Whole Transcriptome Analysis Resulted in the Identification of Chinese Sprangletop (Leptochloa Chinensis) Genes Involved in Cyhalofop-butyl Tolerance

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2021 Jul 9

PMID 34238252

Citations 6

Authors

Ke Chen

Yajun Peng

Liang Zhang

Long Wang

Donghai Mao

Zhenghong Zhao

Lianyang Bai

Lifeng Wang

Affiliations

Soon will be listed here.

Abstract

Background: Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use.

Results: In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR).

Conclusions: This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study.

Citing Articles

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References

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

Gardin J, Gouzy J, Carrere S, Delye C . ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass). BMC Genomics. 2015; 16:590. PMC: 4534104. DOI: 10.1186/s12864-015-1804-x. View

Abdeen A, Miki B . The pleiotropic effects of the bar gene and glufosinate on the Arabidopsis transcriptome. Plant Biotechnol J. 2009; 7(3):266-82. DOI: 10.1111/j.1467-7652.2009.00398.x. View

Yu Q, Powles S . Metabolism-based herbicide resistance and cross-resistance in crop weeds: a threat to herbicide sustainability and global crop production. Plant Physiol. 2014; 166(3):1106-18. PMC: 4226378. DOI: 10.1104/pp.114.242750. View

Young M, Wakefield M, Smyth G, Oshlack A . Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010; 11(2):R14. PMC: 2872874. DOI: 10.1186/gb-2010-11-2-r14. View

Yu J, Gao H, Pan L, Yao Z, Dong L . Mechanism of resistance to cyhalofop-butyl in Chinese sprangletop (Leptochloa chinensis (L.) Nees). Pestic Biochem Physiol. 2017; 143:306-311. DOI: 10.1016/j.pestbp.2016.11.001. View

Saika H, Horita J, Taguchi-Shiobara F, Nonaka S, Nishizawa-Yokoi A, Iwakami S . A novel rice cytochrome P450 gene, CYP72A31, confers tolerance to acetolactate synthase-inhibiting herbicides in rice and Arabidopsis. Plant Physiol. 2014; 166(3):1232-40. PMC: 4226355. DOI: 10.1104/pp.113.231266. View

Chen G, Xu H, Zhang T, Bai C, Dong L . Fenoxaprop-P-ethyl resistance conferred by cytochrome P450s and target site mutation in Alopecurus japonicus. Pest Manag Sci. 2018; 74(7):1694-1703. DOI: 10.1002/ps.4863. View

Pan G, Zhang X, Liu K, Zhang J, Wu X, Zhu J . Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides. Plant Mol Biol. 2006; 61(6):933-43. DOI: 10.1007/s11103-006-0058-z. View

10.

Powles S, Yu Q . Evolution in action: plants resistant to herbicides. Annu Rev Plant Biol. 2010; 61:317-47. DOI: 10.1146/annurev-arplant-042809-112119. View

11.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

12.

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

13.

Yang Q, Deng W, Li X, Yu Q, Bai L, Zheng M . Target-site and non-target-site based resistance to the herbicide tribenuron-methyl in flixweed (Descurainia sophia L.). BMC Genomics. 2016; 17:551. PMC: 4974779. DOI: 10.1186/s12864-016-2915-8. View

14.

Hart J, DiTomaso J, Linscott D, Kochian L . Transport Interactions between Paraquat and Polyamines in Roots of Intact Maize Seedlings. Plant Physiol. 1992; 99(4):1400-5. PMC: 1080639. DOI: 10.1104/pp.99.4.1400. View

15.

Duhoux A, Carrere S, Gouzy J, Bonin L, Delye C . RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. Plant Mol Biol. 2015; 87(4-5):473-87. DOI: 10.1007/s11103-015-0292-3. View

16.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

17.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

18.

Eddy S . A new generation of homology search tools based on probabilistic inference. Genome Inform. 2010; 23(1):205-11. View

19.

Choi J, Seo Y, Kim S, Kim W, Shin J . Constitutive expression of CaXTH3, a hot pepper xyloglucan endotransglucosylase/hydrolase, enhanced tolerance to salt and drought stresses without phenotypic defects in tomato plants (Solanum lycopersicum cv. Dotaerang). Plant Cell Rep. 2011; 30(5):867-77. DOI: 10.1007/s00299-010-0989-3. View

20.

Deng W, Cai J, Zhang J, Chen Y, Chen Y, Di Y . Molecular basis of resistance to ACCase-inhibiting herbicide cyhalofop-butyl in Chinese sprangletop (Leptochloa chinensis (L.) Nees) from China. Pestic Biochem Physiol. 2019; 158:143-148. DOI: 10.1016/j.pestbp.2019.05.004. View