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Switchgrass (Panicum virgatum L.) has been subject to breeding to improve its yield and composition for bioenergy. Increased tolerance of environmental stress is another factor that can improve yields over the life span of a field plot. Natural ploidy series act as somewhat distinct gene pools in switchgrass that maintain differences with respect to tolerance of environmental stress and which can only be bridged through whole genome reduction or duplication events. In order to document potential wide-ranging effects of whole genome duplication, we examined the effects of water stress on growth, physiology, and gene expression in individual tetraploid clones of the switchgrass cultivar “Liberty” as well as neo-octoploid lines derived from it. The neo-octoploids behaved similarly to Liberty under water stress and recovery conditions: Water-stressed plants had approximately 50% or greater reduction of biomass, plant height, and node numbers. Tiller number and photosynthesis rates of stressed plants were reduced by up to 50%, while proline levels were significantly higher in stressed plants than well-watered plants. A total of 6134 differentially expressed genes (8% of the annotated genes with detectable expression in crown tissue) were detected under water-deficit stress, while 3310 differentially expressed genes were detected in crown tissue after 1 week of recovery from water-deficit stress relative to well-watered treatments. Only 187 genes were identified as being differentially expressed between 4x Liberty and its 8x derivatives. This study indicates neo-octoploids could be viable 8x-equivalent Liberty stand-ins for future breeding assays.

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.) 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.

Background 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (10.1186/s12870-018-1360-z) contains supplementary material, which is available to authorized users.

‘CPCL 05-1102’ (Reg. No. CV-157, PI 667556) sugarcane (a complex hybrid of spp.) is the product of research initiated by the United States Sugar Corporation (USSC) and completed cooperatively by the USDA-ARS, the University of Florida, and the Florida Sugar Cane League, Inc. CPCL 05-1102 was released to growers in Florida on 16 Oct. 2012. CPCL 05-1102 was selected from a cross between the USSC proprietary cultivars CL 89-5189 (female) and CL 88-4730 (male) made at Clewiston, FL on 18 Dec. 2000. CL 89-5189 was adapted to muck soils, where it was used only briefly in commercial plantings of USSC due to yield losses to ratoon stunt (caused by subsp.). CL 88-4730 is widely used on commercial plantings of USSC, particularly on sand soils. CPCL 05-1102 has acceptable resistance to leaf scald (caused by Ashby, Dowson), strain E (mosaic), smut (caused by Sydow & P. Sydow), orange rust (caused by E.J. Butler), and brown rust (caused by H. & P. Sydow). 1, a major gene for resistance to brown rust, was not detected in the DNA of CPCL 05-1102. CPCL 05-1102 has high cane and sucrose yields and excellent freeze tolerance and is expected to be used on muck soils in Florida.

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%) ...

CPCL 00-4111' (Reg. No. CV-144, PI 660673) sugarcane (a complex hybrid of Saccharum spp.) is the latest in a series of commercial sugarcane cultivar releases developed by the United States Sugar Corporation (USSC) and completed by the cooperative Canal Point sugarcane breeding and selection program, which included the USDA-ARS, the University of Florida, and the Florida Sugar Cane League, Inc. CPCL 00-4111, which was released in Florida on 18 Feb. 2011, was selected from a cross of genotype CL 83-3431 × CL 89-5189 made at Clewiston, FL on 4 Dec. 1998. The female and male parents, CL 83-3431 and CL 89-5189, respectively, are proprietary genotypes of USSC. CPCL 00-4111 was released because of its high cane yield and commercial recoverable sucrose on organic (muck) soils and because of its resistance to brown rust (caused by Puccinia melanocephala H. & P. Sydow), orange rust (caused by Puccinia kuehnii E.J. Butler), smut (caused by Ustilago scitaminea H. & P. Sydow), and Sugarcane mosaic virus strain E (the causal agent of mosaic), as well as its moderate resistance to leaf scald (caused by Xanthomonas albilineans (Ashby) Dowson). All of these diseases are of economic importance to sugarcane production in Florida.

Research to develop ‘CPCL 99–4455’ (Reg. No. CV-142; PI 659802) sugarcane (a complex hybrid of Saccharum spp.) was initiated by the United States Sugar Corporation (USSC) and completed cooperatively by the USDA-ARS, the University of Florida, and the Florida Sugarcane League, Inc. CPCL 99–4455 was released to growers in Florida on 15 Dec. 2009. CPCL 99–4455 was selected from a cross of the USSC proprietary genotype CL 90–4643 × ‘CP 84–1198’ made at Clewiston, FL on 22 Dec. 1998. The female parent, CL 90–4643, has high yields of cane and sucrose but it is not used commercially by the USSC because of susceptibility to Sugarcane mosaic virus strain E. The male parent, cultivar CP 84–1198, has moderately high commercial recoverable sucrose (CRS) and cane yields and has been grown commercially on about 1–5% of Florida’s sugarcane acreage since 1996. CPCL 99–4455 is moderately resistant to smut (caused by Ustilago scitaminea Sydow & P. Sydow), brown rust (caused by Puccinia melanocephala H. & P. Sydow), orange rust (caused by Puccinia kuehnii E.J. Butler), leaf scald (caused by Xanthomonas albilineans Ashby, Dowson), and Sugarcane mosaic virus strain E. CPCL 99–4455 is expected to be used mostly on organic (muck) soils in Florida, where it had high CRS and acceptable yields of cane in our tests.

The Canal Point (CP) sugarcane (Saccharum spp.) breeding program has developed highyielding 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 fi nal-stage (Stage 4) selection effi ciency 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, fi rst-ratoon, and second-ratoon data, from 7 yr and fi ve 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 signifi cant for cane and sugar yields for all series and crops, but most genotype × soil interactions were nonsignifi cant. 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. USDA-ARS, Sugarcane Field Station, 12990 US Hwy. 441 N., Canal Point, FL 33438. Received 23 Sept. 2009. *Corresponding author (ali

Research to develop ‘CPCL 97-2730’ (Reg. No. CV-137, PI 655943) sugarcane (a complex hybrid of Saccharum spp.) was initiated by the United States Sugar Corporation (USSC) and completed cooperatively by the USDA–ARS, the University of Florida, and the Florida Sugar Cane League, Inc. CPCL 97-2730 was released to growers in Florida in December 2008. CPCL 97-2730 was selected from a cross of USSC proprietary genotypes CL 75-0853 × CL 88-4730 made at Clewiston, FL, in December 1996. The female parent, CL 75-0853, had high commercial recoverable sucrose (CRS) but because of low cane yields was not used extensively by USSC. The male parent, CL 88-4730, is a high-yielding genotype that USSC is evaluating in commercial fi elds with sand and muck soils for possible extended use. CPCL 97-2730 was released because of its acceptable yields of cane and CRS on sand soils and its resistance to smut (caused by Ustilago scitaminea Syd. & P. Syd.), brown rust (caused by Puccinia melanocephala Syd. & P. Syd.), orange rust [caused by P. kuehnii (Kruger) E. Butler], leaf scald [caused by Xanthomonas albilineans (Ashby) Dowson], and sugarcane mosaic virus strain E.

'CP 01-1372' (Reg. No. CV-136, PI 655942) sugarcane (a complex hybrid of Saccharum spp.) was developed through cooperative research conducted by the USDA―ARS, the University of Florida, and the Florida Sugar Cane League, Inc., and was released to growers in Florida in December 2008. CP 01-1372 was selected from a cross of genotype CP 94-1200 x 'CP 89-2143' made at Canal Point, FL, in December 1998. The female parent, CP 94-1200, was advanced to the final selection stage (Stage 4) of the Canal Point sugarcane cultivar breeding and selection program. The male parent, CP 89-2143, is a major sugarcane cultivar in Florida. CP 01-1372 was released because of its high cane yield and commercial recoverable sucrose on both organic and sand soils, and its acceptable levels of resistance to brown rust (caused by Puccinia melanocephala Syd. & P. Syd.), orange rust [caused by P. kuehnii (Kruger) E. Butler], leaf scald [caused by Xanthomonas albilineans (Ashby) Dowson], Sugarcane mosaic virus strain E (mosaic), and ratoon stunt (caused by Clavibacterxyli subsp. xyli Davis et al.) in Florida.

CP 00-1446' (Reg. No CV-133, PI 654092) sugarcane (a complex hybrid of Saccharum spp.) was developed through cooperative research conducted by the USDA-ARS, the University of Florida, and the Florida Sugar Cane League, Inc., and was released to growers in Florida in September 2007. CP 00-1446 was selected from a cross of genotypes CP 93-1607 × CP 91-1150 made at Canal Point, FL, in January 1998. The female and male parents were advanced to the penultimate selection stage (Stage 3) and the fi nal stage (Stage 4), respectively, of the Canal Point sugarcane cultivar breeding and selection program. CP 00-1446 was released and recommended for sand soils in Florida because of its high plant cane and acceptable ratoon per hectare yields of cane and sucrose and commercial recoverable sucrose on sand soils, and its acceptable disease reactions to smut (caused by Ustilago scitaminea (Sydow & P. Sydow)) (moderately susceptible), brown rust (caused by Puccinia melanocephala H. & P. Sydow) (moderately resistant), orange rust (caused by Puccinia kuehnii E.J. Butler) (moderately resistant), leaf scald (caused by Xanthomonas albilineans Ashby, Dowson) (resistant), Sugarcane mosaic virus strain E (mosaic) (moderately susceptible), and ratoon stunting disease (caused by Clavibacter xyli subsp. xyli Davis) (resistant) in Florida.

'CP 00-2180' (Reg. No. CV-134, PI 654093) sugarcane (a complex hybrid of Saccharum spp.) was developed through cooperative research conducted by the USDA-ARS, the University of Florida, and the Florida Sugar Cane League, Inc., and was released to growers in Florida in September 2007. CP 00-2180 was selected from a self-cross of cultivar HoCP 91-552 made at Canal Point, FL, in January 1998. Based on its high cane yields and fiber content (16%), HoCP 91-552 was released as a cultivar for bioenergy in Louisiana. CP 00-2180 was released and recommended for sand soils in Florida because of its high plant cane and acceptable ratoon per hectare yields of cane and sucrose and commercial recoverable sucrose on sand soils, and its resistance to smut [caused by Ustilago scitaminea (Sydow & P. Sydow)], brown rust (caused by Puccinia melanocephala H. & P. Sydow), orange rust (caused by Puccinia kuehnii E.J. Butler), leaf scald [caused by Xanthomonas albilineans (Ashby) Dowson], Sugarcane mosaic virus strain E, and ratoon stunting disease (caused by Clavibacter xyli subsp. xyli Davis) in Florida.

'CP 88-1165' (Reg. No. CV-131, PI 651884) sugarcane (a complex hybrid of Saccharum spp.) was developed through cooperative research conducted by the USDA-ARS, the Centro Guatemalteco de Investigacion y Capacitacion de la Cana de Azucar, and the University of Florida. It was released to growers in Guatemala in September 2004. CP 88-1165 was selected from the cross 'CL 61-620' x CP 81-1302 made at Canal Point, FL, in January 1986. The female parent, CL 61-620, formerly a major commercial cultivar in Florida, was developed by a private breeding program in Clewiston, FL, conducted by the United States Sugar Corp. The male parent, CP 81-1302, was advanced to the final testing stage (Stage 4) of the Canal Point (CP) cultivar development program but was not released due to susceptibility to brown rust (caused by Puccinia melanocephala Syd. & P. Syd.). CP 88-1165 was not released in Florida because of its susceptibility to brown rust and low yield of commercial recoverable sucrose. However, after testing in Guatemala, CP 88-1165 was released there because of its high plant cane and ratoon per hectare yields of cane and sucrose and its acceptable resistance or tolerance to smut [caused by Ustilago scitaminea (Sydow & P. Sydow], brown rust, Sugarcane mosaic virus strain E (mosaic), Sugarcane yellow leaf virus, and red stripe (Acidovorax avenae subsp. avenae) in Guatemala.

Sugarcane (interspecific hybrids of Saccharum spp.) in the Everglades Agricultural Area (EAA) in Florida is frequently subjected to periods of higher-than-desired water levels. This study was conducted to evaluate yields of nine sugarcane cultivars subjected to two higher-than-conventional water tables in the EAA during the summer rainy season from the plant cane through the second-ratoon annual crop cydes. Field experiments were planted in February 1997 and January 1998. During the summers from 1997 through 1999, we sought to maintain water