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

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.

Weak population differentiation and high diversity in Salsola tragus in the inland Pacific Northwest, USA.

BACKGROUND: Salsola tragus is a widespread and problematic weed of semi-arid wheat production globally, and in the inland Pacific Northwest region of the USA. The species exhibits high levels of phenotypic diversity across its range and, at least in California USA, previous work has described cryptic diversity comprising a multi-species complex. Such cryptic diversity could suggest the potential for a differential response to management inputs between groups, and have important implications for the spread of herbicide resistance or other adaptive traits within populations. We used a genotyping-by-sequencing approach to characterize the population structure of S. tragus in the inland Pacific Northwest. RESULTS: Our results indicated that the population in this region is comprised of a single, tetraploid species (S. tragus sensu latu) with weak population structure on a regional scale. Isolation-by-distance appears to be the primary pattern of structure, but an independent set of weakly differentiated clusters of unknown origin were also apparent, along with a mixed mating system and high levels of largely unstructured genetic diversity. CONCLUSIONS: Despite considerable phenotypic variability within S. tragus in the region, agronomic weed managers can likely consider it as a single entity across the region, rather than a collection of cryptic subgroups with possible differential responses to management inputs or agroecosystem conditions. A lack of strong barriers to migration and gene flow mean that adaptive traits, such as herbicide resistance, can be expected to spread rapidly through populations across the region. © 2022 Society of Chemical Industry.

Genetic diversity and population structure of a global invader Mayweed chamomile (Anthemis cotula): management implications.

Mayweed chamomile (Anthemis cotula) is a globally invasive, troublesome annual weed but knowledge of its genetic diversity, population structure in invaded regions and invasion patterns remains unstudied. Therefore, germplasm from 19 A. cotula populations (sites) from three geographically distinct invaded regions: the Walla Walla Basin (located in southern Washington) and the Palouse (located in both northern Idaho and eastern Washington), Pacific Northwest, USA and Kashmir Valley, India were grown in the greenhouse for DNA extraction and sequencing. A total of 18 829 single-nucleotide polymorphisms were called and filtered for each of 89 samples. Pairwise F ST, Nei's genetic distance, heterozygosity, Wright's inbreeding coefficient (F) and self-fertilization rates were estimated for populations within and among the three regions with a total of 19 populations comprised of 89 individuals. Overall measurements of genetic variation were low but significant among regions, populations and individuals. Despite the weak genetic structure, two main genetic clusters were evident, one comprised of populations from Palouse and Kashmir Valley, the other comprised of populations from the Walla Walla Basin. Significant selfing was observed in populations from the Walla Walla Basin and Palouse but not from Kashmir Valley, indicating that Mayweed chamomile in the Pacific Northwest, USA could persist with low pollinator or pollen donor densities. Although F ST values between the regions indicate Palouse populations are more closely related to Kashmir Valley than to Walla Walla Basin populations, based on Migrate-n analysis, panmixis was the most likely model, suggesting an unrestricted gene flow among all three regions. Our study indicated that Kashmir Valley populations either originated from or shared the origin with the Palouse populations, suggesting human-mediated migration of A. cotula between regions.

An ALA122 THR substitution in the AHAS/ALS gene confers imazamox-resistance in Aegilops cylindrica.

BACKGROUND: Wheat growers have limited herbicide options to manage Aegilops cylindrica Host (jointed goatgrass), with many relying on mesosulfuron or imazamox in Clearfield™ winter wheat. Both imazamox and mesosulfuron inhibit acetohydroxyacid synthase/acetolactate synthase (AHAS/ALS). In 2015, a suspected imazamox resistant biotype of Ae. cylindrica was found in eastern Washington. RESULTS: Imazamox and mesosulfuron were applied to the suspected resistant and susceptible Ae. cylindrica biotypes in increasing application rates to evaluate herbicide dose needed to cause 50% growth reduction (GR50 ). The imazamox resistant biotype had a GR50 of 308.5 g ai ha-1 and was more than 5000 times more resistant to imazamox than a known susceptible biotype with a GR50 of 0.06 g ai ha-1 . The Ae. cylindrica resistant biotype was also resistant to mesosulfuron, with an GR50 of 46.82 g ai ha-1 , which was five times more than the susceptible GR50 of 8.6 g ai ha-1 . Sequencing of the AHAS/ALS gene revealed an Ala122 Thr substitution in the herbicide binding region of the AHAS/ALS gene on the D genome of Ae. cylindrica. The resistance trait was inherited as a dominant trait, and the Ala122 Thr co-segregates with the resistance phenotype. CONCLUSIONS: An Ala122 Thr substitution in the AHAS/ALS gene on the D genome of Ae. cylindrica confers resistance to imazamox in Ae. cylindrica. © 2021 Society of Chemical Industry.

Water and Temperature Stresses Impact Canola (Brassica napus L.) Fatty Acid, Protein, and Yield over Nitrogen and Sulfur.

Interactive effects of weather and soil nutrient status often control crop productivity. An experiment was conducted to determine effects of nitrogen (N) and sulfur (S) fertilizer rate, soil water, and atmospheric temperature on canola (Brassica napus L.) fatty acid (FA), total oil, protein, and grain yield. Nitrogen and sulfur were assessed in a 4-yr study with two locations, five N rates (0, 45, 90, 135, and 180 kg ha-1), and two S rates (0 and 17 kg ha-1). Water and temperature were assessed using variability across 12 site-years of dryland canola production. Effects of N and S were inconsistent. Unsaturated FA, oleic acid, grain oil, protein, and theoretical maximum grain yield were highly related to water and temperature variability across the site-years. A nonlinear model identified water and temperature conditions that enabled production of maximum unsaturated FA content, oleic acid content, total oil, protein, and theoretical maximum grain yield. Water and temperature variability played a larger role than soil nutrient status on canola grain constituents and yield.

Population structure and genetic diversity of Bromus tectorum within the small grain production region of the Pacific Northwest.

Bromus tectorum L. is an invasive winter annual grass naturalized across the United States. Numerous studies have investigated B. tectorum population structure and genetics in the context of B. tectorum as an ecological invader of natural areas and rangeland. Despite the wealth of information regarding B. tectorum, previous studies have not focused on, or made comparisons to, B. tectorum as it persists in individual agroecosystems. The objectives of this study were to assess the genetic diversity and structure, the occurrence of generalist and specialist genotypes, and the influence of climate on distribution of B. tectorum sourced exclusively from within small grain production regions of the Pacific Northwest. Genetic diversity of B. tectorum sourced from agronomic fields was found to be similar to what has been observed from other land use histories. Six distinct genetic clusters of B. tectorum were identified, with no evidence to indicate that any of the genetic clusters were better adapted to a particular geographical area or climate within the region. Given the apparent random spatial distribution of B. tectorum genetic clusters at the spatial scale of this analysis, unique genotypes may be well mixed within region, similar to what was reported for other inbreeding weedy grass species.

Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.).

BACKGROUND: 5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous copies of the allohexaploid wheat EPSPS gene were cloned and characterized. METHODS: Genomic and coding DNA sequences of EPSPS from the three related genomes of allohexaploid wheat were isolated using PCR and inverse PCR approaches from soft white spring "Louise'. Development of genome-specific primers allowed the mapping and expression analysis of TaEPSPS-7A1, TaEPSPS-7D1, and TaEPSPS-4A1 on chromosomes 7A, 7D, and 4A, respectively. Sequence alignments of cDNA sequences from wheat and wheat relatives served as a basis for phylogenetic analysis. RESULTS: The three genomic copies of wheat EPSPS differed by insertion/deletion and single nucleotide polymorphisms (SNPs), largely in intron sequences. RT-PCR analysis and cDNA cloning revealed that EPSPS is expressed from all three genomic copies. However, TaEPSPS-4A1 is expressed at much lower levels than TaEPSPS-7A1 and TaEPSPS-7D1 in wheat seedlings. Phylogenetic analysis of 1190-bp cDNA clones from wheat and wheat relatives revealed that: 1) TaEPSPS-7A1 is most similar to EPSPS from the tetraploid AB genome donor, T. turgidum (99.7 % identity); 2) TaEPSPS-7D1 most resembles EPSPS from the diploid D genome donor, Aegilops tauschii (100 % identity); and 3) TaEPSPS-4A1 resembles EPSPS from the diploid B genome relative, Ae. speltoides (97.7 % identity). Thus, EPSPS sequences in allohexaploid wheat are preserved from the most two recent ancestors. The wheat EPSPS genes are more closely related to Lolium multiflorum and Brachypodium distachyon than to Oryza sativa (rice). CONCLUSIONS: The three related EPSPS homoeologues of wheat exhibited conservation of the exon/intron structure and of coding region sequence, but contained significant sequence variation within intron regions. The genome-specific primers developed will enable future characterization of natural and induced variation in EPSPS sequence and expression. This can be useful in investigating new causes of glyphosate herbicide resistance.

Genetic and biochemical evaluation of natural rubber from Eastern Washington prickly lettuce (Lactuca serriola L.).

Alternative sources of natural rubber are of importance due to economic, biological, and political threats that could diminish supplies of this resource. Prickly lettuce (Lactuca serriola L.) synthesizes long-chain natural rubber and was studied to determine underlying genetic and phenotypic characteristics of rubber biosynthesis. Genotypic and phenotypic analysis of an F2 segregating population using EST-SSR markers led to the discovery of genetic regions linked to natural rubber production. Interval mapping (IM) and multiple QTL mapping (MQM) identified several QTL in the mapping population that had significance based on LOD score thresholds. The discovered QTL and the corresponding local markers are genetic resources for understanding rubber biosynthesis in prickly lettuce and could be used in marker-assisted selection (MAS) breeding. Prickly lettuce is an excellent candidate for elucidating the rubber synthesis mechanism and has potential as a crop plant for rubber production.

Interactions between the root pathogen Rhizoctonia solani AG-8 and acetolactate-synthase-inhibiting herbicides in barley.

BACKGROUND: The widespread acceptance of reduced-tillage farming in cereal cropping systems in the Pacific Northwest of the United States has resulted in increased use of herbicides for weed control. However, soil residual concentrations of widely used imidazalone herbicides limit the cultivation of barley, which is more sensitive than wheat. In addition, increased severity of the root rot disease caused by Rhizoctonia solani is associated with reduction in tillage. Many crops exhibit altered disease responses after application of registered herbicides. In this study, the injury symptoms in barley caused by sublethal rates of two acetolactate synthase (ALS)-inhibiting herbicides, imazamox and propoxycarbazone-sodium, were assessed in factorial combinations with a range of inoculum concentrations of the root rot pathogen Rhizoctonia solani AG-8. RESULTS: Both herbicides and pathogen had negative impacts on plant growth parameters such as root and shoot dry weight, shoot height and first leaf length, and interactions between pathogen and herbicide were detected. CONCLUSIONS: The results suggested that sublethal rates of herbicides and R. solani could alter severity of injury symptoms, possibly owing to the herbicide predisposing the plant to the pathogen.

Inheritance and physiological basis for 2,4-D resistance in prickly lettuce (Lactuca serriola L.).

Experiments were conducted to determine the inheritance and physiological basis for resistance to the synthetic auxinic herbicide (2,4-dichlorophenoxy)acetic acid (2,4-D) in a prickly lettuce biotype. Inheritance of 2,4-D resistance in prickly lettuce is governed by a single codominant gene. Absorption and translocation were conducted using (14)C-2,4-D applied to 2,4-D-resistant and -susceptible biotypes. At 96 h after treatment (HAT), the resistant biotype absorbed less applied 2,4-D and retained more 2,4-D in the treated portion of the leaf compared to the susceptible biotype. The resistant biotype translocated less applied 2,4-D to leaves above the treated leaf and crown at 96 HAT compared to the susceptible biotype. No difference in the rate of metabolism of 2,4-D was observed between the two biotypes. Resistance to 2,4-D appears to originate from a reduced growth deregulatory and overstimulation response compared to the susceptible biotype, resulting in lower translocation of 2,4-D in the resistant prickly lettuce biotype.

Uptake, translocation and metabolism of aminocyclopyrachlor in prickly lettuce, rush skeletonweed and yellow starthistle.

BACKGROUND: Aminocyclopyrachlor is a new herbicide proposed to control broadleaf weeds and shrubs in non-crop and rangeland systems. To gain a better understanding of observed field efficacy, the uptake and translocation of foliar-applied aminocyclopyrachlor (DPX-MAT28) and aminocyclopyrachlor methyl ester (DPX-KJM44) were evaluated in two annuals, prickly lettuce (Lactuca serriola L.) and yellow starthistle (Centaurea solstitialis L.), and one perennial, rush skeletonweed (Chondrilla juncea L.). RESULTS: Absorption and translocation varied between species. While absorption of DPX-KJM44 was greater than absorption of DPX-MAT28, rush skeletonweed absorbed the most, followed by yellow starthistle and prickly lettuce. Overall, the total translocation of either herbicide was highest in yellow starthistle, followed by rush skeletonweed and prickly lettuce. Proportional herbicide movement between species was similar, with the majority translocating to developing shoots. However, in rush skeletonweed, early translocation was directed to root tissue. In rush skeletonweed, no DPX-MAT28 metabolism occurred, while DPX-KJM44 was rapidly de-esterified and translocated as DPX-MAT28. CONCLUSION: Aminocyclopyrachlor absorption and translocation are dependent on active ingredient structure and species sensitivity. Highly sensitive species such as prickly lettuce absorb and translocate less material than relatively less sensitive species such as rush skeletonweed. De-esterification of DPX-KJM44 appears to delay translocation of the resulting acid in yellow starthistle and rush skeletonweed.

EST-SSR development from 5 Lactuca species and their use in studying genetic diversity among L. serriola biotypes.

Prickly lettuce (Lactuca serriola L.) is a problematic weed of Pacific Northwest and recently developed resistance to the auxinic herbicide 2,4-D. There are no publically available simple sequence repeat (SSR) markers to tag 2,4-D resistance genes in L. serriola. Therefore, a study was conducted to develop SSR markers from expressed sequence tags (ESTs) of 5 Lactuca species. A total of 15,970 SSRs were identified among 57,126 EST assemblies belonging to 5 Lactuca species. SSR-containing ESTs (SSR-ESTs) ranged from 6.23% to 7.87%, and SSR densities ranged from 1.28 to 2.51 kb(-1) among the ESTs of 5 Lactuca species. Trinucleotide repeats were the most abundant SSRs detected during the study. As a representative sample, 45 ESTs carrying class I SSRs (≥ 20 nucleotides) were selected for designing primers and were also searched against the dbEST entries for L. sativa and Helianthus annuus (≤ 10(-50); score ≥ 100). In silico analysis of 45 SSR-ESTs showed 82% conservation across species and 68% conservation across genera. Primer pairs synthesized for the above 45 EST-SSRs were used to study genetic diversity among a collection of 22 L. serriola biotypes. Comparison of the resultant dendrogram to that developed using phenotypic evaluation of the same subset of lines showed limited correspondence. Taken together, this study reported a collection of useful SSR markers for L. serriola, confirmed transferability of these markers within and across genera, and demonstrated their usefulness in studying genetic diversity.

Evidence for cross-adaptation between s-triazine herbicides resulting in reduced efficacy under field conditions.

BACKGROUND: Enhanced atrazine degradation has been observed in agricultural soils from around the globe. Soils exhibiting enhanced atrazine degradation may be cross-adapted with other s-triazine herbicides, thereby reducing their control of sensitive weed species. The aims of this study were (1) to determine the field persistence of simazine in atrazine-adapted and non-adapted soils, (2) to compare mineralization of ring-labeled (14)C-simazine and (14)C-atrazine between atrazine-adapted and non-adapted soils and (3) to evaluate prickly sida control with simazine in atrazine-adapted and non-adapted soils. RESULTS: Pooled over two pre-emergent (PRE) application dates, simazine field persistence was 1.4-fold lower in atrazine-adapted than in non-adapted soils. For both simazine and atrazine, the mineralization lag phase was 4.3-fold shorter and the mineralization rate constant was 3.5-fold higher in atrazine-adapted than in non-adapted soils. Collectively, the persistence and mineralization data confirm cross-adaptation between these s-triazine herbicides. In non-adapted soils, simazine PRE at the 15 March and 17 April planting dates reduced prickly sida density at least 5.4-fold compared with the no simazine PRE treatment. Conversely, in atrazine-adapted soils, prickly sida densities were not statistically different between simazine PRE and no simazine PRE at either planting date, thereby indicating reduced simazine efficacy in atrazine-adapted soils. CONCLUSIONS: Results demonstrate the potential for cross-adaptation among s-triazine herbicides and the subsequent reduction in the control of otherwise sensitive weed species.