1 INTRODUCTION
In natural ecosystems, the dynamics of plant interactions with other living organisms are complex. This is especially true for organisms that rely on plants for shelter, nutrition, and reproduction, such as fungi and insects (Chisholm, Coaker, Day, & Staskawicz, 2006; Panda & Khush, 1995). Although fungi and insects can provide some of the same useful services in return, those that do not can be extremely harmful to plant productivity. To mitigate the effects of biotic stress, plants employ a diverse set of defense mechanisms including chemical, protein-derived molecules, and physical barriers (Panda & Khush, 1995). Insects and fungi must develop strategies in parallel to overcome these obstacles to survive (Chisholm et al., 2006; Mello & Silva-Filho, 2002). The theory of gene-for-gene coevolution has frequently been used to describe this host plant genetic relationship to its arthropod and fungal communities (Chisholm et al., 2006; Ehrlich & Raven, 1964; Mello & Silva-Filho, 2002; Thompson, 1988).
The gene-for-gene theory suggests a very simple dynamic for the genetic interactions that occur between two species. A gene in the host plant that is important in biotic relationships has a corresponding, coevolving gene from a pathogen/insect which can lead to resistance or susceptibility depending on the life history of the pathogen/insect (Flor, 1971; Friesen, Meinhardt, & Faris, 2007). Much of the evidence for these interactions has been found in crop systems where plant species often have dominant, single-gene resistance to feeding (Thompson, 1988). For example, there are over twenty different genes in wheat (Triticum aestivum L.) that each confer resistance to the Hessian fly, Mayetiola destructor (Thompson & Burdon, 1992). Exposure of Hessian fly populations to these resistant varieties of wheat created selection pressure that led to increased virulent gene combinations in the pest (Gallun, 1977; Panda & Khush, 1995). Similarly, in plant-fungal systems breeding for dominant resistance in cereal crops resulted in new selective forces that increased virulent gene frequencies in Puccinia spp. cereal rusts (X. M. Chen, 2005; Pretorius, Singh, Wagoire, & Payne, 2000). This in turn can lead to an evolutionary arms race between plants, insects, and fungi with the continual development of mechanisms to overcome both genetic defenses and virulent attacks (Bergelson, Kreitman, Stahl, & Tian, 2001; Thompson & Burdon, 1992).
The relationships of host plant genetics and biotic association can also be more complex than these crop breeding systems suggest, and they can leave a lasting impact on genome structure (Lefebvre & Chèvre, 1995). Host plant and biotic associations can lead to the expansion of gene families responsible for the host plant response to biotic stress. For example, the Kunitz protease inhibitors (KPIs) in Populus are important in defense responses against insects by inhibition of herbivore digestion (Haruta, Major, Christopher, Patton, & Constabel, 2001; Major & Constabel, 2008). The KPI gene family has greatly expanded in response to insect attack through tandem duplication events (Philippe, Ralph, Külheim, Jancsik, & Bohlmann, 2009). Similarly, plant resistance (R ) genes, which are important in the defense response of plants to fungal pathogen attack, have also expanded through tandem and segmental duplication events due to biotic pressures (Hulbert, Webb, Smith, & Sun, 2001; Leister, 2004). Analyzing how the genome is structured in the host plant when it associates with fungi and insects is important for studying these relationships and understanding the complexities of their genetic interactions.
Given their rapid growth and vegetative reproduction, Populusspecies have become a focus for research into biofuel production making them a valuable commercial crop (Meilan et al., 2002; Stanton, B. Neale, & Li, 2010; Taylor, 2002). Populus has also become an important genetic model for research into a wide variety of ecological and adaptive traits (McKown et al., 2014), including interactions with the biotic community (Crutsinger et al., 2014; Whitham et al., 2006). In particular, interspecific hybrids of P. trichocarpa x P. deltoides segregate for a wide variety of traits including resistance to insect and fungal attack (G. Newcombe, 1998; George Newcombe & Ostry, 2001b). Such hybrid family crosses can be used to identify regions of the genome that are important in mediating biotic stress.
In this study, we investigated the genome composition of loci associated with insect and fungal species in an interspecific Populusfamily. We surveyed insects and fungal pathogens in a P. deltoides x P. trichocarpa pseudo-backcross family and used quantitative trait locus (QTL) analysis and comparative genomics to address three main questions: (1) Is there heritable, host genetic control of fungal and insect species? (2) What protein domains and gene ontology terms are enriched in the QTL intervals in the genomes of each Populusspecies? (3) What candidate genes in the intervals are unique to each species when comparing the P. trichocarpa and P. deltoidesgenomes?