Panicum hallii cultivar:hallii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA454989 | ENA |
REPOSITORIES: ENA
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR7816836_1.fastq.gz | Fastqsanger.gz | |||
| SRR7816836_2.fastq.gz | Fastqsanger.gz |
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Project description:The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as a result of genetic colocalization either by pleiotropy or genetic linkage. The self-fertilizing C4 grass species Panicum hallii includes two major ecotypes found in xeric (var. hallii) or mesic (var. filipes) habitats. We constructed the first linkage map for P. hallii by genotyping a reduced representation genomic library of an F2 population derived from an intercross of var. hallii and filipes. We then evaluated the genetic architecture of divergence between these ecotypes through quantitative trait locus (QTL) mapping. Overall, we mapped QTLs for nine morphological traits that are involved in the divergence between the ecotypes. QTLs for five key ecotype-differentiating traits all colocalized to the same region of linkage group five. Leaf physiological traits were less divergent between ecotypes, but we still mapped five physiological QTLs. We also discovered a two-locus Dobzhansky-Muller hybrid incompatibility. Our study suggests that ecotype-differentiating traits may evolve in tandem as a result of genetic colocalization.
| S-EPMC4265272 | BioStudies
Project description:<h4>Background</h4>Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to be understood through population genomic studies. We used whole genome sequencing combined with association study of climate to discover the drivers of differentiation in the perennial C4 grass Panicum hallii.<h4>Results</h4>Sequencing of 89 natural accessions of P.hallii revealed complex population structure across the species range. Major population genomic separation was found between subspecies P.hallii var. hallii and var. filipes as well as between at least four major unrecognized subgroups within var. hallii. At least 139 genomic SNPs were significantly associated with temperature or precipitation across the range and these SNPs were enriched for non-synonymous substitutions. SNPs associated with temperature and aridity were more often found in or near genes than expected by chance and enriched for putative involvement in dormancy processes, seed maturation, response to hyperosmosis and salinity, abscisic acid metabolism, hormone metabolism, and drought recovery.<h4>Conclusions</h4>Both geography and climate adaptation contribute significantly to patterns of genome-wide variation in P.hallii. Population subgroups within P.hallii may represent early stages in the formation of ecotypes. Climate associated loci identified here represent promising targets for future research in this and other perennial grasses.
| S-EPMC6211516 | BioStudies
Project description:Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C<sub>4</sub> grass <i>Panicum hallii</i> across its complex natural distribution in North America. We sampled extensively across the natural range of <i>P. hallii</i> in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of <i>P. hallii</i>, <i>P. hallii</i> var. <i>filipes</i> and <i>P. hallii</i> var. <i>hallii</i> as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.
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Project description:<h4>Background</h4>Panicum hallii Vasey (Hall's panicgrass) is a compact, perennial C<sub>4</sub> grass in the family Poaceae, which has potential to enable bioenergy research for switchgrass (Panicum virgatum L.). Unlike P. hallii, switchgrass has a large genome, allopolyploidy, self-incompatibility, a long life cycle, and large stature-all suboptimal traits for rapid genetics research. Herein we improved tissue culture methodologies for two inbred P. hallii populations: FIL2 and HAL2, to enable further development of P. hallii as a model C<sub>4</sub> plant.<h4>Results</h4>The optimal seed-derived callus induction medium was determined to be Murashige and Skoog (MS) medium supplemented with 40 mg L<sup>-1</sup> L-cysteine, 300 mg L<sup>-1</sup> L-proline, 3% sucrose, 1 g L<sup>-1</sup> casein hydrolysate, 3 mg L<sup>-1</sup> 2,4-dichlorophenoxyacetic acid (2,4-D), and 45 ?g L<sup>-1</sup> 6-benzylaminopurine (BAP), which resulted in callus induction of 51?±?29% for FIL2 and 81?±?19% for HAL2. The optimal inflorescence-derived callus induction was observed on MP medium (MS medium supplemented with 2 g L<sup>-1</sup> L-proline, 3% maltose, 5 mg L<sup>-1</sup> 2,4-D, and 500 ?g L<sup>-1</sup> BAP), resulting in callus induction of 100?±?0.0% for FIL2 and 84?±?2.4% for HAL2. Shoot regeneration rates of 11.5?±?0.8 shoots/gram for FIL2 and 11.3?±?0.6 shoots/gram for HAL2 were achieved using seed-induced callus, whereas shoot regeneration rates of 26.2?±?2.6 shoots/gram for FIL2 and 29.3?±?3.6 shoots/gram for HAL2 were achieved from inflorescence-induced callus. Further, cell suspension cultures of P. hallii were established from seed-derived callus, providing faster generation of callus tissue compared with culture using solidified media (1.41-fold increase for FIL2 and 3.00-fold increase for HAL2).<h4>Conclusions</h4>Aside from abbreviated tissue culture times from callus induction to plant regeneration for HAL2, we noted no apparent differences between FIL2 and HAL2 populations in tissue culture performance. For both populations, the cell suspension cultures outperformed tissue cultures on solidified media. Using the methods developed in this work, P. hallii callus was induced from seeds immediately after harvest in a shorter time and with higher frequencies than switchgrass. For clonal propagation, P. hallii callus was established from R1 inflorescences, similar to switchgrass, which further strengthens the potential of this plant as a C<sub>4</sub> model for genetic studies. The rapid cycling (seed-to-seed time) and ease of culture, further demonstrate the potential utility of P. hallii as a C<sub>4</sub> model plant.
| S-EPMC5408410 | BioStudies
Project description:Panicum hallii var. hallii Transcriptome - 92 PAN
| PRJNA455373 | ENA
Project description:Panicum hallii var. hallii Transcriptome - 92 RT
| PRJNA620407 | ENA
Project description:Panicum hallii var. hallii Transcriptome - 92 LF
| PRJNA455138 | ENA
Project description:Background:Biofuels derived from lignocellulosic plant material are an important component of current renewable energy strategies. Improvement efforts in biofuel feedstock crops have been primarily focused on increasing biomass yield with less consideration for tissue quality or composition. Four primary components found in the plant cell wall contribute to the overall quality of plant tissue and conversion characteristics, cellulose and hemicellulose polysaccharides are the primary targets for fuel conversion, while lignin and ash provide structure and defense. We explore the genetic architecture of tissue characteristics using a quantitative trait loci (QTL) mapping approach in Panicum hallii, a model lignocellulosic grass system. Diversity in the mapping population was generated by crossing xeric and mesic varietals, comparative to northern upland and southern lowland ecotypes in switchgrass. We use near-infrared spectroscopy with a primary analytical method to create a P. hallii specific calibration model to quickly quantify cell wall components. Results:Ash, lignin, glucan, and xylan comprise 68% of total dry biomass in P. hallii: comparable to other feedstocks. We identified 14 QTL and one epistatic interaction across these four cell wall traits and found almost half of the QTL to localize to a single linkage group. Conclusions:Panicum hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (P. virgatum). We used high throughput phenotyping to map genomic regions that impact natural variation in leaf tissue composition. Understanding the genetic architecture of tissue traits in a tractable model grass system will lead to a better understanding of cell wall structure as well as provide genomic resources for bioenergy crop breeding programs.
| S-EPMC5797396 | BioStudies
Project description:Panicum hallii var. hallii Transcriptome - 23 SL
| PRJNA454934 | ENA
Project description:Panicum hallii var. hallii Transcriptome - 29 SL
| PRJNA454939 | ENA