Experimental evaluation of genomic selection prediction for rust resistance in sugarcane.

The total sugarcane (Saccharum L.) production has increased worldwide; however, the rate of growth is lower compared with other major crops, mainly due to a plateauing of genetic gain. Genomic selection (GS) has proven to substantially increase the rate of genetic gain in many crops. To investigate the utility of GS in future sugarcane breeding, a field trial was conducted using 432 sugarcane clones using an augmented design with two replications. Two major diseases in sugarcane, brown and orange rust (BR and OR), were screened artificially using whorl inoculation method in the field over two crop cycles. The genotypic data were generated through target enrichment sequencing technologies. After filtering, a set of 8,825 single nucleotide polymorphic markers were used to assess the prediction accuracy of multiple GS models. Using fivefold cross-validation, we observed GS prediction accuracies for BR and OR that ranged from 0.28 to 0.43 and 0.13 to 0.29, respectively, across two crop cycles and combined cycles. The prediction ability further improved by including a known major gene for resistance to BR as a fixed effect in the GS model. It also substantially reduced the minimum number of markers and training population size required for GS. The nonparametric GS models outperformed the parametric GS suggesting that nonadditive genetic effects could contribute genomic sources underlying BR and OR. This study demonstrated that GS could potentially predict the genomic estimated breeding value for selecting the desired germplasm for sugarcane breeding for disease resistance.

Sugarcane cultivar response to glyphosate and trinexapac-ethyl ripeners in Louisiana.

Sugarcane ripening in Louisiana is necessary to ensure adequate sucrose levels in early-season harvested sugarcane. The response of nine sugarcane cultivar's yield components to glyphosate and trinexapac-ethyl ripeners was determined in field trials. Glyphosate (210 g ae ha-1) and trinexapac-ethyl (200 g ai ha-1) treatments failed to increase sucrose yields more than non-ripened sugarcane. Sugarcane ripened with glyphosate or trinexapac-ethyl increased theoretical recoverable sucrose (TRS) 4 to 12% more than non-ripened sugarcane in seven out of nine cultivars, but greater TRS values were counterpoised by lower sugarcane stalk weight. An unintentional consequence of reduced late-season vegetative growth may benefit growers by allowing them to harvest more sugarcane hectares to meet their daily load quota and exposes fewer hectares to a freeze event. The cultivars HoCP 00-950, Ho 09-804, and HoCP 09-840 were not responsive to glyphosate or trinexapac-ethyl ripeners and should not be treated. A delayed harvest from 28 to 49 days after treatment (DAT) coincided with greater TRS values and 17% more sucrose yield.

Confirmation of herbicide resistance mutations Trp574Leu, ΔG210, and EPSPS gene amplification and control of multiple herbicide-resistant Palmer amaranth (Amaranthus palmeri) with chlorimuron-ethyl, fomesafen, and glyphosate.

Herbicide-resistant weeds, especially Palmer amaranth (Amaranthus palmeri S. Watson), are problematic in row-crop producing areas of the United States. The objectives of this study were to determine if chlorimuron-ethyl, fomesafen, and glyphosate applied separately and in mixtures control A. palmeri and confirm the presence of various genotypes surviving two- and three-way herbicide mixtures. Fifteen percent of A. palmeri treated with the three-way herbicide mixture survived. Mixing fomesafen with chlorimuron-ethyl or fomesafen with glyphosate to create a two-way mixture reduced A. palmeri survival 22 to 24% and 60 to 62% more than glyphosate and chlorimuron-ethyl alone, respectively. Previously characterized mutations associated with A. palmeri survival to chlorimuron-ethyl, fomesafen, and glyphosate Trp574Leu, a missing glycine codon at position 210 of the PPX2L gene (ΔG210), and 5-enolpyruvylshikimate-3-phosphase synthase (EPSPS) gene amplification; respectively, were present in surviving plants. However, 37% of plants treated with chlorimuron-ethyl did not contain heterozygous or homozygous alleles for the Trp574Leu mutation, suggesting alternative genotypes contributed to plant survival. All surviving A. palmeri treated with fomesafen or glyphosate possessed genotypes previously documented to confer resistance. Indiana soybean [Glycine max (L.) Merr] fields infested with A. palmeri possessed diverse genotypes and herbicide surviving plants are likely to produce seed and spread if alternative control measures are not implemented.

Effect of growing media and fertilization on sugarcane flowering under artificial photoperiod.

The USDA-ARS Sugarcane Variety Development Program in Houma, LA aims to maximize the number of panicles available for crossing through artificial manipulation of the environment. In a three-year study, the effect of growing media, fertilizer treatment, and their interaction on sugarcane flowering (% of panicles emerged), and number of days to flowering (DTF) under an artificial photoperiod treatment were assessed. The commercially-available sugarcane cultivar, 'HoCP 96-540' was planted in 2.8-L pots and subjected to the standard local photoperiod treatment. The cultivar was planted in four growing media (RediEarth Seedling and Germination Mix, Fafard, Metro-Mix®902, and Metro-Mix®900) and subjected to three different fertilizer applications. In the control treatment, fertilizer application was stopped prior to the commencement of the photoperiod treatment as practiced in some sugarcane breeding programs. The continuous treatment consisted of an application of a 10 ml solution of a NPK three times a week between June and October. The partial treatment consisted of applications of the same NPK solution applied post-initiation between September and October. Nitrogen starvation prior to the commencement of the photoperiod treatment is generally accepted to improve flower initiation; thus the standard practice is to cease nitrogen application two weeks prior to beginning a photoperiod regime. The growing media used in this study did not have a significant effect on days to flowering or percent panicle emergence. In our study, the control fertilizer treatment showed a flowering percentage across all growing media types of 21.2% less than a continuous fertilization regime. Furthermore, a significant trend was observed between fertilization treatments and days to flowering, with the continuous treatment producing panicles, on average across growing media, four days earlier than the control treatment, and six days earlier than the partial treatment. Evidence across this three-year experiment indicates that we should consider modifying plant nutrition management as soil fertility was found to be inadequate.