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Identification of the most suitable reference gene for gene expression studies with development and abiotic stress response in Bromus sterilis

. 2021 Jun 28 ; 11 (1) : 13393. [epub] 20210628

Language English Country Great Britain, England Media electronic

Document type Journal Article, Research Support, Non-U.S. Gov't

Links

PubMed 34183710
PubMed Central PMC8238991
DOI 10.1038/s41598-021-92780-1
PII: 10.1038/s41598-021-92780-1
Knihovny.cz E-resources

Bromus sterilis is an annual weedy grass, causing high yield losses in winter cereals. Frequent use of herbicides had led to the evolution of herbicide resistance in this species. Mechanisms underlying herbicide resistance in B. sterilis must be uncovered because this problem is becoming a global threat. qRT-PCR and the next-generation sequencing technologies can elucidate the resistance mechanisms. Although qRT-PCR can calculate precise fold changes, its preciseness depends on the expression of reference genes. Regardless of stable expression in any given condition, no gene can act as a universal reference gene. Hence, it is necessary to identify the suitable reference gene for each species. To our knowledge, there are no reports on the suitable reference gene in any brome species so far. Thus, in this paper, the stability of eight genes was evaluated using qRT-PCR experiments followed by expression stability ranking via five most commonly used software for reference gene selection. Our findings suggest using a combination of 18S rRNA and ACCase to normalise the qRT-PCR data in B. sterilis. Besides, reference genes are also recommended for different experimental conditions. The present study outcomes will facilitate future molecular work in B. sterilis and other related grass species.

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Žd’árková V, Hamouzová K, Holec J, Janků J, Soukup J. Seed ecology of Bromus sterilis L. Julius-Kühn-Arch. 2014;443:156–164.

Jursík M, Kolářová M, Soukup J, Žďárková V. Effects of adjuvants and carriers on propoxycarbazone and pyroxsulam efficacy on Bromus sterilis in winter wheat. Plant Soil Environ. 2016;62:447–452. doi: 10.17221/273/2016-PSE. DOI

Žďárková V, Hamouzová K, Kolářová M, Soukup J. Germination responses to water potential in Bromus sterilis L. under different temperatures and light regimes. Plant Soil Environ. 2017;63:368–374. doi: 10.17221/406/2017-PSE. DOI

Davies LR, Hull R, Moss S, Neve P. The first cases of evolving glyphosate resistance in UK poverty brome (Bromus sterilis) populations. Weed Sci. 2019;67:41–47. doi: 10.1017/wsc.2018.61. DOI

Gaines TA, et al. Gene amplification confers glyphosate resistance in Amaranthus palmeri. PNAS. 2010;107:1029–1034. doi: 10.1073/pnas.0906649107. PubMed DOI PMC

Salas RA, Scott RC, Dayan FE, Burgos NR. EPSPS gene amplification in glyphosate-resistant Italian ryegrass (Lolium perenne ssp. multiflorum) populations from arkansas (United States) J. Agric. Food Chem. 2015;63:5885–5893. doi: 10.1021/acs.jafc.5b00018. PubMed DOI

Gaines TA, et al. RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum. Plant J. 2014;78:865–876. doi: 10.1111/tpj.12514. PubMed DOI

Chen J, et al. Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress. Sci. Rep. 2017;7:46494. doi: 10.1038/srep46494. PubMed DOI PMC

Joseph JT, Poolakkalody NJ, Shah JM. Plant reference genes for development and stress response studies. J. Biosci. 2018;43:173–187. doi: 10.1007/s12038-017-9728-z. PubMed DOI

Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat. Protoc. 2006;1:1559–1582. doi: 10.1038/nprot.2006.236. PubMed DOI

Ginzinger DG. Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Exp. Hematol. 2002;30:503–512. doi: 10.1016/S0301-472X(02)00806-8. PubMed DOI

Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005;6:279–284. doi: 10.1038/sj.gene.6364190. PubMed DOI

Guénin S, et al. Normalisation of qRT-PCR data: The necessity of adopting a systematic, experimental conditions-specific, validation of references. J. Exp. Bot. 2009;60:487–493. doi: 10.1093/jxb/ern305. PubMed DOI

Bustin S. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems. J. Mol. Endocrinol. 2002;29:23–39. doi: 10.1677/jme.0.0290023. PubMed DOI

Rocha AJ, Monteiro-Júnior JE, Freire JEC, Sousa AJS, Fonteles CSR. Real time PCR: The use of reference genes and essential rules required to obtain normalisation data reliable to quantitative gene expression. J. Mol. Biol. Res. 2015;5:45. doi: 10.5539/jmbr.v5n1p45. DOI

Chapman JR, Waldenström J. With reference to reference genes: A systematic review of endogenous controls in gene expression studies. PLoS ONE. 2015;10:e0141853. doi: 10.1371/journal.pone.0141853. PubMed DOI PMC

Nestorov J, Matić G, Elaković I, Tanić N. Gene expression studies: How to obtain accurate and reliable data by quantitative real-time RT PCR/izučavanje ekspresije gena: kako dobiti tačne i pouzdane podatke kvantitativnim rt pcr-om u realnom vremenu. J. Med. Biochem. 2013;32:325–338. doi: 10.2478/jomb-2014-0001. DOI

Kozera B, Rapacz M. Reference genes in real-time PCR. J. Appl. Genet. 2013;54:391–406. doi: 10.1007/s13353-013-0173-x. PubMed DOI PMC

Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R. Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis. Plant Physiol. 2005;139:5–17. doi: 10.1104/pp.105.063743. PubMed DOI PMC

Xu H, et al. Identification of reference genes for studying herbicide resistance mechanisms in Japanese foxtail (Alopecurus japonicus) Weed Sci. 2017;65:557–566. doi: 10.1017/wsc.2017.19. DOI

Hong S-Y, Seo PJ, Yang M-S, Xiang F, Park C-M. Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol. 2008;8:112. doi: 10.1186/1471-2229-8-112. PubMed DOI PMC

Gutierrez L, et al. The lack of a systematic validation of reference genes: A serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol. J. 2008;6:609–618. doi: 10.1111/j.1467-7652.2008.00346.x. PubMed DOI

Tong Z, Gao Z, Wang F, Zhou J, Zhang Z. Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol. Biol. 2009;10:71. doi: 10.1186/1471-2199-10-71. PubMed DOI PMC

Ramesh K, Matloob A, Aslam F, Florentine SK, Chauhan BS. Weeds in a changing climate: Vulnerabilities, consequences, and implications for future weed management. Front. Plant Sci. 2017;8:95. doi: 10.3389/fpls.2017.00095. PubMed DOI PMC

Sen MK, et al. Enhanced metabolism and target gene overexpression confer resistance against acetolactate synthase-inhibiting herbicides in Bromus sterilis. Pest Manag. Sci. 2021;77(4):2122–2128. doi: 10.1002/ps.6241. PubMed DOI

Davies LR, Onkokesung N, Brazier-Hicks M, Edwards R, Moss S. Detection and characterisation of resistance to acetolactate synthase inhibiting herbicides in Anisantha and Bromus species in the United Kingdom. Pest Manag. Sci. 2020;76:2473–2482. doi: 10.1002/ps.5788. PubMed DOI

Anthimidou E, Ntoanidou S, Madesis P, Eleftherohorinos I. Mechanisms of Lolium rigidum multiple resistance to ALS- and ACCase-inhibiting herbicides and their impact on plant fitness. Pestic. Biochem. Physiol. 2020;164:65–72. doi: 10.1016/j.pestbp.2019.12.010. PubMed DOI

Gaines TA, et al. Mechanisms of evolved herbicide resistance. J. Biol. Chem. 2020;295:10307–10330. doi: 10.1074/jbc.REV120.013572. PubMed DOI PMC

Pan L, Gao H, Xia W, Zhang T, Dong L. Establishing a herbicide-metabolising enzyme library in Beckmannia syzigachne to identify genes associated with metabolic resistance. J. Exp. Bot. 2016;67:1745–1757. doi: 10.1093/jxb/erv565. PubMed DOI

Jugulam M, Shyam C. Non-target-site resistance to herbicides: Recent developments. Plants. 2019;8:417. doi: 10.3390/plants8100417. PubMed DOI PMC

Akbarabadi A, Ismaili A, Kahrizi D, Firouzabadi FN. Validation of expression stability of reference genes in response to herbicide stress in wild oat (Avena ludoviciana) Cell Mol. Biol. (Noisy-le-grand) 2018;64:113–118. doi: 10.14715/cmb/2018.64.4.19. PubMed DOI

Ruduś I, Kępczyński J. Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L.) caryopses by RT-qPCR method. PLoS ONE. 2018;13:e0192343. doi: 10.1371/journal.pone.0192343. PubMed DOI PMC

Wrzesińska B, Kierzek R, Obrępalska-Stęplowska A. Evaluation of six commonly used reference genes for gene expression studies in herbicide-resistant Avena fatua biotypes. Weed Res. 2016;56:284–292. doi: 10.1111/wre.12209. DOI

Xu X, et al. Selection of relatively exact reference genes for gene expression studies in flixweed (Descurainia sophia) by quantitative real-time polymerase chain reaction. Pestic. Biochem. Physiol. 2016;127:59–66. doi: 10.1016/j.pestbp.2015.09.007. PubMed DOI

Jain M, Nijhawan A, Tyagi AK, Khurana JP. Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem. Biophys. Res. Commun. 2006;345:646–651. doi: 10.1016/j.bbrc.2006.04.140. PubMed DOI

Petit C, Pernin F, Heydel J-M, Délye C. Validation of a set of reference genes to study response to herbicide stress in grasses. BMC Res. Notes. 2012;5:18. doi: 10.1186/1756-0500-5-18. PubMed DOI PMC

Liu J, et al. Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua Linn. Plant Protect. Sci. 2018;55:61–71. doi: 10.17221/20/2018-PPS. DOI

Roy A, Palli SR. Epigenetic modifications acetylation and deacetylation play important roles in juvenile hormone action. BMC Genomics. 2018;19:934. doi: 10.1186/s12864-018-5323-4. PubMed DOI PMC

Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25:402–408. doi: 10.1006/meth.2001.1262. PubMed DOI

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