Cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation

As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. Using the next generation sequencing (NGS) Illumina MiSeq and HiSeq, we performed RNA-seq profiling in roots with disease progression of 10 days and collected from 23 days old plants of SJ2, WMJJ, and NemX. With three biological replicates of each treatment from each cultivar, plants were subjected to RKN-infestation and non-infested control developing a total of 18 RNA-seq libraries Overall design: Three cotton genotypes (Acala SJ-2 (RKN-susceptible), Wild Mexico Jack Jones (WMJJ; moderately tolerant to RKN) and Acala NemX (RKN-resistant)) and 2 treatments (Control, RKN-infested) were tested. 3 biological replicates for each treatment and genotype.