DNA markers and gene expression polymorphisms associated with growth habit quantitative trait loci in Leymus wildryes

Studies have shown the synteny of the Triticeae linkage group 3 and rice chromosome 1. The objectives of the project were a. ) the development and mapping of ESTs in perennial Leymus wildryes and b. ) comparative analysis of the collinearity of the expressed sequence tag microsatellite markers (EST-SSRs) on Leymus linkage group 3 with rice chromosome 1 and wheat linkage group 3. A total of 228 of 1,798 Leymus ESTSSRs were aligned to rice chromosome 1. From 67 polymorphic EST-SSRs in Leymus, the genetic map order of 23 LG3a and 17 LG3b Leymus EST or STS markers was strictly collinear with homologous sequences on rice chromosome 1. Mapping of three EST-SSR sequences on both LG3a and LG3b also confirmed the homoeology of two linkage groups. A total of 44% of the ESTs present on rice chromosome 1 showed significant sequence homology with wheat EST sequences. About 32% of all Leymus ESTs homologous to rice chromosome 1 were also hon~ologous to wheat group 3 ESTs at a threshold value of E'~ . Identification of Leymus linkage group 3 chromoso~nes in wheatLeynzus addition lines using Leynzus linkage group 3 ESTs refuted the assertion of partitioning chromosome 3 into two parts. Introduction Conservation of gene content and order (collinearity) in related genomes has been studied in several model species such as rice and Arabidopsis in the past few years. The information obtained from these model plants is successfully being used in the related plant species (Devos and Gale 1997,2000). This allows us to design effective strategies for map-based gene cloning from plant species with large and complex genomes. Several exceptions of collinearity among grass genomes exist (Guyot et al. 2004; Li and Gill 2002; Rarnakrishna et al. 2002), which may result from changes in chromosome number and genome size or sequence changes such as insertions, deletions, duplications, and translocations, making the use of these model species for cross-species comparisons with other grasses a complicated process (Sorrells et al. 2003). Leymus wildryes are medium-to large-statured perennial Triticeae grasses, members of Poaceae, and comprising important staple crops such as rice (Oryza spp.), maize (Zea mays), barley (Hordeum vulgare) and wheat (Triticum spp.). Cool-season Leynzus grasses are remarkably well adapted to harsh conditions such as polar, saline, desert, and erosion-prone environments in North America. The genus Leymus comprises about 30 long-lived perennial grass species, distributed throughout the temperate regions of Asia, Europe, and America (Dewey 1984). Leymus cinereus and L. ~riticoides are allotetraploid (2n=4x=28), and display disomic inheritance (Wu et al. 2003). Leynzus triticoides is characterized by the presence of aggressive subterranean rhizomes and are well adapted to poorly drained, alkaline sites of the western United States. Conversely, L. cinereus is a tall conspicuous bunchgrass growing strictly upright with high biomass potential adapted to well-drained soils of western North America (Wu et al. 2003; Larson et al. 2006). Hybrids of L. cinereus and L. triticoides display regular meiosis and stainable pollen (Dewey 1972; Hole et al. 1999). High-density molecular genetic linkage maps have been constructed for two fullsib mapping families, TTC 1 and TTC2 (Wu et al. 2003). The 164-sib TTC 1 and 170-sib TTC2 were derived from two different L. triticoides x L. cinereus F1 hybrids, TC 1 and TC2, crossed to the same clones of L. tviticoides T-tester genotype. The initial parents were derived from two outcrossing and inherentlylheterogenous accessions; Acc:636 and Acc:641 (L. cinereus and L. tviticoides, respectively). Thus TCl and TC2 hybrids are genetically different (Wu et al. 2003). The TTCl and TTC2 families segregate for growth habit and other characteristics of the L. cinereus and L. triticoides source populations and thus can be used for gene discovery research and development of molecular markers in perennial grasses. Over 1,583 AFLP barkers and 67 anchor markers were previously mapped to the Leymus TTCl and/or TTC2 molecular genetic linkage maps (Wu et al. 2003; Larson et al. 2006). Recently, Larson et al. (2006) exploited the two families to discover quantitative trait loci (QTLs) controlling growth habit, plant height, and flowering traits. Growth habit QTLs near the VP1 loci on linkage group LG3a and LG3b, in both TTCl and TTC2 families, suggest that the growth habit QTL is controlled by homoeologous copies of the same gene on Triticeae homoeologous group 3 (Larson et al. 2006). However, only two anchor markers (SIP1 and VP1) were available to align LG3a and LG3b to each other and other Poaceae species (Wu et al. 2003). Linkage group 3 is highly conserved among Triticeae grasses (Devos and Gale