Comparative Transcriptome Analysis of Near Isogenic Lines for Root-Knot Resistance QTLs, Qmi-C11 and Qmi-C14

Southern root-knot nematode (Meloidogyne incognita; RKN) is the most significant pathogen of Upland cotton in the United States and host plant resistance is the only practical means of combating RKN infestation. Quantitative trait loci qMi-C11 and qMi-C14 provide genetic resistance to RKN at two different stages of pathogen development. Histopathological study with near isogenic lines (isolines carrying different QTLs) has documented different modes of action. qMi-C11 induced increase in RKN emigration (at J2 stage) from cotton roots or the nematodes fail to develop beyond the SJ2 stage, while qMi-C14 caused nematodes cease to develop beyond the J4 stage. Here, we present our approach towards comparative transcriptome analysis using RNA-seq to decipher differential gene expression in the resistant isolines and their susceptible recurrent parent (Coker 201) at different timepoints after infection.