Restriction fragment length polymorphism (RFLP) linkage maps have been constructed in several major diploid crops. However, construction of RFLP maps directly in polyploids has lagged behind for several reasons: (1) there are a large number of possible genotypes for each DNA probe expected in a segregating population, and these genotypes cannot always be identified readily by their banding phenotypes; and (2) the genome constitutions (allopolyploidy versus autopolyploidy) in many high polyploids are not clearly understood. We present here an analysis of these problems and propose a general method for mapping polyploids based on segregation of single-dose restriction fragments (SDRFS). SDRFs segregate 1:1 (presence: absence) in gametes of heterozygous plants. Hypothetical allopolyploid and autopolyploid species with four ploidy levels of 2n = 4x, 6x, 8x, and 10x, are used to illustrate the procedures for identifying SDRFs, detecting linkages among SDRFs, and distinguishing allopolyploid versus autopolyploids from polyploids of unknown genome constitution. Family size required, probability of linkage, and attributes of different mapping populations are discussed. We estimate that a population size of 75 is required to identify SDRFs with 98% level of confidence for the four ploidy levels. This population size is also adequate for detecting and estimating linkages in the coupling phase for both allopolyploids and autopolyploids, but linkages in the repulsion phase can be estimated only in allopolyploids. For autopolyploids, it is impractical to estimate meaningful linkages in repulsion because very large family sizes (>750) are required. For high-level polyploids of unknown genome constitution, the ratio between the number of detected repulsion versus coupling linkages may provide a crude measurement of preferential chromosome pairing, which can be used to distinguish allopolyploidy from autopolyploidy. To create a mapping population, one parent (P1) should have high heterozygosity to ensure a high frequency of SDRFs, and the second parent (P2) should have a low level of heterozygosity to increase the probability of detecting polymorphic fragments. This condition could be satisfied by choosing outcrossed hybrids as one parental type and inbreds, haploids, or doubled haploids as the other parental type.

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Current knowledge of yield potential and best agronomic management practices for perennial bioenergy grasses is primarily derived from small-scale and short-term studies, yet these studies inform policy at the national scale. In an effort to learn more about how bioenergy grasses perform across multiple locations and years, the U.S. Department of Energy (US DOE)/Sun Grant Initiative Regional Feedstock Partnership was initiated in 2008. The objectives of the Feedstock Partnership were to (1) provide a wide range of information for feedstock selection (species choice) and management practice options for a variety of regions and (2) develop national maps of potential feedstock yield for each of the herbaceous species evaluated. The Feedstock Partnership expands our previous understanding of the bioenergy potential of switchgrass, Miscanthus, sorghum, energycane, and prairie mixtures on Conservation Reserve Program land by conducting long-term, replicated trials of each species at diverse environments in the U.S. Trials were initiated between 2008 and 2010 and completed between 2012 and 2015 depending on species. Field-scale plots were utilized for switchgrass and Conservation Reserve Program trials to use traditional agricultural machinery. This is important as we know that the smaller scale studies often overestimated yield potential of some of these species. Insufficient vegetative propagules of energycane and Miscanthus prohibited farm-scale trials of these species. The Feedstock Partnership studies also confirmed that environmental differences across years and across sites had a large impact on biomass production. Nitrogen application had variable effects across feedstocks, but some nitrogen fertilizer generally had a positive effect. National yield potential maps were developed using PRISM-ELM for each species in the Feedstock Partnership. This manuscript, with the accompanying supplemental data, will be useful in making decisions about feedstock selection as well as agronomic practices across a wide region of the country.

Sugarcane, a significant component of the economy of many countries in the tropics and subtropics, is a large, tropical grass that stores sucrose in its stem and serves as an important food and bioenergy crop. It has long been recognized as one of the world's most efficient crops in converting solar energy into chemical energy harvestable as sucrose and biomass. Current taxonomy divides sugarcane into six species, two of which are wild and always recognized (Saccharum spontaneum L. and Saccharum robustum Brandes and Jewiet ex Grassl). The other species are cultivated and classified variously. Of the four domesticated species of sugarcane, S. officinarum L. was the first named and is the primary species for production of sugar. Recent genomic data for evaluating genetic diversity within Saccharum suggest relationships among accessions that may ultimately produce a definitive classification for the group. Cultivated sugarcanes of today are complex interspecific hybrids primarily between Saccharum officinarum, known as the noble cane, and Saccharum spontaneum, with contributions from S. robustum, S. sinense, S. barberi, and related grass genera such as Miscanthus, Narenga, and Erianthus. Understanding the source and range of diversity of sugarcane species and cultivars can enable breeders in the development of new varieties improved for high productivity with low inputs and wide adaptation to varied environments.