The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar 'Kanlow' and upland cultivar Summer are distinct and can be exploited for trait ...improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown 'Kanlow', and 'Summer' plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.
Switchgrass (Panicum virgatum L.) can be infected by the rust pathogen (Puccinia novopanici) and results in lowering biomass yields and quality. Label-free quantitative proteomics was conducted on ...leaf extracts harvested from non-infected and infected plants from a susceptible cultivar (Summer) at 7, 11, and 18 days after inoculation (DAI) to follow the progression of disease and evaluate any plant compensatory mechanisms to infection. Some pustules were evident at 7 DAI, and their numbers increased with time. However, fungal DNA loads did not appreciably change over the course of this experiment in the infected plants. In total, 3830 proteins were identified at 1% false discovery rate, with 3632 mapped to the switchgrass proteome and 198 proteins mapped to different Puccinia proteomes. Across all comparisons, 1825 differentially accumulated switchgrass proteins were identified and subjected to a STRING analysis using Arabidopsis (A. thaliana L.) orthologs to deduce switchgrass cellular pathways impacted by rust infection. Proteins associated with plastid functions and primary metabolism were diminished in infected Summer plants at all harvest dates, whereas proteins associated with immunity, chaperone functions, and phenylpropanoid biosynthesis were significantly enriched. At 18 DAI, 1105 and 151 proteins were significantly enriched or diminished, respectively. Many of the enriched proteins were associated with mitigation of cellular stress and defense.
Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. ...One way to achieve this is through genomic selection. However, the heritability of traits needs to be determined as well as the accuracy of prediction in order to determine if efficient selection is possible.
Using five distinct switchgrass populations comprised of three lowland, one upland and one hybrid accession, the accuracy of genomic predictions under different cross-validation strategies and prediction methods was investigated. Individual genotypes were collected using GBS while kin-BLUP, partial least squares, sparse partial least squares, and BayesB methods were employed to predict yield, morphological, and NIRS-based compositional data collected in 2012-2013 from a replicated Nebraska field trial. Population structure was assessed by F statistics which ranged from 0.3952 between lowland and upland accessions to 0.0131 among the lowland accessions. Prediction accuracy ranged from 0.57-0.52 for cell wall soluble glucose and fructose respectively, to insignificant for traits with low repeatability. Ratios of heritability across to within-population ranged from 15 to 0.6.
Accuracy was significantly affected by both cross-validation strategy and trait. Accounting for population structure with a cross-validation strategy constrained by accession resulted in accuracies that were 69% lower than apparent accuracies using unconstrained cross-validation. Less accurate genomic selection is anticipated when most of the phenotypic variation exists between populations such as with spring regreening and yield phenotypes.
Maintaining low levels of rust incidence (caused by Puccinia novopanici) in switchgrass (Panicum virgatum L.) breeding populations is a priority for the USDA-ARS program engaged in improving ...cultivars for high biomass yield and quality. Essential to this goal is the unbiased and accurate estimation of genetic parameters to predict the merits of parents and progeny. Spores of the fungus were inoculated in greenhouse-grown seedling progeny of 31 half-sib families in generation 2 (Gen 2) of a composite Summer × Kanlow population for evaluation of rust incidence on the leaves with a 0–9 rating scale. Two parents were later chosen to cross and develop a linkage mapping population as Gen 3. The Gen 2, 3, and Kanlow seedlings were transplanted into the field located near Mead, NE, in early June 2020 and laid out as a replicated row–column design with six blocks of single-row plots of five plants each. The field trial was rated in September 2021 and 2022 with a 0–4 scale. Lab and field data were subjected to univariate linear mixed models via the restricted maximum likelihood to extract the variance components needed to predict the breeding values. The additive genetic variation was substantial (p < 0.01), enough to result in high heritability estimates ranging from 0.42 ± 14 to 0.73 ± 0.09 at the individual and family mean levels. This result implies that rust resistance is under strong genetic control to use mass selection for obtaining satisfactory gains. A possible rust incidence x year interaction was detected with a Spearman correlation of breeding values of −0.38, caused by significant rank changes of the Gen 3 genotypes in 2022 (a high heat and drought year). Genetic gains were predicted to reduce rust incidence scores by at least two points on the rating scale when selecting backwards, and by one point when selecting individual candidates as parents of the next generation. Faster gains (31 and 59%) were realized relative to the second generation by respectively selecting the top 10% of the families in Gen 3 or the top 10% of genotypes within this group. Based on these results, strategies for controlling the incidence of rust will be developed to optimize gains in the other traits of economic importance.
Summary
Switchgrass (Panicum virgatum), a perennial, polyploid, C4 warm‐season grass is among the foremost herbaceous species being advanced as a source of biomass for biofuel end uses. At the end of ...every growing season, the aerial tissues senesce, and the below‐ground rhizomes become dormant. Future growth is dependent on the successful over‐wintering of the rhizomes. Although the importance of rhizome health to overall year‐upon‐year plant productivity has been long recognized, there is limited information on seasonal changes occurring during dormancy at both the transcriptome and metabolite levels. Here, global changes in transcriptomes and metabolites were investigated over two growing seasons in rhizomes harvested from field‐grown plants. The objectives were: (a) synthesize information on cellular processes that lead to dormancy; and (b) provide models that could account for major metabolic pathways present in dormant switchgrass rhizomes. Overall, metabolism during dormancy appeared to involve discrete but interrelated events. One was a response to abscisic acid that resulted in dehydration, increases in osmolytes and upregulation of autophagic processes, likely through the target of rapamycin complex and sucrose non‐fermentative‐related kinase‐based signaling cascades. Another was a recalibration of energy transduction through apparent reductions in mitochondrial oxidative phosphorylation, increases in substrate level generation of ATP and reducing equivalents, and recycling of N and possibly CO2 through refixation. Lastly, transcript abundances indicated that cold‐related signaling was also occurring. Altogether, these data provide a detailed overview of rhizome metabolism, especially during dormancy, which can be exploited in the future to improve winter survival in switchgrass.
Significance Statement
This research synthesizes information on cellular processes that regulate seasonal metabolism of switchgrass rhizomes and provide models for explaining the major metabolic pathways involved in dormancy. This detailed overview of rhizome metabolism provides mechanistic information that can be used to improve winter survival in switchgrass.
High-biomass-yielding southerly adapted switchgrasses (
L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring ...regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow-which is a significant source of genetics for yield improvement-was studied over a growing season at a northern site. Metabolite levels and transcript abundances were combined to develop physiological profiles accompanying greening through the onset of dormancy in Kanlow rhizomes. Next, comparisons of the data to rhizome metabolism occurring in the adapted upland cultivar Summer were performed. These data revealed both similarities as well as numerous differences in rhizome metabolism that were indicative of physiological adaptations unique to each cultivar. Similarities included elevated ABA levels and accumulation of starch in rhizomes during dormancy onset. Notable differences were observed in the accumulation of specific metabolites, the expression of genes encoding transcription factors, and several enzymes linked to primary metabolism.
Freeze stress negatively affects sucrose yield in sugarcane (Saccharum spp. hybrids), particularly during the harvest season. To understand its impact on the performance of genotypes in the Canal ...Point (CP) breeding program, the genotype-environment (GxE) interaction was appraised via additive main effects and multiplicative interactions (AMMI) analysis and group-based trajectory modeling (GTM). Forty-five selections of the CP01, CP02, and CP03 series and three cultivars were examined in replicated field tests at Hague and Canal Point, Florida, in the plant-cane (CP01-CP02 in 2006-07) or through the first ratoon (CP03 in 2007-09). Profile analyses of Brix, pol, and sucrose content (SC) were developed from stalks sampled at different times of year to follow their deterioration. Hague experienced more intense freeze nights (17-22 d yr
−1
with temperatures T
C
from −0.4 °C to −8 °C) than CP (2 nights, rarely down to −2 °C). Temperatures ≥−2 °C increased SC in a majority of the genotypes and T
C
≤ −4 °C hastened juice deterioration. The response was nonlinear when T
C
gradually declined from 0 ° to −4 °C, but linear after early freeze of ≤−4 °C. The AMMI analysis was appropriate for interpreting the GxE interaction variation, indicating a greater contribution from environments (location-year-sampling combinations) than from G or GxE interaction. The AMMI and GTM identified two to four reaction norms as differential performance under freeze: a susceptible group in the minority with SC declining constantly with T
C
; the other groups typifying the common profile had an increase in SC with T
C
≥ −2 °C and a decline with T
C
≤ −4 °C. Genotypes with the highest SC at the onset of freeze tended to hold this level longer than those with the lowest content. The identification of different reaction norms suggests that a genetic component may underpin freeze adaptation in modern sugarcane cultivars relative to the old tropical hybrids. However, breeding efforts to increase the tolerance of sugarcane cultivars to temperatures <−3 °C must be given due consideration.
The Canal Point (CP) sugarcane (Saccharum spp.) breeding program has developed high-yielding cultivars for the organic soils of South Florida, but cultivar development has not been as successful for ...sand soils in this region. Our objectives were to improve final-stage (Stage 4) selection efficiency of this program by assessing interactions among genotypes, soils, and locations and other sources of variation and by comparing the relationship between repeatability and number of replications as a measure of precision for testing sugarcane genotypes on sand and muck soils. Sources of variation were partitioned for plant-cane, first-ratoon, and second-ratoon data, from 7 yr and five CP series in Stage 4 tested at eight locations on muck soils and two locations on sand soils. Variation related to genotype × location (soil) was highly significant for cane and sugar yields for all series and crops, but most genotype × soil interactions were nonsignificant. This suggested that planting more Stage-4 tests on sand may improve genotype selection for these soils. The six replications used routinely in Stage 4 provided elevated levels of precision for both soil types. All locations with muck and sand soils in Stage 4 have ample testing resources for discriminating among genotypes. Our results indicate that, to improve sugarcane genotype selection for sand soils, increasing the number of sand locations would be a more successful strategy than increasing replications within locations.
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