Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insect Bemisia tabaci (whitefly)

Abstract

SummaryThe whitefly (Bemisia tabaci) causes tremendous damage to cotton production worldwide. However, very limited information is available about how plants perceive and defend themselves from this destructive pest. In this study, the transcriptomic differences between two cotton cultivars that exhibit either strong resistance (HR) or sensitivity (ZS) to whitefly were compared at different time points (0, 12, 24 and 48 h after infection) using RNA‐Seq. Approximately one billion paired‐end reads were obtained by Illumina sequencing technology. Gene ontology and KEGG pathway analysis indicated that the cotton transcriptional response to whitefly infestation involves genes encoding protein kinases, transcription factors, metabolite synthesis, and phytohormone signalling. Furthermore, a weighted gene co‐expression network constructed from RNA‐Seq datasets showed that WRKY40 and copper transport protein are hub genes that may regulate cotton defenses to whitefly infestation. Silencing GhMPK3 by virus‐induced gene silencing (VIGS) resulted in suppression of the MPK‐WRKY‐JA and ET pathways and lead to enhanced whitefly susceptibility, suggesting that the candidate insect resistant genes identified in this RNA‐Seq analysis are credible and offer significant utility. Taken together, this study provides comprehensive insights into the cotton defense system to whitefly infestation and has identified several candidate genes for control of phloem‐feeding pests.

Whole genome sequencing reveals rare off‐target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9‐edited cotton plants

“…The sgRNAs were designed according to CRISPR-P web tool (Liu et al, 2017). The AP2, MYB44 and ARC target genes were selected for further analysis (Li et al, 2016). First, we found all possible sgRNA sequences in specific target gene with GC content (40% 60%) and on-target score (score value > 0.6).…”

“…Interestingly, no off-target mutations were detected by targeted deep sequencing in the top 26 potential off-target sites of four sgRNAs, suggesting that the CRISPR/Cas9 system is an efficient and reliable tool for allotetraploid cotton genome editing . To further investigate the specificity of CRISPR/Cas9 system on the genome-wide scale in cotton genome editing, three target genes encoding the AP2/B3-like transcription factor (AP2), MYB44 transcription factor (MYB44) and nucleotide-binding (NB)-ARC domain-containing disease resistance protein (ARC) were edited using CRISPR/Cas9 in this study (Li et al, 2016). We performed whole genome sequencing in T0 generation plants and T1 lines with an approximate 359 sequencing depth (Table S1).…”

Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process

“…Quantitative RT-PCR was performed as previously described to confirm the RNA-Seq data (Li et al, 2016). The relative expression level of each gene was normalized using the cotton Ubiquitin 7 (GhUb7) gene as a reference gene.…”

RNA Interference in Insect Vectors for Plant Viruses

“…Suppressing the terpenoid synthesis in tobacco plants via gene silencing improved whitefly fitness and favored vector–virus mutualism [100]. Similarly, silencing protein kinase ( GhMPK3 ) by VIGS resulted in suppression of the MPK-WRKY-jasmonic acid (JA) and ethylene (ET) pathways and resulted in enhanced whitefly susceptibility and significant effects on eggs and pupa [101]. …”