scholarly journals Identification of phosphorus stress related proteins in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.) using label-free quantitative proteomic analysis

2020 ◽  
Author(s):  
Qianwen Deng ◽  
Liweidan Bai ◽  
Liangfang Dai ◽  
Yaling Chen ◽  
Jun Fang ◽  
...  
Keyword(s):  
Wild Rice ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Oryza Rufipogon ◽  
Available Phosphorus ◽  
Label Free ◽  
Response Mechanism ◽  
Cultivated Rice ◽  
P Deficiency ◽  
Dongxiang Wild Rice

Abstract Background: The lack of available phosphorus (P) in soil is one of the important factors restricting rice growth. Previous studies indicated that Dongxiang wild rice (DXWR, O. rufipogon Griff.) was resistant to low-P stress. So far, the research of resistance mechanism in DXWR was very limited.Results: The results showed that 3589 significant differential accumulation proteins were identified between low P and the normal P treated root samples. 60 up-regulated and 15 down-regulated proteins were identified with ≥ 1.5-fold changes as an additional standard. Furthermore, among 75 significantly different expression proteins (SDEPs), 24 proteins also detected in previous transcriptome dataset verified by qRT-PCR, including OsPT2, OsPT8, OsPAP10c, OsPAP10a and OsPHF1. Through comprehensive analysis, it was found that DXWR could increase PAPs, membrane location of PTs, rhizosphere area, alternative splicing and decrease ROS activity to deal with low-P stress. Moreover, among the genes corresponding to 75 SDEPs, 7 uncharacterized genes were located in previous P related QTL intervals, of which two genes (LOC_Os12g09620 and LOC_Os03g40670) have been detected at both transcriptome and proteome levels. In addition, the expression patterns of OsPHR1, OsPHR2, OsPHO1 and NAT-OsPHO1 in DXWR were different in cultivated rice, suggesting that the response mechanism of some low-P tolerance in DXWR might be different from that in cultivated rice.Conclusions: This study screened out some candidate genes for low-P resistance and preliminarily verified that there might be a different low-P response mechanism in DXWR than in cultivated rice, which would provide insights in cloning the P-deficiency genes from wild rice, as well as elucidating the molecular mechanism of low-P resistance in DXWR.

scholarly journals Identification of Phosphorus Stress Related Proteins in the Seedlings of Dongxiang Wild Rice (Oryza Rufipogon Griff.) Using Label-Free Quantitative Proteomic Analysis

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 108
Author(s):  
Qianwen Deng ◽  
Liangfang Dai ◽  
Yaling Chen ◽  
Decai Wu ◽  
Yu Shen ◽  
...  
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Joint Analysis ◽  
Regulation Mechanism ◽  
Label Free ◽  
Transcriptome Data ◽  
P Deficiency ◽  
Proteomic Approach ◽  
Dongxiang Wild Rice ◽  
Related Proteins

Phosphorus (P) deficiency tolerance in rice is a complex character controlled by polygenes. Through proteomics analysis, we could find more low P tolerance related proteins in unique P-deficiency tolerance germplasm Dongxiang wild rice (Oryza Rufipogon, DXWR), which will provide the basis for the research of its regulation mechanism. In this study, a proteomic approach as well as joint analysis with transcriptome data were conducted to identify potential unique low P response genes in DXWR during seedlings. The results showed that 3589 significant differential accumulation proteins were identified between the low P and the normal P treated root samples of DXWR. The degree of change was more than 1.5 times, including 60 up-regulated and 15 downregulated proteins, 24 of which also detected expression changes of more than 1.5-fold in the transcriptome data. Through quantitative trait locus (QTLs) matching analysis, seven genes corresponding to the significantly different expression proteins identified in this study were found to be uncharacterized and distributed in the QTLs interval related to low P tolerance, two of which (LOC_Os12g09620 and LOC_Os03g40670) were detected at both transcriptome and proteome levels. Based on the comprehensive analysis, it was found that DXWR could increase the expression of purple acid phosphatases (PAPs), membrane location of P transporters (PTs), rhizosphere area, and alternative splicing, and it could decrease reactive oxygen species (ROS) activity to deal with low P stress. This study would provide some useful insights in cloning the P-deficiency tolerance genes from wild rice, as well as elucidating the molecular mechanism of low P resistance in DXWR.

Genome-wide genic SSR marker development for the endangered Dongxiang wild rice (Oryza rufipogon)

2016 ◽  
Vol 15 (6) ◽  
pp. 566-569
Author(s):  
Jiankun Xie ◽  
Meng Zhang ◽  
Jia Sun ◽  
Fantao Zhang
Keyword(s):  
Ssr Markers ◽  
Wild Rice ◽  
Pcr Amplification ◽  
Oryza Rufipogon ◽  
Sequencing Technology ◽  
Cultivated Rice ◽  
Genic Ssr ◽  
Genome Wide ◽  
Dongxiang Wild Rice ◽  
Simple Sequence

AbstractDongxiang wild rice (Oryza rufipogon, DXWR), one of the species of common wild rice, is regarded as an important genetic resource for the improvement of cultivated rice (Oryza sativa). Molecular markers are reliable tools that can greatly accelerate the breeding process and have been widely used in various species. In the present study, a total of 3681 genic simple sequence repeat (SSR) markers were developed for DXWR based on transcriptome sequencing technology. Additionally, 25 primer pairs were randomly selected and synthesized for the verification. Among them, 18 (72%) primer pairs were successfully amplified in PCR amplification with genomic DNA of DXWR and also had abundant polymorphisms between DXWR and cultivated rice. These novel genic SSR markers will enrich current genomic resources for DXWR, and provide an effective tool for genetic study and molecular marker assisted breeding for this valuable and endangered germplasm.

Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)

2017 ◽  
Vol 16 (4) ◽  
pp. 386-389
Author(s):  
Meng Zhang ◽  
Wenyang Huang ◽  
Zijun Xia ◽  
Jiahui Liu ◽  
Jiankun Xie ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Genomic Comparison ◽  
Germplasm Resource ◽  
Genome Wide ◽  
Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.

Phosphate Solubilizing Rhizospherebacterial T21 Isolated from Dongxiang Wild Rice Species Promotes Cultivated Rice Growth

2011 ◽  
Vol 108 ◽  
pp. 167-175 ◽  
Author(s):  
Qing Gui Zeng ◽  
Fei Luo ◽  
Zhi Bin Zhang ◽  
Ri Ming Yan ◽  
Du Zhu
Keyword(s):  
Plant Growth ◽  
Wild Rice ◽  
Pantoea Agglomerans ◽  
Oryza Rufipogon ◽  
Plant Growth Promoting Bacteria ◽  
Cultivated Rice ◽  
Wild Rice Species ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Dongxiang Wild Rice

The capability of bacterial strain T21 isolated from Dongxiang wild rice (Oryza rufipogon) rhizosphere to behave as plant growth promoting bacteria (PGPB) was investigated. Rhizosphere bacteria T21 showed P-solubilizing capability when cultured in the PVK medium amended with tricalcium phosphate. The strain T21 also showed nitrogen-fixing activity in N-free medium, and produced indole-3-acetic (IAA) and siderophore. The strain T21 was identified as Pantoea agglomerans by morphology, physiological and biochemical properties, and 16S rDNA sequence analysis. The strain T21 was formulated as an inoculant in order to evaluate its growth promotion effect in the field when applied on the cultivated rice at the sowing time. It showed a significant plant growth-promoting effect on seedling length, root length, fresh weight and dry weight of the cultivated rice (Oryza sativa). These findings fetched us to conclude that wild rice rhizospheric microorganism Pantoea agglomerans T21 could stimulate the growth of cultivated rice in vivo in poor soil.

Diversity and plant growth promoting activities of the cultivable rhizo-bacteria of Dongxiang wild rice (Oryza rufipogon)

2011 ◽  
Vol 19 (4) ◽  
pp. 476-484 ◽  
Author(s):  
Luo Fei ◽  
Wang Ya ◽  
Zeng Qinggui ◽  
Yan Riming ◽  
Zhang Zhibin ◽  
...  
Keyword(s):  
Plant Growth ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Plant Growth Promoting Activities ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Dongxiang Wild Rice

Genetic Analysis of Cold Tolerance at the Seedling Stage in Dongxiang Wild Rice (Oryza rufipogon)

2011 ◽  
Vol 46 (1) ◽  
pp. 21-27
Author(s):  
Jian Shuirong ◽  
Wan Yong ◽  
Luo Xiangdong ◽  
Fang Jun ◽  
Chu Chengcai ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Seedling Stage ◽  
Dongxiang Wild Rice

Identification of novel insertion–deletion markers for Dongxiang wild rice (Oryza rufipogon Griff.) using high-throughput sequencing technology

2015 ◽  
Vol 94 (S2) ◽  
pp. 51-55 ◽  
Author(s):  
FANTAO ZHANG ◽  
LIANGXING ZHANG ◽  
FENGLEI CUI ◽  
XIANGDONG LUO ◽  
YI ZHOU ◽  
...  
Keyword(s):  
High Throughput ◽  
Wild Rice ◽  
High Throughput Sequencing ◽  
Oryza Rufipogon ◽  
Sequencing Technology ◽  
Oryza Rufipogon Griff ◽  
Dongxiang Wild Rice

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

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.

scholarly journals Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1412
Author(s):  
Ruchi Bansal ◽  
Nitika Rana ◽  
Akshay Singh ◽  
Pallavi Dhiman ◽  
Rushil Mandlik ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Rice ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
North East ◽  
Wild Rice Species

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

Sign in / Sign up

Export Citation Format

Share Document