Inferring Plant and Nematode Interaction Networks with Genetical Genomics Data - Built upon Enhanced Genetic Resources for the Model Organism, Meloidogyne hapla

Root-knot nematodes (RKN) are plant parasites that infect a wide range of plant species and cause substantial loss to agricultural production. Understanding the genetic interaction between host and parasites holds the key to development of effective control methods, but is a complex and multi-dimensional problem. Powered by rapid technological development, genetical genomics studies that integrate genetic and transcriptomic profiles have brought many successes in understanding the genetic basis of complex traits and disease susceptibility. This dissertation analyzes genetical genomics data from a cross-species experiment where plants with an identical genetic background were inoculated by offspring of a cross between two nematode inbred lines. Through reconstruction of a genetic interaction network, this work uncovers important regulatory mechanisms between host plants and RKNs.;In the introduction chapter, we first summarize current knowledge about RKNs and their infectious biology, as well as the model plant-pathogen system used in this study: Medicago truncatula infected with Meloidogyne hapla. We further introduce statistical methods available for integrating markers genotypes and gene expression profiles in a network analysis. For this project, these profiles were derived from short reads generated by RNA-sequencing, representing the transcribed regions of the genome. Based on the mapped genome location of these transcribed regions, in chapter 2, we present an improved gene structural annotation for the model nematode species, M. hapla. Additionally we evaluate trans-splicing events in this species using the same data. In chapter 3, we construct a dense genetic map for M. hapla with approximately 5,000 high quality SNP markers that are anchored to the existed physical map. Collinearity of the genetic and physical maps suggests the veracity of both maps. We further characterize the recombination rate and identify recombination hot spots for this species. Built upon these improved genetic resources, in chapter 4, we reconstruct the genetic regulation network with a focus on between-species interactions. Results reinforce some of the current knowledge on RKN infectious biology, and further discover novel regulatory mechanism between plant and nematode.