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 world's 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.

Comparative Transcriptomics Among Four White Pine Species.

Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

Sequence of the Sugar Pine Megagenome.

Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1 We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.

Seed shattering in a wild sorghum is conferred by a locus unrelated to domestication.

Suppression of seed shattering was a key step during crop domestication that we have previously suggested to be convergent among independent cereal lineages. Positional, association, expression, and mutant complementation data all implicate a WRKY transcription factor, SpWRKY, in conferring shattering to a wild sorghum relative, Sorghum propinquum. We hypothesize that SpWRKY functions in a manner analogous to Medicago and Arabidopsis homologs that regulate cell wall biosynthesis genes, with low expression toward the end of floral development derepressing downstream cell wall biosynthesis genes to allow deposition of lignin that initiates the abscission zone in the seed-pedicel junction. The recent discovery of a YABBY locus that confers shattering within Sorghum bicolor and other cereals validated our prior hypothesis that some parallel domestication may have been convergent. Ironically, however, the shattering allele of SpWRKY appears to be recently evolved in S. propinquum and illustrates a case in which the genetic control of a trait in a wild relative fails to extrapolate even to closely related crops. Remarkably, the SpWRKY and YABBY loci lie only 300 kb apart and may have appeared to be a single genetic locus in some sorghum populations.

Proximity is not a proxy for parentage in an animal-dispersed Neotropical canopy palm.

We used parentage analysis to estimate seedling recruitment distances and genetic composition of seedling patches centred around reproductive trees of the animal-dispersed Neotropical canopy palm Iriartea deltoidea in two 0.5 ha plots within second-growth forest and one 0.5 ha plot in adjacent old-growth forest at La Selva Biological Field Station in north-eastern Costa Rica. Seedlings were significantly spatially aggregated in all plots, but this pattern was not due to dispersal limitation. More than 70 per cent of seedlings were dispersed at least 50 m from parent trees. Few seedlings were offspring of the closest reproductive trees. Seedling patches observed beneath reproductive trees originate from dozens of parental trees. Observed patterns of seedling distribution and spatial genetic structure are largely determined by the behaviour of vertebrate seed dispersers rather than by spatial proximity to parental trees.

Multigenerational genetic analysis of tropical secondary regeneration in a canopy palm.

Iriartea deltoidea (Arecaceae) is an abundant canopy palm with a wide geographic distribution in Neotropical wet forests. We analyzed the genetic profile across three generations of Iriartea within a 43-ha area encompassing two areas of second-growth and adjoining old-growth forest at La Selva Biological Field Station in northeastern Costa Rica. A total of 311 reproductively mature trees, 99 large saplings, 207 small saplings, and 601 seedlings were genotyped using 141 AFLP loci. Parentage analysis revealed high dispersal distances, both for seed (over 2.3 km) and pollen (over 3.8 km), indicating a large genetic neighborhood within La Selva Biological Station. In a 20-ha area of second growth, the founding palm population was dominated by a small number of parental trees located in the adjacent old-growth forest; two old-growth trees contributed 48% of the second-growth genes. The genetic diversity of reproductively mature trees in this second-growth forest was significantly reduced compared to adjacent old-growth forest. Within 400 m of the border with old-growth forest, we observed a similar reduction of genetic diversity in saplings, and an even greater loss of genetic diversity in the second generation of seedlings. Nearly half of these seedlings were offspring of local parents. In contrast, in the distant portion of second-growth forest (400-800 m from the old-growth border), parentage analysis showed that 40% of seedlings originated from outside the study area and only 10% were offspring of local parents. These high levels of gene flow maintained genetic diversity in saplings and seedlings similar to levels observed in old-growth forest. Our findings highlight the importance of gene flow from diverse seed and pollen sources for sustaining levels of genetic diversity of tree populations in second-growth forests.

Genetic consequences of tropical second-growth forest regeneration.

Secondary forests are more extensive than old-growth forests in many tropical regions, yet the genetic composition of colonizing populations is poorly understood. We analyzed the parentage of a founder population of 130 individuals of the canopy palm Iriartea deltoidea in a 24-year-old second-growth forest in lowland Costa Rica. Among 66 trees in adjacent old-growth forest, only two individuals contributed 56% of the genes in founders. Second-growth trees had lower genetic diversity and larger patches of similar genotypes than old-growth trees. Recovery of genetic diversity of populations in tropical second-growth forests may take many generations and will require continued dispersal from genetically diverse source populations.