Dataset Information

Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study.

ABSTRACT: A variety of adverse conditions including drought stress severely affect rice production. Root system plays a critical role in drought avoidance, which is one of the major mechanisms of drought resistance. In this study, we adopted genome-wide association study (GWAS) to dissect the genetic basis controlling various root traits by using a natural population consisting of 529 representative rice accessions. A total of 413 suggestive associations, containing 143 significant associations, were identified for 21 root traits, such as maximum root length, root volume, and root dry weight under normal and drought stress conditions at the maturation stage. More than 80 percent of the suggestive loci were located in the region of reported QTLs for root traits, while about 20 percent of suggestive loci were novel loci detected in this study. Besides, 11 reported root-related genes, including DRO1, WOX11, and OsPID, were found to co-locate with the association loci. We further proved that the association results can facilitate the efficient identification of causal genes for root traits by the two case studies of Nal1 and OsJAZ1. These loci and their candidate causal genes provide an important basis for the genetic improvement of root traits and drought resistance.

SUBMITTER: Li X

PROVIDER: S-EPMC5521850 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study.

Li Xiaokai X Guo Zilong Z Lv Yan Y Cen Xiang X Ding Xipeng X Wu Hua H Li Xianghua X Huang Jianping J Xiong Lizhong L

PLoS genetics 20170707 7

A variety of adverse conditions including drought stress severely affect rice production. Root system plays a critical role in drought avoidance, which is one of the major mechanisms of drought resistance. In this study, we adopted genome-wide association study (GWAS) to dissect the genetic basis controlling various root traits by using a natural population consisting of 529 representative rice accessions. A total of 413 suggestive associations, containing 143 significant associations, were iden ...[more]

PMID: 28686596

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Project description:In order to clarify the molecular mechanisms of drought tolerance between different maize (Zea mays L.) varieties at the protein level, iTRAQ (the isobaric tags for relative and absolute quantitation) quantitative proteomics were used for the comparative analysis of protein expression in the seedling roots of the drought-tolerant Chang 7-2 and drought-sensitive TS141 maize varieties under 20% PEG 6000 (polyethylene glycol 6000)-simulated drought stress. A total of 7723 proteins were identified using iTRAQ in the maize seedling roots. We detected 39371 peptides and 30148 unique peptides. The identified protein molecular mass was mainly distributed between 10–60 kDa. COG analysis divided these proteins into 24 categories, among which general function prediction contained the largest number of proteins (19.1%), followed by posttranslational modification, protein turnover, and chaperones (10.52%). In the identified differentially expressed proteins, 1552 of which were significantly differentially expressed. Of these, 1249 were differentially expressed in Chang 7-2 following drought stress, 577 of which were up-regulated and 672 were down-regulated. Four hundred and twenty five differentially expressed proteins were identified in TS141, 249 of which were up-regulated and 176 were down-regulated. Of these proteins, 32 demonstrated opposite expression levels in the two varieties, and there were 56 up-regulated proteins that were common between the two varieties. Comparing the Chang 7-2 treatment group and control group, the DEPS in the cellular component category were mainly enriched in cytoplasmic membrane-bounded vesicles, cytoplasmic vesicles, membrane-bound vesicles and vesicles; in the molecular function category, the DEPs were mainly enriched in cation binding and metal ion binding; and in the biological process category, the major enriched categories included phosphate-containing compound metabolic process, single-organism transport cellular component organization or biogenesis, carbohydrate metabolic process, and cellular component organization. Comparing the TS141 treatment group and control group, the DEPS in the cellular component category were primarily enriched in cytoplasmic membrane-bounded vesicles, cytoplasmic vesicles, membrane-bound vesicles, and vesicle; in the molecular function category, the DEPs were mainly enriched in cation binding and metal ion binding; and in the biological process category, the major enrichment categories included oxidation-reduction process and carbohydrate metabolic process. In Chang 7-2, the differentially expressed proteins were associated with ribosome pathway, glycolysis/gluconeogenesis pathway, and amino sugar and nucleotide sugar metabolism. In TS141, the differentially expressed proteins were associated with metabolic pathway, phenylpropanoid biosynthesis pathway, and starch and sucrose metabolism.

Project description:Background Abiotic and biotic stresses induce oxidative processes in plant cells that this process starts with the production of ROSs which cause damage to the proteins. Therefore, plants have increased their antioxidant activity to defend against this oxidative stress to be able to handle stress better. In this research, 14 different tea accessions in a randomized complete block design with two replications were evaluated in two normal and drought stress conditions, and their antioxidant activity was measured by DPPH-free radicals’ assay and gene expression analysis. Results The results of gene expression analysis showed that the 100 and 399 accessions and Bazri cultivar had high values for most of the antioxidant enzymes, ascorbate peroxidase, superoxide dismutase, catalase, and peroxidase under drought stress conditions while the 278 and 276 accessions had the lowest amount of antioxidant enzymes in the same situation. Results showed that the IC50 of the BHT combination was 90.12 μg/ ml. Also, The IC50 of accessions ranged from 218 to 261 μg/ml and 201–264 μg/ml at normal and drought stress conditions, respectively. The 100 and 399 accessions showed the lowest IC50 under normal and drought stress conditions, while 278 and 276 accessions had the highest value for IC50. The antioxidant activity of tea accession extracts under normal conditions was ranged from 25 to 69% for accessions 278 and 100, respectively. While, the antioxidant activities of extracts under drought stress condition was 12 to 83% for accessions 276 and 100, respectively. So, according to the results, 100 and 399 accessions exhibited the least IC50 and more antioxidant activity under drought stress conditions and were identified as stress-tolerant accessions. However, 278 and 276 accessions did not show much antioxidant activity and were recognized as sensitive accessions under drought stress conditions. Conclusions These results demonstrate that total phenol content, antioxidant activity, and the oxygen-scavenging system can be used as a descriptor for identifying drought-tolerant accessions.

Project description:BACKGROUND: Plant roots are important organs to uptake soil water and nutrients, perceiving and transducing of soil water deficit signals to shoot. The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress. RESULTS: Global gene expression analysis showed that about 55% of genes differentially expressed in roots of rice in response to drought stress treatments. The number of differentially expressed genes (DEGs) increased in NILs as the level of water deficits, increased from mild to severe condition, suggesting that more genes were affected by increasing drought stress. Gene onthology (GO) test and biological pathway analysis indicated that activated genes in the drought tolerant NILs IR77298-14-1-2-B-10 and IR77298-5-6-B-18 were mostly involved in secondary metabolism, amino acid metabolism, response to stimulus, defence response, transcription and signal transduction, and down-regulated genes were involved in photosynthesis and cell wall growth. We also observed gibberellic acid (GA) and auxin crosstalk modulating lateral root formation in the tolerant NILs. CONCLUSIONS: Transcriptome analysis on two pairs of NILs with a common genetic background (~97%) showed distinctive differences in gene expression profiles and could be effective to unravel genes involved in drought tolerance. In comparison with the moderately tolerant NIL IR77298-5-6-B-18 and other susceptible NILs, the tolerant NIL IR77298-14-1-2-B-10 showed a greater number of DEGs for cell growth, hormone biosynthesis, cellular transports, amino acid metabolism, signalling, transcription factors and carbohydrate metabolism in response to drought stress treatments. Thus, different mechanisms are achieving tolerance in the two tolerant lines.

Dataset Information

Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study.

Publications

Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study.

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