Comparative Transcriptome Analysis Highlights the Crucial Roles of Photosynthetic System in Drought Stress Adaptation in Upland Rice

Overview

Journal Sci Rep

Specialty Science

Date 2016 Jan 19

PMID 26777777

Citations 36

Authors

Zheng-Feng Zhang

Yuan-Yuan Li

Ben-Ze Xiao

Affiliations

Soon will be listed here.

Abstract

Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice.

Citing Articles

Comparative analysis of the mitochondrial genomes of four species (Orchidaceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing.

Wang L, Liu X, Wang Y, Ming X, Qi J, Zhou Y Front Plant Sci. 2024; 15:1429545.

PMID: 39139720 PMC: 11319272. DOI: 10.3389/fpls.2024.1429545.

Exploring the dynamic adaptive responses of Epimedium pubescens to phosphorus deficiency by Integrated transcriptome and miRNA analysis.

Liu S, An X, Xu C, Guo B, Li X, Chen C BMC Plant Biol. 2024; 24(1):480.

PMID: 38816792 PMC: 11138043. DOI: 10.1186/s12870-024-05063-y.

Genetic Analysis of Partially Resistant and Susceptible Chickpea Cultivars in Response to Infection.

Deokar A, Sagi M, Taran B Int J Mol Sci. 2024; 25(2).

PMID: 38279360 PMC: 10816841. DOI: 10.3390/ijms25021360.

Panicle transcriptome of high-yield mutant indica rice reveals physiological mechanisms and novel candidate regulatory genes for yield under reproductive stage drought stress.

Eragam A, Mohapatra A, Shukla V, Kadumuri R, George A, Putta L BMC Plant Biol. 2023; 23(1):493.

PMID: 37833626 PMC: 10571340. DOI: 10.1186/s12870-023-04507-1.

A multi-level approach reveals key physiological and molecular traits in the response of two rice genotypes subjected to water deficit at the reproductive stage.

Favreau B, Gaal C, Pereira de Lima I, Droc G, Roques S, Sotillo A Plant Environ Interact. 2023; 4(5):229-257.

PMID: 37822730 PMC: 10564380. DOI: 10.1002/pei3.10121.

References

Lian H, Yu X, Ye Q, Ding X, Kitagawa Y, Kwak S . The role of aquaporin RWC3 in drought avoidance in rice. Plant Cell Physiol. 2004; 45(4):481-9. DOI: 10.1093/pcp/pch058. View

Pena-Fronteras J, Villalobos M, Baltazar A, Merca F, Ismail A, Johnson D . Adaptation to flooding in upland and lowland ecotypes of Cyperus rotundus, a troublesome sedge weed of rice: tuber morphology and carbohydrate metabolism. Ann Bot. 2008; 103(2):295-302. PMC: 2707299. DOI: 10.1093/aob/mcn085. View

Du Z, Zhou X, Ling Y, Zhang Z, Su Z . agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010; 38(Web Server issue):W64-70. PMC: 2896167. DOI: 10.1093/nar/gkq310. View

Dong Y, Wang C, Han X, Tang S, Liu S, Xia X . A novel bHLH transcription factor PebHLH35 from Populus euphratica confers drought tolerance through regulating stomatal development, photosynthesis and growth in Arabidopsis. Biochem Biophys Res Commun. 2014; 450(1):453-8. DOI: 10.1016/j.bbrc.2014.05.139. View

Fu B, Xiong J, Zhu L, Zhao X, Xu H, Gao Y . Identification of functional candidate genes for drought tolerance in rice. Mol Genet Genomics. 2007; 278(6):599-609. DOI: 10.1007/s00438-007-0276-3. View

Sprecher C, Puers C, Lins A, Schumm J . General approach to analysis of polymorphic short tandem repeat loci. Biotechniques. 1996; 20(2):266-76. DOI: 10.2144/96202rr04. View

Parida S, Mukerji M, Singh A, Singh N, Mohapatra T . SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure. BMC Genomics. 2012; 13:426. PMC: 3562522. DOI: 10.1186/1471-2164-13-426. View

Ding X, Li X, Xiong L . Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet. 2011; 123(5):815-26. DOI: 10.1007/s00122-011-1629-1. View

Ding X, Li X, Xiong L . Insight into differential responses of upland and paddy rice to drought stress by comparative expression profiling analysis. Int J Mol Sci. 2013; 14(3):5214-38. PMC: 3634487. DOI: 10.3390/ijms14035214. View

10.

Gu J, Yin X, Struik P, Stomph T, Wang H . Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions. J Exp Bot. 2011; 63(1):455-69. PMC: 3245479. DOI: 10.1093/jxb/err292. View

11.

Boyer J . Plant productivity and environment. Science. 1982; 218(4571):443-8. DOI: 10.1126/science.218.4571.443. View

12.

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

13.

Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K . Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics. 2005; 172(2):1213-28. PMC: 1456219. DOI: 10.1534/genetics.105.045062. View

14.

Wang H, Zhang H, Gao F, Li J, Li Z . Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray. Theor Appl Genet. 2007; 115(8):1109-26. DOI: 10.1007/s00122-007-0637-7. View

15.

Murray M, Thompson W . Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980; 8(19):4321-5. PMC: 324241. DOI: 10.1093/nar/8.19.4321. View

16.

Lyu J, Li B, He W, Zhang S, Gou Z, Zhang J . A genomic perspective on the important genetic mechanisms of upland adaptation of rice. BMC Plant Biol. 2014; 14:160. PMC: 4074872. DOI: 10.1186/1471-2229-14-160. View

17.

Ji K, Wang Y, Sun W, Lou Q, Mei H, Shen S . Drought-responsive mechanisms in rice genotypes with contrasting drought tolerance during reproductive stage. J Plant Physiol. 2011; 169(4):336-44. DOI: 10.1016/j.jplph.2011.10.010. View

18.

Trapnell C, Pachter L, Salzberg S . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. PMC: 2672628. DOI: 10.1093/bioinformatics/btp120. View

19.

Voesenek L, Pierik R . Plant science. Plant stress profiles. Science. 2008; 320(5878):880-1. DOI: 10.1126/science.1158720. View

20.

Osakabe Y, Osakabe K, Shinozaki K, Tran L . Response of plants to water stress. Front Plant Sci. 2014; 5:86. PMC: 3952189. DOI: 10.3389/fpls.2014.00086. View