Genetic, Geographic, and Climate Diversity of a Weedy Species: The Brachypodium distachyon Species Complex

The Introduction of novel species into non-native environments can have biodiversity and agricultural effects on landscapes costing billions of dollars in damage each year. Approximately 1.2 million hectares of land are currently deemed unusable globally because of invasive plants. The likelihood of introduced species becoming invasive isn't always understood, nor the effect of introductions immediately apparent. The environment is the primary selection force for screening habitability and is the primary selector for adaptation, but measuring all its components is complex. Therefor climate factors, precipitation and temperature, are the primary variables for determining a species distribution. The three model grasses in the Brachypodium distachyon complex species were used in this study because of their small sequenced genomes, classified as weedy and invasive in some regions, and were once native to the circum-Mediterranean, now global distributed. Genotyping by sequencing was used on 1,573 individuals to determine species identification and genetic diversity of each complex member. A total of 125 unique genotypes of B. distachyon were found from 479 individuals, eight unique genotypes of B. stacei from 50 individuals, and 80 unique genotypes of B. hybridum from 1,015 individuals. MaxEnt distribution modelling was used to find potential area using a training specificity equals sensitivity threshold both natively and globally. B. stacei was the most rare having the smallest potential area in its native range at 2,458,837 square kilometers and 3,207,524 globally. B. distachyon had the largest native potential area at 5,098,573 square kilometers, but rare outside its native range, Australia only. B. hybridum was modelled to have 3,935,266 square kilometers natively, but 6,705,946 square kilometers globally leaving 2,770,680 of potential habitat non-natively. Common genotypes of the polyploid complex member B. hybridum were permutation tested for global abundance across groups of regions, with the genotype NRD-1 being significantly more abundant geographically than random. NRD-1 was also used for global distribution modelling to determine global suitable regions that would be sensitive to NRD-1 introduction. The three complex species were compared for climate breadth where B. hybridum had the widest climate breadth of the three group members. The genotype NRD-1 was also compared to B. hybridum as a whole to see if the NRD-1 genotype had a similar climate breadth as the whole species, possibly defining the species climate breadth. The climate diversity within each species was used to designate climate type identities for sample locations to measure climate range a genotype occupies and the climate diversity of geographic space. The B. hybridum genotype NRD-1 was found in the most climate types through permutation testing and found to have a significantly larger climate breadth than average p-value <0.01. Geographic regions with high climate diversity were also found to have the most genotypes. As B. hybridum was found to be the most widely distributed of the three study species, many specific genotypes occurred in numerous climate types and were sampled on multiple continents, particularly genotype NRD-1, thus were concluded as the most widely adapted B. hybridum and all other B. distachyon complex species genotypes

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence.

Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation

Global diversity of the Brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.We are grateful for funding and support from the Australian Research Council Centre of Excellence in Plant Energy Biology (CE140100008). Australian Plant Phenomics Facility is supported under the National Collaborative Research Infrastructure Strategy of the Australian Government. The research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI), which is supported by the Australian Government

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence

Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation

Quinoa phenotyping methodologies: An international consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.Fil: Stanschewski, Clara S.. King Abdullah University of Science and Technology; Arabia SauditaFil: Rey, Elodie. King Abdullah University of Science and Technology; Arabia SauditaFil: Fiene, Gabriele. King Abdullah University of Science and Technology; Arabia SauditaFil: Craine, Evan B.. Washington State University; Estados UnidosFil: Wellman, Gordon. King Abdullah University of Science and Technology; Arabia SauditaFil: Melino, Vanessa J.. King Abdullah University of Science and Technology; Arabia SauditaFil: Patiranage, Dilan S. R.. King Abdullah University of Science and Technology; Arabia SauditaFil: Johansen, Kasper. King Abdullah University of Science and Technology; Arabia SauditaFil: Schmöckel, Sandra M.. King Abdullah University of Science and Technology; Arabia SauditaFil: Bertero, Hector Daniel. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal. Cátedra de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Oakey, Helena. University of Adelaide; AustraliaFil: Colque Little, Carla. Universidad de Copenhagen; DinamarcaFil: Afzal, Irfan. University of Agriculture; PakistánFil: Raubach, Sebastian. The James Hutton Institute; Reino UnidoFil: Miller, Nathan. University of Wisconsin; Estados UnidosFil: Streich, Jared. Oak Ridge National Laboratory; Estados UnidosFil: Amby, Daniel Buchvaldt. Universidad de Copenhagen; DinamarcaFil: Emrani, Nazgol. Christian-albrechts-universität Zu Kiel; AlemaniaFil: Warmington, Mark. Agriculture And Food; AustraliaFil: Mousa, Magdi A. A.. Assiut University; Arabia Saudita. King Abdullah University of Science and Technology; Arabia SauditaFil: Wu, David. Shanxi Jiaqi Agri-Tech Co.; ChinaFil: Jacobson, Daniel. Oak Ridge National Laboratory; Estados UnidosFil: Andreasen, Christian. Universidad de Copenhagen; DinamarcaFil: Jung, Christian. Christian-albrechts-universität Zu Kiel; AlemaniaFil: Murphy, Kevin. Washington State University; Estados UnidosFil: Bazile, Didier. Savoirs, Environnement, Sociétés; Francia. Universite Paul-valery Montpellier Iii; FranciaFil: Tester, Mark. King Abdullah University of Science and Technology; Arabia Saudit

Rare inland reindeer lichens at Mima Mounds in southwest Washington State

Isolated populations of four reindeer lichen species and varieties co-occur in a unique relict prairie habitat at Mima Mounds Natural Area Preserve, southwest Washington State, USA. The prairie is the type locality for mima mounds, unusual geologic features providing topographical variation that influences vegetation patterns. Reindeer lichens (Cladonia subgenus Cladina) are very rare in inland valley habitats of the western states outside of Alaska; one study species, C. ciliata, is apparently rare in North America and is not known south of the site. The current study establishes distributional, ecological, chemotypic, and phylogenetic analyses for the study species. We found that topography was not as important as recent fire history in explaining reindeer lichen distribution; in the future, prescribed fire is likely to benefit reindeer lichens so long as it preserves pockets of refugia as propagule sources. We also detected moderate air pollution stress, which is projected to have impacts on lichen abundances and community compositions in the near future. Chemotype analysis revealed 6 reindeer lichen chemotypes, of which 2 are rare (C. ciliata var. tenuis and C. portentosa subsp. pacifica f. decolorans). Phylogenetic analyses supported previous species concepts, showing C. portentosa is distinct from the closely-related group that includes C. rangiferina and two varieties of C. ciliata. We suggested that the four target taxa described herein may benefit from continued future monitoring and cataloging as state sensitive species

Using iterative random forest to find geospatial environmental and Sociodemographic predictors of suicide attempts

IntroductionDespite a recent global decrease in suicide rates, death by suicide has increased in the United States. It is therefore imperative to identify the risk factors associated with suicide attempts to combat this growing epidemic. In this study, we aim to identify potential risk factors of suicide attempt using geospatial features in an Artificial intelligence framework.MethodsWe use iterative Random Forest, an explainable artificial intelligence method, to predict suicide attempts using data from the Million Veteran Program. This cohort incorporated 405,540 patients with 391,409 controls and 14,131 attempts. Our predictive model incorporates multiple climatic features at ZIP-code-level geospatial resolution. We additionally consider demographic features from the American Community Survey as well as the number of firearms and alcohol vendors per 10,000 people to assess the contributions of proximal environment, access to means, and restraint decrease to suicide attempts. In total 1,784 features were included in the predictive model.ResultsOur results show that geographic areas with higher concentrations of married males living with spouses are predictive of lower rates of suicide attempts, whereas geographic areas where males are more likely to live alone and to rent housing are predictive of higher rates of suicide attempts. We also identified climatic features that were associated with suicide attempt risk by age group. Additionally, we observed that firearms and alcohol vendors were associated with increased risk for suicide attempts irrespective of the age group examined, but that their effects were small in comparison to the top features.DiscussionTaken together, our findings highlight the importance of social determinants and environmental factors in understanding suicide risk among veterans

Trait data for 12 Brachypodium hybridum populations

This file includes the biomass (and its CV) data measured from the common garden experiment for the 12 invasive Californian Brachypodium hybridum populations