The Evolution of an Invasive Plant, Sorghum halepense L. (Johnsongrass).

From noble beginnings as a prospective forage, polyploid Sorghum halepense (Johnsongrass) is both an invasive species and one of the worlds worst agricultural weeds. Formed by S. bicolor x S. propinquum hybridization, we show S. halepense to have S. bicolor-enriched allele composition and striking mutations in 5,957 genes that differentiate it from representatives of its progenitor species and an outgroup. The spread of S. halepense may have been facilitated by introgression from closely-related cultivated sorghum near genetic loci affecting rhizome development, seed size, and levels of lutein, a photochemical protectant and abscisic acid precursor. Rhizomes, subterranean stems that store carbohydrates and spawn clonal propagules, have growth correlated with reproductive rather than other vegetative tissues, and increase survival of both temperate cold seasons and tropical dry seasons. Rhizomes of S. halepense are more extensive than those of its rhizomatous progenitor S. propinquum, with gene expression including many alleles from its non-rhizomatous S. bicolor progenitor. The first surviving polyploid in its lineage in ∼96 million years, its post-Columbian spread across six continents carried rich genetic diversity that in the United States has facilitated transition from agricultural to non-agricultural niches. Projected to spread another 200-600 km northward in the coming century, despite its drawbacks S. halepense may offer novel alleles and traits of value to improvement of sorghum

Genetic Analysis of Stem Diameter and Water Contents To Improve Sorghum Bioenergy Efficiency

Biofuel made from agricultural products has the potential in contribute to a stable supply of fuel for growing energy demands. Some salient plant traits, such as stem diameter and water content, and their relationship to other important biomass-related traits are so far poorly understood. Here, we performed QTL mapping for three stem diameter and two water content traits in a S. bicolor BTx623 x IS3620c recombinant inbred line population of 399 genotypes, and validated the genomic regions identified using genome-wide association studies (GWAS) in a diversity panel of 354 accessions. The discovery of both co-localized and non-overlapping loci affecting stem diameter traits suggests that stem widths at different heights share some common genetic control, but also have some distinct genetic influences. Co-localizations of stem diameter and water content traits with other biomass traits including plant height, flowering time and the ‘dry’ trait, suggest that their inheritance may be linked functionally (pleiotropy) or physically (linkage disequilibrium). Water content QTL in homeologous regions resulting from an ancient duplication event may have been retained and continue to have related functions for an estimated 96 million years. Integration of QTL and GWAS data advanced knowledge of the genetic basis of stem diameter and water content components in sorghum, which may lead to tools and strategies for either enhancing or suppressing these traits, supporting advances toward improved quality of plant-based biomass for biofuel production

Data from: Reconstructing changes in the genotype, phenotype, and climatic niche of an introduced species

An introduced species must contend with enormous environmental variation in its introduced range. In this study, we use niche models and ordination analyses to reconstruct changes in genotype, phenotype, and climatic niche of Johnsongrass (Sorghum halepense), which is regarded as one of the world's most threatening invasive plants. In the United States, Johnsongrass has rapidly evolved within- and among-population genetic diversity; our results show that genetic differentiation in expanding Johnsongrass populations has resulted in phenotypic variation that is consistent with habitat and climatic variation encountered during its expansion. Moreover, Johnsongrass expanded from agricultural to non-agricultural habitat, and now, despite occupying overlapping ranges, extant agricultural and non-agricultural populations are genetically and phenotypically distinct and manifest different plastic responses when encountering environmental variation. Non-agricultural accessions are broadly distributed in climatic and geographic space and their fitness traits demonstrate plastic responses to common garden conditions that are consistent with local specialization. In contrast, agricultural accessions demonstrate “general purpose” plastic responses and have more restricted climatic niches and geographic distributions. They also grow much larger than non-agricultural accessions. If these differences are adaptive, our results suggest that adaptation to local habitat variation plays a crucial role in the ecology of this invader. Further, its success relates to its ability to succeed on dual fronts, by responding simultaneously to habitat and climate variability and by capitalizing on differential responses to these factors during its range expansion

AtwaterEtAl2015EcographyData

This .zip file contains the data used for this paper, along with a ReadMe file describing each data set

Data from: Types, levels, and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

To explore types, levels, and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA, and SSR loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, while ESTs are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars

Data from: Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)

Background: Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice. Results: We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved ‘hotspots’ in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum. Conclusions: Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice

Supplemental Tables

This file includes four supplemental tables which are relevant to the paper. The supplemental table 1 lists the locus name, GenBank accession number, primer sequence and annealing temperature for all loci studied in this research. Supplemental table 2 is about the diversities revealed in the pair wise comparison including extended and single deletion, insertion, SNP, polymorphic sites, and polymorphic base pairs. Supplemental table 3 is about SNPs, polymorphic sites, and polymorphic base pairs between A and D ancestral genomes. Supplemental table 4 is about diversities revealed in the three way comparison including extended and single deletion, insertion, SNP, polymorphic sites, and polymorphic base pairs

Supplemental Figures

This file includes three supplemental figures which are related to the paper. The figure legends are given below each figure

Figure_1b_tree

Newick file for figure 1b. Neighbor-joining tree of 502 sorghum accessions for 265,487 SNP