Transcriptome Analysis of Upland Cotton Roots at Two Critical stages of Meloidogyne incognita infection and development.

Working group session: 
Structural Genomics
Presentation type: 
15 minute Oral
Authors: 
Kumar, Pawan
Da Silva, Mychele
Singh, Rippy
Davis, Richard F.
Nichols, Robert L.
Chee, Peng W.
Author Affliation: 
Cotton Molecular Breeding Laboratory, University of Georgia, Tifton, GA 31793, USA
Cotton Molecular Breeding Laboratory, University of Georgia, Tifton, GA 31793, USA
Cotton Molecular Breeding Laboratory, University of Georgia, Tifton, GA 31793, USA
USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA 31793, USA
Cotton Incorporated, Cary, NC 27513, USA
Cotton Molecular Breeding Laboratory, University of Georgia, Tifton, GA 31793, USA
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 pest 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 coincide with the establishment of a feeding site and at the late stage of RKN development that coincide 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 down regulated in susceptible genotype at the late stage of RKN development while 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 resistant genotype at qMi-C11 and qMi-C14 loci displayed higher expression compared to the DEGs in susceptible genotypes.