽  
Oryza Sativa L ◽  
Wild Type ◽  
High Affinity ◽  
Functional Characterisation ◽  
Overexpression Line ◽  
Net Uptake ◽  
Transgenic Lines ◽  
Responsive Gene

In rice (Oryza sativa L.) OsAMT1.1 is the most active and / or most N-responsive gene responsible for high-affinity NH4+ transport (HATS) activity. We measured 13NH4+ influx and plant biomass in transgenic overexpression lines and two wild type cultivars of rice, Jarrah and Taipei, with one or more copies of OsAMT1.1. 13NH4+ influx was higher for the overexpression lines of Jarrah line when grown at 10 µm external NH4+ concentration, but not for the overexpression lines of Taipei. For seedlings grown at 2 mm external NH4+ concentration Jarrah lines 77-1 and 75-4 showed an increased influx; however, two overexpression lines of Taipei showed reduced influx rates. The biomasses of the transgenic lines grown at low and high external NH4+ concentrations were either reduced or showed no statistically significant differences compared with wild type lines. While 13NH4+ influx into roots of Jarrah line 75-4 grown at 10 µm external NH4+ concentration was significantly higher than in wild type, measurements of 13NH efflux revealed no differences, and thus net uptake of NH4+ was higher in this overexpression line.

scholarly journals Silicon Modulates Molecular and Physiological Activities in Lsi1 Transgenic and Wild Rice Seedlings under Arsenic Stress

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1532
Author(s):  
Mohammad Reza Boorboori ◽  
Wenxiong Lin ◽  
Yanyang Jiao ◽  
Changxun Fang
Keyword(s):  
Calcium Binding ◽  
Dry Weight ◽  
Silicon Concentration ◽  
Rna Seq ◽  
Wild Type ◽  
Rice Seedlings ◽  
Rnai Line ◽  
Overexpression Line ◽  
Arsenic Stress ◽  
Hydroponic Conditions

Arsenic is one of the most dangerous metalloids, and silicon is a helpful element supporting plants to withstand stress. In this study, three factors were considered, including rice accessions with three different lines, including Lsi1-RNAi line (LE-R), Lsi1 overexpression line (LE-OE), and their wild type (LE-WT), and silicon and arsenic treatments with two different levels. Analysis of variance in dry weight biomass, protein content, arsenic, and silicon concentration has shown a significant interaction between three factors. Further analysis showed that the silicon concentration of all rice seedlings under silicon treatments increased significantly. The LE-OE line has shown a higher ability to absorb silicon in hydroponic conditions than the wild type, and when the seedlings were exposed to arsenic, the concentration of arsenic in all lines increased significantly. Adding silicon to over-expressed rice lines with the Lsi1 gene creates better arsenic resistance than their wild type. These findings confirmed antagonism between silicon and arsenic, and seedlings exposed to arsenic showed a reduction in silicon concentration in all rice lines. RNA-seq analysis showed 106 differentially expressed genes in the LE-OE line, including 75 up-regulated genes and 31 down-regulated genes. DEGs in the LE-R line were 449 genes, including 190 up-regulated and 259 down-regulated genes. Adding treatment has changed the expression of Calcium-binding EGF domain-containing, Os10g0530500, Os05g0240200 in both LE-OE and LE-R roots. They showed that transgenic cultivars were more resistant to arsenic than wild-type, especially when silicon was added to the culture medium.

scholarly journals Gene Mapping, Genome-Wide Transcriptome Analysis, and WGCNA Reveals the Molecular Mechanism for Triggering Programmed Cell Death in Rice Mutant pir1

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1607
Author(s):  
Xinyu Chen ◽  
Qiong Mei ◽  
Weifang Liang ◽  
Jia Sun ◽  
Xuming Wang ◽  
...  
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Molecular Mechanism ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Biotic And Abiotic Stress ◽  
Alpha Linolenic Acid ◽  
Rice Mutant ◽  
Phenylpropanoid Biosynthesis ◽  
Physiological Analysis

Programmed cell death (PCD) is involved in plant growth and development and in resistance to biotic and abiotic stress. To understand the molecular mechanism that triggers PCD, phenotypic and physiological analysis was conducted using the first three leaves of mutant rice PCD-induced-resistance 1(pir1) and its wild-type ZJ22. The 2nd and 3rd leaves of pir1 had a lesion mimic phenotype, which was shown to be an expression of PCD induced by H2O2-accumulation. The PIR1 gene was mapped in a 498 kb-interval between the molecular markers RM3321 and RM3616 on chromosome 5, and further analysis suggested that the PCD phenotype of pir1 is controlled by a novel gene for rice PCD. By comparing the mutant with wild type rice, 1679, 6019, and 4500 differentially expressed genes (DEGs) were identified in the three leaf positions, respectively. KEGG analysis revealed that DEGs were most highly enriched in phenylpropanoid biosynthesis, alpha-linolenic acid metabolism, and brassinosteroid biosynthesis. In addition, conjoint analysis of transcriptome data by weighted gene co-expression network analysis (WGCNA) showed that the turquoise module of the 18 identified modules may be related to PCD. There are close interactions or indirect cross-regulations between the differential genes that are significantly enriched in the phenylpropanoid biosynthesis pathway and the hormone biosynthesis pathway in this module, which indicates that these genes may respond to and trigger PCD.

scholarly journals OsPGIP1-Mediated Resistance to Bacterial Leaf Streak in Rice is Beyond Responsive to the Polygalacturonase of Xanthomonas oryzae pv. oryzicola

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Tao Wu ◽  
Chune Peng ◽  
Beibei Li ◽  
Wei Wu ◽  
Lingguang Kong ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Xanthomonas Oryzae ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Bacterial Leaf Streak ◽  
Wild Type ◽  
Transcription Factor Genes ◽  
Ja Signaling

AbstractPolygalacturonase-inhibiting proteins (PGIPs) have been shown to recognize fungal polygalacturonases (PGs), which initiate innate immunity in various plant species. Notably, the connection between rice OsPGIPs and PGs in Xanthomonas oryzae pv. oryzicola (Xoc), which causes bacterial leaf streak (BLS), remains unclear. Here, we show that OsPGIP1 was strongly induced after inoculating rice with the Xoc strain RS105. Furthermore, OsPGIP1-overexpressing (OV) and RNA interference (RNAi) rice lines increased and decreased, respectively, the resistance of rice to RS105, indicating that OsPGIP1 contributes to BLS resistance. Subsequently, we generated the unique PG mutant RS105Δpg, the virulence of which is attenuated compared to that of RS105. Surprisingly, the lesion lengths caused by RS105Δpg were similar to those caused by RS105 in the OV lines compared with wild-type ZH11 with reduced Xoc susceptibility. However, the lesion lengths caused by RS105Δpg were still significantly shorter in the OV lines than in ZH11, implying that OsPGIP1-mediated BLS resistance could respond to other virulence factors in addition to PGs. To explore the OsPGIP1-mediated resistance, RNA-seq analysis were performed and showed that many plant cell wall-associated genes and several MYB transcription factor genes were specifically expressed or more highly induced in the OV lines compared to ZH11 postinoculation with RS105. Consistent with the expression of the differentially expressed genes, the OV plants accumulated a higher content of jasmonic acid (JA) than ZH11 postinoculation with RS105, suggesting that the OsPGIP1-mediated resistance to BLS is mainly dependent on the plant cell wall-associated immunity and the JA signaling pathway.

scholarly journals Impaired Expression of Chloroplast HSP90C Chaperone Activates Plant Defense Responses with a Possible Link to a Disease-Symptom-Like Phenotype

2020 ◽  
Vol 21 (12) ◽  
pp. 4202 ◽  
Author(s):  
Shaikhul Islam ◽  
Sachin Ashok Bhor ◽  
Keisuke Tanaka ◽  
Hikaru Sakamoto ◽  
Takashi Yaeno ◽  
...  
Keyword(s):  
Cell Death ◽  
Immune Responses ◽  
Tobacco Plant ◽  
Defense Responses ◽  
Blue Staining ◽  
H2o2 Production ◽  
Gene Ontology Analysis ◽  
Rna Seq ◽  
Plant Defense Responses ◽  
Cell Death Pathways

RNA-seq analysis of a transgenic tobacco plant, i-hpHSP90C, in which chloroplast HSP90C genes can be silenced in an artificially inducible manner resulting in the development of chlorosis, revealed the up- and downregulation of 2746 and 3490 genes, respectively. Gene ontology analysis of these differentially expressed genes indicated the upregulation of ROS-responsive genes; the activation of the innate immunity and cell death pathways; and the downregulation of genes involved in photosynthesis, plastid organization, and cell cycle. Cell death was confirmed by trypan blue staining and electrolyte leakage assay, and the H2O2 production was confirmed by diaminobenzidine staining. The results collectively suggest that the reduced levels of HSP90C chaperone lead the plant to develop chlorosis primarily through the global downregulation of chloroplast- and photosynthesis-related genes and additionally through the light-dependent production of ROS, followed by the activation of immune responses, including cell death.

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