Brachypodium - Bioenergy Crop Plants - page 597

large genomes. Fortunately, the now-sequenced 272-Mbp diploid Brachypodium genome is one of
the smallest of any grass (International Brachypodium Initiative 2010). Brachypodium is self-fertile
and does not typically outcross (Vogel et al. 2009). This feature is useful for breeding homozygous
lines for many applications that require the maintenance of large numbers of independent genotypes
(i.e., mapping experiments, mutant analysis, and studies of natural diversity). Furthermore, within
the genus Brachypodium , there are species that may be useful to study polyploidy and perenniality.
23.2.1 p hylogEnEtic and S yntEnic r ElationShipS
of B rachypodium to o thEr g raSSES
The phylogenetic relationship between Brachypodium and the other grasses has been evaluated a
number of times with increasing amounts of data. Reports based on internal transcribed spacer (ITS)
and 5.8S ribosomal DNA (rDNA) sequence, genomic restriction fragment length polymorphism (RFLP)
and random amplified polymorphic DNA (RAPD) markers, and ITS sequence plus the chloroplast
ndfH gene all placed Brachypodium between rice and a clade containing temperate grains such as
wheat, barley, and Secale (Hsaio et al. 1994). Additional examinations of a much broader spectrum of
grasses used ITS and the ndfH sequence, as well as morphological data and chloroplast restriction sites
(Kellogg 2001) or the sequence of the matK chloroplast gene (Döring et al. 2007). These studies placed
Brachypodium in the subfamily Pooideae just below the radiation of the small grains and forage and turf
grasses, making Brachypodium a “sister” to this economically important group of grasses. However,
phylogenies based on single genes or small sets of genes can produce inconsistent phylogenetic trees
(Rokas et al. 2003), and this phenomenon has been observed with rice (Kellogg 1998). Therefore, it was
important to examine the phylogenetic relationships of Brachypodium using larger data sets. Analysis
of a data set comprising 11 kb of sequence from 20 highly expressed genes verified the relationship
between Brachypodium and the small grains (Vogel et al. 2006a). An even larger data set that is based
on 335 bacterial artificial chromosome (BAC) end sequences provides further evidence to confirm the
placement of Brachypodium within the grass family tree (Huo et al. 2007).
Several genomic regions of B. distachyon and B. sylvaticum have been compared to rice and
wheat, and these have shown general colinearity. One comparison of a 371-kb genomic sequence from
B. sylvaticum to the orthologous regions of rice and wheat showed perfect macrocolinearity between
the three genomes. The order of the shared genes was the same in B. sylvaticum and wheat, whereas
there was an approximately 220-kb inversion in rice, demonstrating variation in microcolinearity
(Bossolini et al. 2007). Markers from a 140-kb region of rice also were compared with B. sylvaticum
and wheat sequences in efforts to map the Ph1 locus that controls the pairing of homologous
chromosomes in wheat. In this case, the colinearity of B. sylvaticum and rice sequences permitted
the localization of Ph1 to a 2.5-Mb interstitial region of wheat chromosome 5B (Griffiths et al. 2006).
Furthermore, only 17% of the genes from 55,221 paired B. distachyon BAC end sequences were not
colinear with the orthologous regions in rice. A Brachypodium physical map covered 88% of the rice
sequence and showed conservation of synteny across these genomes (Gu et al. 2009).
23.2.2 r ElatEd b rAchypodium S pEciES
The genus Brachypodium contains a relatively small number of grasses and is estimated to have
diverged from Tr iticeae and Poeae 35-40 million years ago (Bossolini et al. 2007). The genus has
been assigned to its own tribe, Brachypodieae , within the subfamily Pooideae (Catalan et al. 1995;
Catalán and Olmstead 2000). Most of the 12-15 described Brachypodium species have been collected
from Mediterranean and Eurasian locations, but representatives of this genus have been identified
worldwide (Catalan et al. 1995; Catalán and Olmstead 2000). Species originating in the Mediterranean
include B. distachyon (Figure 23.1 c-e), B. retusum , and B. phoenicoides . B. sylvaticum (Figure 23.1, e
and f), B. glaucovirens , and B. pinnatum are from Eurasian locations, and the European representative