Apart from linkage analysis and QTL mapping, association mapping is another commonly used tool for genetic analysis of genetic factors for quantitative characteristics. In contrast to QTL analysis, which has been typically derived from a bi-parentally crossed population, association mapping takes advantage of the fact that historic recombination within a population which has decreased linkage disequilibrium (LD) to short chromosomal intervals, enabling potentially statistically strong and robust marker-trait associations to be detected. It offers three advantages over QTL analysis: 1) much higher mapping resolution; 2) greater allele number and broader reference population; and 3) less research time in establishing an association (Yu and Buckler 2006). However, two major drawbacks exist in association mapping. First, false positive associations between markers and traits can be obtained due to the presence of population structure. Population structure can be assessed with marker information from genome-wide genetic markers (such as SSRs), and then association tests can be conditioned on the population structure to reduce the false positive rate (Pritchard et al. 2000). Second, a higher density of markers is needed to identify linked QTL because LD spans over shorter distances in the genome, compared to linkage-based QTL mapping analyses. Loci that are more closely located on a chromosome (or that have a low level of recombination between them) will be more likely to be in LD than loci located further apart. The genetic distance over which LD is present along a chromosome depends on the population history: populations that have undergone many rounds of recombination will show less LD than populations that have had little recombination (Yu and Buckler 2006).

In the first attempt of association mapping study in plants, DNA sequence polymorphisms within the D8 locus were associated with flowering time (Thornsberry et al. 2001). Later it has also been used to associate candidate gene Y1 with maize endosperm color (Palaisa et al. 2004). In forage crops, association mapping successfully identified flowering time genes in natural populations of perennial ryegrass (Skot et al. 2005). Several SSR markers were found related to yield and quality in an elite alfalfa breeding population by associated mapping (Li et al. 2011). In Switchgrass, a project about association mapping of cell wall synthesis regulatory genes and cell wall quality is in progress (http://www. switchgrassgenomics. org//research. shtml). Although the complexity of the switchgrass genome (polyploidy, repeat-sequence rich, and highly heterozygous) poses significant challenges to the application of association mapping, ongoing genome sequencing projects will ultimately allow for a thorough genome­wide examination of nucleotide polymorphism-trait association. Two association mapping collections were assembled. One is an upland collection created by E. Buckler, M. Casler and colleagues (Casler et al. 2011). The other one is a southern collection of most lowland genotypes and some upland genotypes made by M. Saha, E. C. Brummer and colleagues at the Noble Foundation (Personal communication 2012). M. Saha and collaborators have also established a switchgrass nested association mapping (NAM) population, which was selected for funding by DOE in 2012 (http:// genomicscience. energy. gov/research/DOEUSDA/2012awards. shtml). It is expected a large amount of information will be available from these projects for associations among economically important traits and DNA markers in the near future.