Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome

Abstract

Abstract Bromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares and costs land managers and growers through lost yield, land utility, and increased incidence of fire. Invasion success is often related to avoidance of abiotic stress and human management. Early flowering is a complex but heritable trait utilized by B. tectorum that enables the species to temporally monopolize limited resources and thus outcompete native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies – regardless of the invaded ecosystem. To study flowering time traits in B. tectorum, we assembled the first chromosome scale reference genome using PacBio long reads, assembled using the Canu assembler, and scaffolded using Omni-C chromatin contact mapping technology. The final assembly spanned 2.482 Gb in length and has an N50 and L50 of 357 Mb and 4, respectively. To assess the utility of the assembled genome for trait discovery, 121 diverse B. tectorum accessions were phenotyped in replicated greenhouse trials, genotyped by sequencing and subjected to a genome wide association study (GWAS). Significantly (q < 0.05) associated QTLs were identified for height, days to first joint (J1), days to first visible panicle (VPN), and days to first ripe seed (FRS). Overlap between significant QTLs was present between traits, suggesting pleiotropy or closely linked QTLs for life cycle related traits. Candidate genes, representing homologs of an array of genes that have been previously associated with plant height or flowering phenology traits in related species, were located near significant QTLs. The GWAS, combined with a well annotated genome, is a viable method for identifying candidate genes associated with weedy characteristics in invasive weeds. This is the first study using high-resolution GWAS to identify phenology related genes in a weedy species and represents a significant step forward in our understanding of the mechanisms underlying genetic plasticity in one of the most successful invasive weed species in the world.