Transcriptome analysis of a nematode resistant and susceptible upland cotton line at two critical stages of Meloidogyne incognita infection and development

Authors: KUMAR, PAWAN - University Of Georgia; KHANAL, SAMEER - University Of Georgia; DA SILVA, MYCHELE - University Of Georgia; SINGH, RIPPY - University Of Georgia; Davis, Richard; NICHOLS, ROBERT - Cotton, Inc; CHEE, PENG - University Of Georgia

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/6/2019
Publication Date: 9/10/2019
Citation: Kumar, P., Da Silva, M., Singh, R., Davis, R.F., Nichols, R., Chee, P. 2019. Transcriptome analysis of a nematode resistant and susceptible upland cotton line at two critical stages of Meloidogyne incognita infection and development. PLoS One. 14(9). https://doi.org/10.1371/journal.pone.0221328.
DOI: https://doi.org/10.1371/journal.pone.0221328

Interpretive Summary: Host plant resistance is the most practical approach to control the Southern root-knot nematode (Meloidogyne incognita; RKN), which is one of the most serious economic pests of Upland cotton. Previous genetic analysis identified a section of DNA on chromosome 11 (a quantitative trait locus [QTL] named qMi-C11) associated with reduced galling and another QTL on chromosome-14 (qMi-C14) associated with reduced egg production. Although these two QTL regions were fine mapped, there is no information suggesting which genes may be involved in this resistance phenomenon. We applied the comparative transcriptomic approach to compare the expression profiles of genes between RKN susceptible and resistant genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. A total of 1239 differentially expressed genes (DEGs) were identified between the RKN-infected susceptible and resistant cotton genotypes. A large number of DEGs were found to be down regulated (suppressed activity) in the susceptible genotype at the late stage of RKN development whereas several genes were upregulated (increased activity) in the resistant genotype. Key enriched categories of genes included transcription factor activity, defense response, response to hormones, cell wall organization, and protein serine/threonine kinase activity. Our results show that the DEGs in the resistant genotype at the qMi-C11 and qMi-C14 loci displayed higher expression compared to the DEGs in the susceptible genotype, which supports the conclusion that these QTLs are involved in the resistance response. We found that the RKN resistance in M120 might not only be due to induction of genotype-specific genes but also due to greater magnitude in expression of defense response genes that are common to both genotypes.

Technical Abstract: Host plant resistance is the most practical approach to control the Southern root-knot nematode (Meloidogyne incognita; RKN), which has emerged as one of the most serious economic pests of Upland cotton (Gossypium hirsutum L.). Linkage analysis of an interspecific F2:3 population has identified a resistance locus on chromosome 11 (qMi-C11) affecting galling and another locus on chromosome-14 (qMi-C14) affecting egg production. Although these two QTL regions were fine mapped, there are no expression profiling of genes that may account for this phenomenon. We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of six cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome. A total of 1239 differentially expressed genes (DEGs) were identified and clustered according to their expression profiles. A large number of DEGs were found to be down regulated in the susceptible genotype at the late stage of RKN development whereas several genes were upregulated in the resistant genotype. Key enriched categories included transcription factor activity, defense response, response to hormones, cell wall organization, and protein serine/threonine kinase activity. Zeatin biosynthesis and biosynthesis of secondary metabolites are among the enriched KEGG pathway. Our results also show that the DEGs in the resistant genotype at qMi-C11 and qMi-C14 loci displayed higher expression compared to the DEGs in the susceptible genotype.