Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages.

Switchgrass (Panicum virgatum L.) is an important crop for bioenergy feedstock development. Switchgrass has two main ecotypes: the lowland ecotype being exclusively tetraploid (2n = 4x = 36) and the upland ecotype being mainly tetraploid and octaploid (2n = 8x = 72). Because there is a significant difference in ploidy, morphology, growth pattern, and zone of adaptation between and within the upland and lowland ecotypes, it is important to discriminate switchgrass plants belonging to different genetic pools. We used 55 simple sequence repeats (SSR) loci and six chloroplast sequences to identify patterns of variation between and within 18 switchgrass cultivars representing seven lowland and 11 upland cultivars from different geographic regions and of varying ploidy levels. We report consistent discrimination of switchgrass cultivars into ecotype membership and demonstrate unambiguous molecular differentiation among switchgrass ploidy levels using genetic markers. Also, SSR and chloroplast markers identified genetic pools related to the geographic origin of the 18 cultivars with respect to ecotype, ploidy, and geographical, and cultivar sources. SSR loci were highly informative for cultivar fingerprinting and to classify plants of unknown origin. This classification system is the first step toward developing switchgrass complementary gene pools that can be expected to provide a significant heterotic increase in biomass yield.

Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 3503 coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed.

The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.

Recent increases in glyphosate use in perennial crops of California, USA, are hypothesized to have led to an increase in selection and evolution of resistance to the herbicide in Conyza canadensis populations. To gain insight into the evolutionary origins and spread of resistance and to inform glyphosate resistance management strategies, we investigated the geographical distribution of glyphosate resistance in C. canadensis across and surrounding the Central Valley, its spatial relationship to groundwater protection areas (GWPA), and the genetic diversity and population structure and history using microsatellite markers. Frequencies of resistant individuals in 42 sampled populations were positively correlated with the size of GWPA within counties. Analyses of population genetic structure also supported spread of resistance in these areas. Bayesian clustering and approximate Bayesian computation (ABC) analyses revealed multiple independent origins of resistance within the Central Valley. Based on parameter estimation in the ABC analyses, resistant genotypes underwent expansion after glyphosate use began in agriculture, but many years before it was detected. Thus, diversity in weed control practices prior to herbicide regulation in GWPA probably kept resistance frequencies low. Regionally coordinated efforts to reduce seed dispersal and selection pressure are needed to manage glyphosate resistance in C. canadensis.

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Understanding the genetic mechanisms that contribute to range expansion and colonization success within novel environments is important for both invasion biology and predicting species-level responses to changing environments. If populations are adapted to local climates across a species' native range, then climate matching may predict which genotypes will successfully establish in novel environments. We examine evidence for climate adaptation and its role in colonization of novel environments in the model species, Arabidopsis thaliana. We review phenotypic and genomic evidence for climate adaptation within the native range and describe new analyses of fitness data from European accessions introduced to Rhode Island, USA, in spring and fall plantings. Accessions from climates similar to the Rhode Island site had higher fitness indicating a potential role for climate pre-adaptation in colonization success. A genomewide association study (GWAS), and genotypic mean correlations of fitness across plantings suggest the genetic basis of fitness in Rhode Island differs between spring and autumn cohorts, and from previous fitness measurements in European field sites. In general, these observations suggest a scenario of conditional neutrality for loci contributing to colonization success, although there was evidence of a fitness trade-off between fall plantings in Norwich, UK, and Rhode Island. GWAS suggested that antagonistic pleiotropy at a few specific loci may contribute to this trade-off, but this conclusion depended upon the accessions included in the analysis. Increased genomic information and phenotypic information make A. thaliana a model system to test for the genetic basis of colonization success in novel environments.

Comparing genetic diversity, genetic differentiation, and performance between native and nonnative populations has advanced our knowledge of contemporary evolution and its ecological consequences. However, such between‐range comparisons can be complicated by high among‐population variation within native and nonnative ranges. For example, native vs. nonnative comparisons between small and non‐representative subsets of populations for species with very large distributions have the potential to mislead because they may not sufficiently account for within‐range adaptation to climatic conditions, and demographic history that may lead to non‐adaptive evolution. We used the cosmopolitan weed Conyza canadensis to study the interplay of adaptive and demographic processes across, to our knowledge, the broadest climatic gradient yet investigated in this context. To examine the distribution of genetic diversity, we genotyped 26 native and 26 nonnative populations at 12 microsatellite loci. Furthermore, we recorded performance traits for 12 native and 13 nonnative populations in the field and in the common garden. To analyze how performance was related to range and/or climate, we fit pedigree mixed‐effects models. These models weighed the population random effect for co‐ancestry to account for the influence of demographic history on phenotypic among‐population differentiation. Genetic diversity was very low, selfing rates were very high, and both were comparable between native and nonnative ranges. Nonnative populations out‐performed native populations in the field. However, our most salient result was that both neutral genetic differentiation and common garden performance were far more correlated with the climatic conditions from which populations originated than native vs. nonnative range affiliation. Including co‐ancestry of our populations in our models greatly increased explained variance and our ability to detect significant main effects for among‐population variation in performance. High propagule pressure and high selfing rates, in concert with the ability to adapt rapidly to climatic gradients, may have facilitated the global success of this weed. Neither native nor nonnative populations were homogeneous groups but responded comparably to similar environments in each range. We suggest that studies of contemporary evolution should consider widely distributed and genotyped populations to disentangle native vs. nonnative range effects from varying adaptive processes within ranges and from potentially confounding effects of demographic history.