RNA-Seq transcriptome analysis of maize inbred carrying nicosulfuron-tolerant and nicosulfuron-susceptible alleles

International Journal of Molecular Sciences
Xiaomin LiuMoran Li

Abstract

Postemergence applications of nicosulfuron can cause great damage to certain maize inbred lines and hybrids. Variation among different responses to nicosulfuron may be attributed to differential rates of herbicide metabolism. We employed RNA-Seq analysis to compare transcriptome responses between nicosulfuron-treated and untreated in both tolerant and susceptible maize plants. A total of 71.8 million paired end Illumina RNA-Seq reads were generated, representing the transcription of around 40,441 unique reads. About 345,171 gene ontology (GO) term assignments were conducted for the annotation in terms of biological process, cellular component and molecular function categories, and 6413 sequences with 108 enzyme commission numbers were assigned to 134 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed within the susceptible and tolerant maize between the nicosulfuron-treated and untreated conditions, 13 genes were selected as the candidates most likely involved in herbicide metabolism, and quantitative RT-PCR validated the RNA-Seq results for eight genes. This transcriptome data may provide opportunities for the study o...Continue Reading

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Citations

Mar 5, 2019·Genome Génome / Conseil National De Recherches Canada·Wassana PrisingkornWei-Min Wang
Feb 23, 2020·Pest Management Science·George GiannakopoulosRobert Edwards
Apr 6, 2020·Pest Management Science·Eunsoo Choe, Martin M Williams
Jan 18, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xiaomin LiuJ Scott McElroy
Mar 2, 2021·Ecotoxicology and Environmental Safety·Jian WangQing Yang

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Methods Mentioned

BETA
glycosylation
targeted modification
RNA-Seq
transgenic
PCR

Software Mentioned

Tophat
blastx
Primer Premier
Bowtie
Blast2GO
EBSeq
Cufflinks
SAM Map
R
SAM

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