Serge J. Edmé

Vigor Rating and Brix for First Clonal Selection Stage of the Canal Point Sugarcane Cultivar Development Program

A better understanding of sugarcane (Saccharum spp.) genetic variability in agronomic performance will help optimize breeding and selection strategies. Vigor ratings and Brix data were collected from the 2009 and 2010 clones in the first clonal selection stage (stage I) of the Canal Point (CP) sugarcane cultivar development program. Stage I individual selection was based on disease resistance and on the product of vigor and Brix. Vigor ratings (from 1 to 9) from all clones and Brix of any clones with a vigor rating ≥6 were collected in the stage I fields and analyzed for relationships between vigor and Brix, for selection rate in each family (i.e., cross), and for their coefficients of variation (CV) within and among families. There was no correlation between vigor and Brix, suggesting that it would be feasible in stage I to select sugarcane clones with both high vigor and high Brix. Variability was high (CV = 59%) for both the number of planted clones and selection rates among families, and vigor (7.2%) had greater CV than Brix (5.4%). Averaged across years, the within-family CVs (9.3% for vigor and 6.3% for Brix) were greater than the among-family CVs (6.3% for vigor and 4.7% for Brix). Results indicated that greater emphasis on family-based than on individual selection in stage I should be avoided, as it would result in the loss of potentially productive clones. However, use of individual selection data on vigor and Brix for analyzing family performance should improve parental selection and optimize crosses.

Field Response of Sugarcane Genotypes to Freeze Stress with Genotype x Environment Effects on Quality Traits

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 [TC] 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 TC ≤ −4 °C hastened juice deterioration. The response was nonlinear when TC 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 TC; the other groups typifying the common profile had an increase in SC with TC ≥ −2 °C and a decline with TC ≤ −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.

Dedicated Herbaceous Biomass Feedstock Genetics and Development

Biofuels and bio-based products can be produced from a wide variety of herbaceous feedstocks. To supply enough biomass to meet the needs of a new bio-based economy, a suite of dedicated biomass species must be developed to accommodate a range of growing environments throughout the USA. Researchers from the US Department of Agriculture’s Agricultural Research Service (USDA-ARS) and collaborators associated with the USDA Regional Biomass Research Centers have made major progress in understanding the genetics of switchgrass, sorghum, and other grass species and have begun to use this knowledge to develop new cultivars with high yields and appropriate traits for efficient conversion to bio-based products. Plant geneticists and breeders have discovered genes that reduce recalcitrance for biochemical conversion to ethanol and drop-in fuels. Progress has also been made in finding genes that improve production under biotic and abiotic stress from diseases, pests, and climatic variations.

Seasonal below-ground metabolism in switchgrass

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.

Generation of Octaploid Switchgrass by Seedling Treatment with Mitotic Inhibitors

Switchgrass (Panicum virgatum L.) exists as multiple cytotypes with octaploid (8x) and tetraploid (4x) populations occupying distinct, overlapping ranges. These cytotypes tend to show differences in adaptation, yield potential, and other characters, but the specific result of whole-genome duplication is not clear and 8x and 4x switchgrass populations are reproductively isolated with limited genetic exchange. To create new opportunities for population improvement and to study the effects of whole genome duplication on switchgrass, seedling treatment of the tetraploid cultivar Liberty with microtubule inhibitors was used to generate an octaploid population. Resulting octaploids, tetraploids, and cytochimeras were resolved by intercrossing octaploid sectors to produce a population of 19 octaploid families. Fertility of octaploid sectors was significantly reduced relative to tetraploid sectors and caryopsis size significantly increased. Cell size was significantly increased which resulted in quantitative changes to leaf anatomy. During seedling and early vegetative growth stages, no differences in vigor or tillering ability were seen. This technique resulted in efficient genome doubling and was simple to perform. However, aneuploids were also identified with both larger and smaller than expected genome sizes.

Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations

BackgroundSwitchgrass 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.ResultsUsing 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.ConclusionsAccuracy 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.