Training Population Optimization for Genomic Selection in Miscanthus.

Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus × giganteus (M×g) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of M×g clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the genomic selection (GS) prediction accuracies within a 538-member diversity panel of predominately Msi individuals and a 598-member diversity panels of Msa individuals. We then assessed the ability of these two diversity panels to train GS models that predict breeding values in an interspecific diploid 216-member M×g F2 panel. Low and negative prediction accuracies were observed when various subsets of the two diversity panels were used to train these GS models. To overcome the drawback of having only one interspecific M×g F2 panel available, we also evaluated prediction accuracies for traits simulated in 50 simulated interspecific M×g F2 panels derived from different sets of Msi and diploid Msa parents. The results revealed that genetic architectures with common causal mutations across Msi and Msa yielded the highest prediction accuracies. Ultimately, these results suggest that the ideal training set should contain the same causal mutations segregating within interspecific M×g populations, and thus efforts should be undertaken to ensure that individuals in the training and validation sets are as closely related as possible.

A footprint of past climate change on the diversity and population structure of Miscanthus sinensis.

BACKGROUND AND AIMS: Miscanthus is a perennial C4 grass that is a leading potential feedstock crop for the emerging bioenergy industry in North America, Europe and China. However, only a single, sterile genotype of M. × giganteus (M×g), a nothospecies derived from diploid M. sinensis (Msi) and tetraploid M. sacchariflorus (Msa), is currently available to farmers for biomass production. To facilitate breeding of Miscanthus, this study characterized genetic diversity and population structure of Msi in its native range of East Asia. METHODS: A total of 767 accessions were studied, including 617 Msi from most of its native range in China, Japan and South Korea, and 77 ornamental cultivars and 43 naturalized individuals from the USA. Accessions were evaluated with 21 207 restriction site-associated DNA sequencing single nucleotide polymorphism (SNP) markers, 424 GoldenGate SNPs and ten plastid microsatellite markers. KEY RESULTS: Six genetic clusters of Msi from geographically distinct regions in Asia were identified. Genetic data indicated that (1) south-eastern China was the origin of Msi populations found in temperate eastern Asia, which is consistent with this area probably having been a refugium during the last glacial maximum (LGM); (2) Msi migrated directly from south-eastern China to Japan before migrating to the same latitudes in China and Korea, which is consistent with the known sequence of warming post-LGM; (3) ornamental Msi cultivars were derived from the southern Japan population, and US naturalized populations were derived from a sub-set of the ornamental cultivars; and (4) many ornamental cultivars previously described as Msi have hybrid ancestry from Msa and Msi, whereas US naturalized populations of Msi do not. CONCLUSIONS: Population structure of Msi was driven by patterns of warming since the LGM, and secondarily by geographical barriers. This study will facilitate germplasm conservation, association analyses and identification of potential heterotic groups for the improvement of Miscanthus as a bioenergy crop.

Establishment and growth of two willow species in a riparian zone impacted by mine tailings.

A field study was initiated to determine survival, growth characteristics, and metal uptake of two montane riparian willow species, Geyer (Salix geyeriana Andersson) and mountain (S. monticola Bebb) willow, grown in amended fluvial mine tailing deposits. Revegetation was done with staked and previously rooted cuttings to determine if planting method had an effect on successful establishment of willows. A second planting was done the following growing season which tested cuttings of different ages. The addition of lime increased the soil pH from 5.0 to 6.5 and effectively reduced bioavailability of most heavy metals below phytotoxic levels. However, both willow species, regardless of planting method, concentrated Cd, Mn, Pb, and Zn in their leaf tissue above levels considered toxic to agronomic plants. Over the course of four growing seasons, prerooted mountain willows had a consistently higher survival rate compared to staked willows. At the end of the fourth growing season, mountain willow had a higher survival rate and produced greater aboveground growth for both planting methods, irrespective of year planted, compared with Geyer willow. Based on growth characteristics, the use of prerooted mountain willows would be recommended for successful revegetation of amended fluvial mine tailing deposits in riparian zones. However, because of the high Cd uptake into aboveground tissues, care should be taken in restoration efforts where wildlife and domestic livestock are likely to browse on the willows.

Manganese and zinc toxicity thresholds for mountain and Geyer willow.

Information on the heavy metal toxicity thresholds of woody species endemic to the western United States is lacking but critical for successful restoration of contaminated riparian areas. Manganese (Mn, 50-10,000 mg l(-1)) and zinc (Zn, 100-1000 mg l(-1)) toxicity thresholds were determined for Geyer (Salix geyeriana Anderss.) and mountain (S. monticola Bebb) willow using a sand-culture technique. The lethal concentration (50%) values were 3117 and 2791 mg Mn l(-1) and 556 and 623 mg Zn l(-1) for Geyer and mountain willow, respectively. The effective concentration (50%) values for shoots were 2263 and 1027 mg Mn l(-1) and 436 and 356 mg Zn l(-1) for Geyer and mountain willow, respectively. Shoot tissue values did not increase with increasing treatment concentrations. However, metals in the roots did increase consistently in response to the treatments. Metal levels in the shoot tissues were low for Zn (65-139 mg kg(-1)) and moderate for Mn (1300-2700 mg kg(-1)). Geyer and mountain willow have good resistance to Mn, possibly due to evolution in hydric soils with increased Mn availability, and may be useful for phytostabilization of soils with high levels of available Mn. Both species were affected to a greater degree by Zn as compared to Mn, but still exhibited good resistance and should be useful in remediating sites with at least moderate levels of available Zn. Based on the thresholds evaluated, Geyer willow had greater resistance to both Mn and Zn as compared to mountain willow, especially at lower concentrations in which growth of Geyer willow was actually stimulated.

Irrigated mountain meadow fertilizer application timing effects on overland flow water quality.

Nonpoint-source pollution from agricultural activities is currently the leading cause of degradation of waterways in the United States. Applying best management practices to flood-irrigated mountain meadows may improve agricultural runoff and return flow water quality. Prior research has focused on fertilizer use for increased hay yields, while few studies have investigated the environmental implications of this practice. We examined the effects of fertilizer application timing on overland flow water quality from an irrigated mountain meadow near Gunnison, Colorado. Application of 40 kg phosphorus (P) and 19 kg nitrogen (N) ha(-1) using monoammonium phosphate (11-52-0, N-P-K) fertilizer to plots in the fall significantly reduced concentrations of reactive P and ammonium N in irrigation overland flow compared with early or late spring fertilization. Reactive P loading was 9 to almost 16 times greater when fertilizer was applied in the early or late spring, respectively, compared with in the fall. Ammonium N followed a similar trend with early spring loading more than 18 times greater and late spring loading more than 34 times greater than loads from fall-fertilized plots. Losses of 45% of the applied P and more than 17% of the N were measured in runoff when fertilizer was applied in the late spring. These results, coupled with those from previous studies, suggest that mountain meadow hay producers should apply fertilizer in the fall, especially P-based fertilizers, to improve hay yields, avoid economic losses from loss of applied fertilizers, and reduce the potential for impacts to water quality.