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.

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.

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

Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon)

2009 ◽  
Vol 57 (4) ◽  
pp. 597-609 ◽  
Author(s):  
J. Xie ◽  
H. A. Agrama ◽  
D. Kong ◽  
J. Zhuang ◽  
B. Hu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Dongxiang Wild Rice

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.

scholarly journals Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

2021 ◽  
Author(s):  
Wanling Yang ◽  
Yuanwei Fan ◽  
Yong Chen ◽  
Gumu Ding ◽  
Hu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Stress Responses ◽  
Wild Rice ◽  
Diversity Index ◽  
Oryza Rufipogon ◽  
Coding Sequences ◽  
Genome Wide ◽  
Ssr Loci ◽  
Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

Identification and Genetic Analysis of Fertility Restoration Ability in Dongxiang Wild Rice (Oryza rufipogon)

Rice Science ◽  
2008 ◽  
Vol 15 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Xiao-rong CHEN ◽  
Kong-song YANG ◽  
Jun-ru FU ◽  
Chang-lan ZHU ◽  
Xiao-song PENG ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Wild Rice ◽  
Fertility Restoration ◽  
Oryza Rufipogon ◽  
Restoration Ability ◽  
Dongxiang Wild Rice
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