Environmental Engineering Reference
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is  B. rupestre . Seven additional taxa are reported from diverse origins: B. arbuscula (Canary Islands),
B. boissieri (southern Spain), B. kawakamii Hayata (Ta iwa n), B. mexicanum (Mexico to Bolivia),
B. pringlei (Central and South America), B. bolusii (Africa), and B. flexum (Africa).
All members of the genus exhibit a set of common features that include lateral stem development
from the coleoptile, small chromosomes, rDNA sequence, repetitive DNA families, and shared
nuclear RFLPs. However, variation in morphology, life-cycle, and cytology is sufficient to
clearly distinguish the species (Catalán and Olmstead 2000). B. distachyon is the only member
to have an annual life-cycle, and it is also self-compatible, a trait that is shared with only two
perennial species— B. mexicanum and B. sylvaticum (Khan and Stace 1999). With the exception of
B. mexicanum , the perennial species are rhizomatous (Catalán and Olmstead 2000).
The phylogenetic relationships between eight Brachypodium species ( B. arbuscula , B. distachyon ,
B. mexicanum , B. phoenicoides , B. pinnatum , B. retusum, B. rupestre , and B. sylvaticum ) have been
evaluated using multiple data sets: RFLP and RAPD markers, a chloroplast ndhF gene sequence, a
nuclear rDNA sequence, and rDNA ITS sequence (Shi et al. 1993; Hsaio et al. 1994; Catalan et al.
1995; Catalán and Olmstead 2000). An Eco RI site was identified in the rDNA of most perennial spe-
cies that could be used to distinguish them from B. distachyon and B. mexicanum , but this approach
failed to identify sufficient variation to resolve the relationship between the perennial species. By
using RAPD data along with ndhF and ITS sequences, B. distachyon was identified as the basal
lineage of the group, followed by the divergence of B. mexicanum , B. arbuscula, B. retusum , B. rup-
estre, B. phoenicoides, B. pinnatum, and then B. sylvaticum (Catalán and Olmstead 2000) .
Polyploidy is common among all taxa, and diploid, tetraploid, hexaploid, and octaploid species
have been reported with base chromosome numbers ranging from 5 to 10 (Robertson 1981). In a
recent report (Wolny and Hasterok 2009), cytogenetic analyses were performed on six species and
two subspecies of Brachypodium . The researchers found that fluorescence in situ hybridization
(FISH) could help identify the small chromosomes found in Brachypodium species that are
otherwise difficult to distinguish. Evolutionary relationships between allopolyploid species were
also  investigated using genomic in situ hybridization (GISH) to assign chromosomes to putative
ancestral genomes. Wolny and Hasterok (2009) concluded that B. pinnatum (2 n = 28) is an interspecific
hybrid between B. distachyon and B. pinnatum (2 n = 18) and suggested that B. distachyon is one
of the putative ancestral species for both of the allopolyploids B. phoenicoides and B. retusum .
Insight into the organization, phylogeny, and evolution of mechanisms that determine variation in
chromosome number will become possible with the development of additional tools such as arm-
and region-specific probes for cytogenetic analyses.
Perenniality and self-incompatibility are traits that are present in the wild grasses being developed
into bioenergy crops (e.g., Miscanthus and switchgrass) and can also be found in a number of species
within the genus Brachypodium (Khan and Stace 1999; DOE and USDA 2005). As a result of the
close relationship between different Brachypodium species, researchers will be able to leverage the
resources developed for B. distachyon to study these traits in other Brachypodium species.
23.3 BrachyPodIum as an exPerImental system
Brachypodium displays many traits that make it a tractable and powerful system for research
targeted at improving grasses for use as food, feed, and fuel. A large collection of diverse accessions
and described inbred lines, simple growth requirements, efficient transformation, and a compact
genome make this small grass an attractive choice for an experimental system to understand basic
questions in grass biology.
23.3.1 g ErmplaSm and n atural d ivErSity
In contrast to the domesticated cereals which have been subjected to human selection for millennia,
Brachypodium is a wild grass. Brachypodium germplasm, for which there are a number of collections,
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