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

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. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.

Fig. 1. Circos synteny plot depicting the synteny between the Bromus tectorum draft reference genome and a previously published barley genome.

Strips and barley chromosomes colored in reference to the corresponding barley chromosomes. Histograms above B. tectorum chromosomes are coded black for gene density and red for telomere repeats for each 1 Mb window of the chromosome.

Fig. 2. Distributions, Spearman correlations, and scatter plots of the genotype BLUEs for height (cm), number of tillers, days until first panicle (VPN), days until 50% rip seed (50%), days until first joint (J1), days until first ripe seed (FRS) used in the GWAS analysis.

Histograms with density ticks and a smoothing line are on the diagonals. The upper diagonal contains the Spearman correlation between BLUEs of traits with “***” denoting a significant level (p < 0.0001) of correlation between traits, where N = 121 genotypes. The lower diagonal contains scatter plots between traits with center dot, a centroid with a standard deviation of 1 and locally estimated scatterplot smoothing (LOESS) smoothing curve.