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Plant Molecular Biology 35: 3–15, 1997.
c 1997 Kluwer Academic Publishers. Printed in Belgium.
Comparative genetics in the grasses
Katrien M. Devos and Michael D. Gale
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
Key words: comparative genetics, synteny, colinearity, grasses
Abstract
Comparative genetic studies have demonstrated that gene content and orders are highly conserved, both at the map
and megabase level, between different species within the grass family. Integration of the genetic maps of rice,
foxtail millet, sugar cane, sorghum, maize, the Triticeae cereals and oats into a single synthesis reveals that some
chromosome arrangements characterise taxonomic groups, while others have arisen during or after speciation. A
detailed analysis of the comparative maps of seven species, belonging to three subfamilies, and their applications
are described below.
Introduction
History of comparative genetics
‘Comparative genetics’ is the science that exploits the
results of ‘comparative mapping’ – two terms that were
unknown to plant geneticists ten years ago. Although
the discovery that genes in related species – and as it
turns out now, quite distantly related species – tend to
be ordered colinearly on chromosomes is quite new,
the concept of conservation has a long history in plant
genetics. In the 1920s Vavilov had already observed
that ‘similar variations’ were to be found in different
species. More recently, of course, DNA studies have
shown that genes of similar function in different species
have remarkably conserved sequences. The discovery
of colinearity by comparative mapping is, however, a
function of the new molecular markers – in particular
RFLPs – employed in plants for the first time in the
mid 1980s. Nevertheless, with the immense effort in
genetic mapping of morphological mutants and, later, protein loci in both plants and animals it is surprising that gene colinearity remained hidden until the
reports in 1988 of convergence of the maps of the three
genomes of hexaploid bread wheat [6] and the similar
convergence between the maps of tomato and potato
[3].
In wheat, evidence for homoeology between the
three genomes had already been provided by cytogeneticists, particularly by the late Prof. Ernie Sears,
who assembled the first set of aneuploid genetic stocks
in wheat. Hexaploid bread wheat (Triticum aestivum,
2n = 6x = 42) is an allopolyploid with genome constitution AABBDD, formed through hybridization of
T. urartu (AA) with a B genome diploid of unknown
origin, and subsequent hybridization, only about 8000
years ago, with a D genome diploid, T. tauschii. The
development of aneuploid stocks in wheat led to the
discovery that an extra dose of a particular chromosome could compensate for the absence of another [57].
This compensating ability of chromosomes of different
ancestral origin defined their relationship, and resulted in the classification of the 21 wheat chromosomes
into 7 homoeologous groups [58]. Similar compensating experiments determined the homoeologous relationships between wheat chromosomes and those of
other Triticeae species such as rye, barley, and several Aegilops ssp. (for catalogue see 60). The ability of
chromosomes to substitute for one another suggested
that they carried similar genes. This was confirmed by
the demonstration that the glutenin storage protein loci
were to be found on chromosomes 1A, 1B and 1D by
Shepherd [59]. Following this aneuploid analysis of
other biochemical markers, and later of DNA markers, showed that most protein, isozyme and RFLP loci
4
are triplicated in the wheat genome. The realisation
that not only gene content but also gene orders were
conserved had, however, to await the construction of
molecular marker-based genetic maps.
Comparative genetics at the map level
Within hexaploid wheat
The application of RFLP markers in plant genetics provided, for the first time, unlimited supplies of markers
of both genic (cDNA probes) and random genomic
(genomic DNA probes) origin to detect variation at the
DNA level. Hybridization of cDNA clones to aneuploid lines of hexaploid bread wheat showed that most
genes were triplicated on the A, B and D genomes
(Figure 1a). Generally, these probes cross-hybridized
strongly under high stringency conditions to wheat relatives such as rye and barley. Genomic clones, on the
other hand, either showed a hybridization behaviour
comparable to cDNA clones, or hybridized to one or
more chromosomes apparently at random (Figure 1b).
The latter ‘non-homoeologous’ probes were found to
be derived from fast evolving regions of the wheat
genome [30] (Figure 1d), and it was therefore not
surprising that these sequences could not be detected
in other Triticeae species under stringent hybridization conditions [16]. Genetic mapping of cDNA-like
or homoeologous sequences in hexaploid bread wheat
clearly demonstrated that, taking into account evolutionary chromosomal rearrangements involving chromosome arms 4AS, 4AL, 5AL and 7BS [41, 15], and
possibly 2BS and 6BS [16], gene orders on the A, B
and D genomes were extremely highly conserved.
In recent years molecular marker technology has
moved to exploit the polymerase chain reaction (PCR).
Microsatellites are now, in fact, the markers of choice
for marker aided applications in breeding programmes.
In contrast to RFLPs these systems, which rely on
complete sequence identity between primer and target DNA, tend to fail to detect homoeoloci across
the three wheat genomes (Figure 1c). This lack of
transferability of PCR-based markers across different
genomes excludes their use for comparative purposes. The evidence for the extensive synteny across the
grasses discussed below stems almost entirely from
cross-mapping of RFLPs.
Within the Poaceae family
The high levels of conservation of gene orders within
polyploid wheat begged the question of how far synteny would extend. In the first instance, analyses were
focused on genomes of species belonging to the same
tribe with major efforts within the Triticeae (Figure 2)
and Andropogonodae tribes. Later, the leading laboratories in grass genome research exploited RFLPs as a
generic tool to broaden their purview of crop species
beyond tribe boundaries (Figure 3). Cornell graduated
from rice to wheat, barley, maize, sugar cane and oats,
while the John Innes Centre (JIC) expanded from wheat
to barley, rye, rice, maize, pearl millet and foxtail millet. Where experience was not immediately available
collaborations provided the necessary materials and
information. Links between the Brookhaven National
Laboratory maize group and Cornell and the Japanese
Rice Genome Programme and JIC were key collaborations which led to the present-day synthesis.
The first publications that demonstrated the breadth
of synteny among the cereals were by Ahn and
Tanksley [1] showing the relationship between rice
and maize, Kurata et al. [39] showing that the wheat
genome could be aligned with rice, and Moore et al.
[45] who showed that all the maps could be combined
in a single synthesis. A recent evaluation of the extent
of synteny is shown in Figure 4 which draws on many,
some as yet conflicting, sources of information.
The alignment in Figure 4 is based on rice, with
the other genomes arranged relative to rice in the most
parsimonious manner. Rice is used as the base simply
because it is the smallest cereal genome analysed in
detail, and that for which we have the densest maps
and most genomic tools available. It is important to
note that the organisation of Figure 4 has no bearing
on the ancestry of the grass genomes. Inferences can,
of course, be made concerning which chromosomal
arrangements are the more primitive.
The integrated grass genome map, which now
includes species belonging to 6 different tribes and
3 different subfamilies, reveals three distinct genome
patterns, provided by rice, a representative of the Bambusoideae, oats and the Triticeae crops of the Pooideae,
and several members of the Panicoideae (Figure 5).
Rice. The rice chromosomes are arranged in a circle
in the order revealed by Moore et al. [46] following a
comparison of the rice and maize genomes. Key information concerning the rice genome map came from
the Rockefeller Rice Biotechnology Programme map
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Figure 1. The chromosomal location in wheat of loci detected with a ‘homoeologous’ RFLP probe (a), a non-homoeologous RFLP probe (b), a microsatellite, all using nullisomic-tetrasomic
aneuploid lines (c), and their map position on the homoeologous group 3 chromosomes (d).
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Figure 2. Hybridization of a wheat cDNA probe, PSR129, to the wheat variety Chinese spring (CS), wheat nullisomic-tetrasomic lines (N7A,
N7B, N7D), barley (cv. Betzes), a wheat/rye amphiploid (CS/Imperial), a CS/Ae. umbellulata amphiploid, and wheat/barley, wheat/rye and
wheat/Ae. umbellulata disomic single chromosome addition lines reveals loci on homoeologous chromosomes in the four Triticeae species.
Figure 3. Differential hybridization behaviour of probes in a range of Triticeae crop species, rye grass (Lolium), maize and pearl millet
(Pennisetum).
made at Cornell by Susan McCouch and colleagues
in an interspecific backcross population derived from
O. sativa and O. longistaminata, two AA genomes
species (5 and updates in RiceGenes, the rice genome
database) and Takuji Sasaki’s group at the Japanese
Rice Genome Program in Tsukuba, using an indica 7
Figure 4. Aligned maps of rice, foxtail millet, sugar cane, sorghum, maize, the Triticeae crops and oats. Chromosome nomenclature: Chromosomes are numbered conventionally – rice
(short and long) after Singh et al. [61]; foxtail millet (top and bottom) after Wang et al. [66]; sugar cane linkage groups (top and bottom) after Dufour [20]; sorghum (top and bottom) after
Dufour [20]; oats (top and bottom) after O’Donoughue et al. [53]. All maps are aligned relative to rice, ends of maps of chromosomes (in some cases telomeres) are shown with coloured
arrows. Where known, the positions of centromeres are marked. Double ended arrows show inversions (relative to rice), open arrows show segments that require transposition to return to
linear chromosome maps. Hatched areas indicate regions of uncertainty where the cross-mapping data does not allow definite alignment with rice. Arrows in solid red indicate ‘evolutionary’
transpositions which define the Panicoideae and Pooideae subfamilies. The intra-genomic duplication of R11b and R12c is considered as part of R12 only in this analysis. All references are
in the text.
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Figure 5. Taxonomic relationships within the grass family.
japonica O. sativa cross (40 and updates in the JRGP
database). These two maps have been merged [43] to
provide in excess of 2000 loci. Discrepancies in marker orders between the maps are few. An earlier comparison between a map of the cultivated AA-genome
species O. sativa and the wild CC-genome O. officinalis showed an 8.6% reduction in map length but
marker orders that were mostly conserved. Two large
inversions were observed in rice chromosome 1, and
several markers appeared to be translocated between
rice 11 and 12 [34].
Locations of the centromeres on the rice maps have
been provided by analysis of tertiary trisomic stocks
by Singh et al. [61]. The construction of detailed maps
has also revealed a number of segmental duplications
within the largely diploid rice genome. More and more
of these are becoming recognised, but only one major
duplication involving the distal short arm segments of
R11 and R12 [47] is taken into account in Figure 4.
Duplications within the rice and other grass genomes
may confound an unequivocal alignment of the species
chromosomes.
Triticeae. Within the Triticeae tribe, comparative
research has determined precise relationships among
the genomes of T. tauschii [26], barley [65, 48], rye [56,
12], T. monococcum [19], and most recently, Aegilops
umbellulata [69], all of which share a basic chromosome number of 7 and a monoploid DNA content of
about 5.5 pg. The genomes of wheat, T. monococcum,
T. tauschii and barley were shown to be highly colinear [62, 16, 48, 19], although the presence of a few
minor inversions is still being debated. The genomes
of rye and Ae. umbellulata, on the other hand, are distinguished from the wheat genomes by a minimum of
7 and 11 rearrangements respectively [12, 69]. Colinearity, however, was conserved within the translocated
segments. The presence of extensive rearrangements
in the rye and Ae. umbellulata genomes was surprising, and there is currently no answer as to why certain
species accumulate and fix rearrangements more readily than others. It is clear that this differential rate
of accumulation of structural changes excludes sheer
numbers of rearrangements as a measure of evolutionary age.
The Triticeae maps in Figure 4 are a consensus of
wheat, barley and rye and the arrangement shown is
that of the D genome of the wheat variety Chinese
Spring. The main wheat maps providing RFLP clones
for comparative mapping were developed at JIC in a
Chinese Spring Synthetic population [13, 16, 68,
35, 15, summarised in 25] and by the Cornell and
Clermont Ferrand groups in the International Triticeae
Mapping Initiative population, derived from the cross
Opata Synthetic [62, 50, 51, 49, 42]. As yet there are
too few points of correspondence to allow these maps
to be closely aligned. The barley maps of the North
America mapping group [38] and the group at Munich
9
[28] are also increasingly providing anchor probes for
comparative mapping.
The Triticeae genomes are characterised, relative
to rice, by the rice 5/10 rearrangement in which rice
10 is inserted into the proximal region of the long arm
of R5 to form the wheat homoeologous group 1 chromosomes. Similarly R8 is inserted into R6 to form
homoeologous group 7 chromosomes and R7 into R4
to form homoeologous group 2 chromosomes. These
rearrangements characterise the species within the Triticeae tribe. Other rearrangements, such as those that
characterise rye and Ae. umbellulata, may be speciesspecific and will have arisen during or after speciation.
Oats. The oat map shown in Figure 4 is from a cross
between two diploid species Avena atlantica and A. hirtula by O’Donoughue et al. [53] which has since been
populated with comparative wheat, rice, barley and
maize markers by Van Deynze et al. [63] and comparisons drawn with rice, maize and wheat. Hexaploid oats
(AACCDD) is characterised by multiple intergenomic
translocations, at least some of which have occurred
after the formation of the AACC tetraploid [33, 52]. A
number of duplications are present in both the diploid
and hexaploid oat maps, indicating that they preceded
polyploidization.
The analysis by Van Deynze et al. [63] shows that
the diploid oat genome can be aligned with that of rice
in only 20 syntenic regions, and with wheat and maize
in 18. Many of the rearrangements, relative to the other
grasses, are however novel. Exceptions are the insertions of R10 into R5 and the R8/R6 rearrangement that
characterise both oats and the Triticeae and demonstrates their relationship as members of the Pooideae.
The Panicoideae group. The foxtail millet, sugar
cane, sorghum and the two maize genomes shown in
Figure 4 are characterised by two common rearrangements relative to rice. These involve, once again, R10
which is inserted into R3, and R9 which is found
inserted into R7. While these evolutionary translocations characterise the group, each species has further
rearrangements which distinguish it from the others.
Maize. The main sources of mapping information are
from the USDA group led by Ed Coe in Columbia,
Missouri (10 and updates in MaizeDB), Ben Burr’s
programme at the Brookhaven National Laboratory (4
and updates in MaizeDB) and Tim Helentjaris [31]
The comparative information has been provided by
Ahn and Tanksley [1] and Devos et al. [14] for maize
chromosome 9. Other information used is from Sorrells
et al. [63, 64] and the CIRAD group at Montpellier [20,
22].
The key observation is that maize is clearly a
tetraploid, probably of relatively recent origin since
most DNA probes hybridise to duplicated loci. Doebley dates the polyploidisation of maize at 16 million
years ago. However, the two ‘genomes’, each with
five chromosomes are, in contrast to wheat, extremely
differentiated in that no completely ‘homoeologous’
chromosomes remain. The fact that most of the larger maize chromosomes (1, 2, 3, 4 and 6) make up
one genome and the smaller chromosomes (5, 7, 8,
9 and 10) make up the other, may relate to differences retained from the time of allotetraploidization.
However, the chromosome size differences could also
be fortuitous. A comparison at the sequence level of
duplicated genes indicated that some duplicated loci
appear to have diverged less (16 million years) than
others (27 million years) (Doebley, pers.comm.). This
could have been achieved if some chromosome pairing
and recombination took place before ‘homoeologous’
pairing was restricted, resulting in segments of the
duplicated genome having been retained from the two
ancestral five-chromosome diploid parents and other
parts representing duplicated segments from one or
other of genomes which have diverged only in the
intervening 16 million years. This theory that maize
is a ‘segmental’ allotetraploid will be supported if the
two types of genes are found to lie in linkage blocks,
but more evidence is yet required.
Several rearrangements and inversions, relative to
both wheat and rice, are apparent in addition to the
common Panicoideae group translocations and these
would appear to have occurred after the divergence of
maize from other members of the subfamily.
Sorghum. Within the Andropogonodae, comparative
research was undertaken to increase the understanding
of sorghum genetics. Several groups established the
relationship between the sorghum and maize genomes
following the lead of Hulbert et al. [32, 67, 44, 55, 29,
22, 20, 54]. The most complete information to date is
provided by Dufour et al. [20] and their synthesis and
chromosome numbering and orientations are used in
Figure 4. Gene orders appear to be largely conserved
between sorghum and maize and only a limited number of rearrangements have been identified. With the
exception of major evolutionary translocations which
characterise the Panicoideae, extreme colinearity also
appears to have been maintained with rice, with seven
10
linkage groups reflecting precisely, within the limits of
the analysis to date, seven rice chromosome linkage
blocks.
The close taxonomic relationship between maize
and sorghum, both with a 10 chromosome haploid
complement, and maize having been shown clearly
to be an allotetraploid as of 16 million years ago, begs
the question as to whether sorghum is also a tetraploid.
Although there are clearly some regions of duplication [55, 9, 20, 21], the evidence for tetraploidy, at
least of recent origin, is not strong. In both Chittenden
et al. [9] and Dufour et al.’s [20] analysis only 8% and
11% respectively of duplicated loci were present on
the map, although the number of probes that detected
more than one hybridizing fragment amounted to 23%
[20]. In maize the equivalent figure is about 70% [67,
18]. Certainly comparative maps of maize and sorghum
show single sorghum linkage groups relating to, usually, two regions of the maize genome, as indicated in
Figure 4. For these reasons sorghum is maintained as
a 2x = 2n = 20 diploid in this review.
Sugar cane. Sugar cane, another important crop
belonging to the Andropogonodae, has a complex
polyploid nature and mapping studies were initiated
at CIRAD to help define its intricate genome structure [29]. Modern sugar cane varieties have originated
through introgression of part of the genome of the wild
species Saccharum spontaneum (x = 8, 2n = 40 to
128) into S. officinarum (x = 10, 2n = 80). Introgressions are mostly complete chromosomes but some
intergenomic translocations have been observed [11].
Due to its genome complexity, the numbers in Figure 4
refer to composite linkage groups rather than chromosomes. Extensive colinearity was maintained between
sugar cane and sorghum.
Foxtail millet. All of the genome information relating to Setaria italica (2x = 2n = 18) derives from
the work of Zhimin Wang from Hebei Academy, China during his PhD work at JIC. In addition to being a
crop of importance in Northern China, foxtail millet
is very attractive as a genetic organism since it has a
genome almost as small as rice with 1C = 490 mb
DNA (O. Panaud, pers.comm.). Maps were constructed in an intraspecific population between two S. italica accessions and an interspecific cross, S. italica S. viridis. Both maps had equivalent genetic lengths
and displayed highly conserved marker orders [66].
The foxtail millet genome also shows extreme colinearity with rice [17] with five entire chromosomes
unchanged in marker content and order. More interesting possibly is the very close relationship between
foxtail millet, which has a haploid chromosome number of 9, and sorghum with n = 10. The difference in
chromosome number is accounted for by the synteny of
foxtail millet chromosome III with sorghum chromosomes E and I. Elsewhere we can currently detect only
one inversion, in sorghum chromosome D, and one
translocation involving foxtail millet chromosomes III
and VII, which differentiate the two species.
Centromeres. The comparative maps of genomes
with chromosome numbers varying between 5 and 12
raises the question as to whether centromeres are syntenic. Plainly they cannot all be completely so.
Precise positioning of the centromeres on the maps
is limited to wheat, maize and rice. Only in these three
species have the appropriate genetic stocks been available to map RFLP markers to chromosome arms and
then to delineate, often very precisely, the locations
of the centromeres. A comparison of maps and centromere positions across these three species indicates
that the centromeres of maize chromosomes 1, 2, 3, 5,
7, 8, 9 and 10 correspond to those of rice chromosomes
8, 4, 1, 2, 7, 1, 6 and 4 respectively. Conservation of
colinearity of the centromeres of maize chromosomes
4 and 6 across rice could not, as yet, be established,
but it is expected that they correspond with the centromeres of either rice chromosomes 2 or 11, and 5
or 6 respectively. Similarly, colinearity between the
centromeres of wheat and rice can be established for
five of the seven wheat chromosomes. Centromeres of
wheat chromosomes 2, 3, 4, 6 and 7 appear to be colinear with those of rice chromosomes 7, 1, 3, 2 and
8.
Conservation of colinearity of centromeres across
grass species could be exploited to predict their location in species such as the millets for which the appropriate genetic stocks are not available. Using the comparative approach, putative centromere positions were
established for foxtail millet chromosomes I, II, IV, V,
VI, VII, VIII and IX [17]. Particularly on chromosomes
I, IV, V, VI and IX, the putative centromere regions
coincide with regions of severe marker clustering. This
is a further indication that these regions indeed contain
centromeres, following the observations in wheat that
reduced recombination results in clustering of markers
on genetic maps around centromeres [7]. Similar arguments have been used to predict the locations of the oat
centromeres [63], five of which are shown in Figure 4.
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Recent research has identified cereal centromerespecific probes [2, 36] and microsatellites that are
indicative of centromere positions [27]. It may thus
soon be feasible to map both functional and redundant
centromeres. This will go some way towards answering
the question of ancestry since, if rice has retained the
more primitive grass genome organisation, then wheat,
for example, should carry five redundant centromeres
in addition to the seven functional centromeres. Moreover these should all be present at predictable locations
in the Triticeae genomes.
Ancestry. The question as to exactly what the genome
of the ancestral grass was like is still open. Of those
grasses studied to date for synteny, rice has the smallest genome which may be an indicator, if we assume
that genomes accumulate repeats, as demonstrated by
Bennetzen [8]. Another pointer may lie in the chromosomal rearrangements that characterise the Pooideae
and Panicoideae subfamilies relative to rice, shown in
red on Figure 4. Each involves the insertion of one rice
linkage group into the centromeric region of another. Rice chromosome 10 is involved in two of these
key rearrangements, inserted in maize into R3 and in
wheat into R5, which may argue that an independent
R10 block is the more primitive. Certainly the argument by Moore et al. [46], which uses the comparison
of the rice and maize genomes and shows that the rice
genome can be equated to a single chromosome stack
of blocks is intriguing. However we must await further
research before assuming there was indeed a single
ancestral grass chromosome.
Comparative genetics at the level of gene organisation
As discussed above there is now overwhelming evidence for the existence of extensive regions of conserved colinearity among grass species at the genetic
map level. This knowledge can already be exploited
to advance marker studies on all grass species and to
extend our knowledge of key syntenic agronomic genes
as they become placed on the genetic maps. Application of comparative genome research as a tool for gene
isolation, however, also requires that conservation of
gene presence and organisation is maintained at the
megabase level. Dunford et al. [23] demonstrated that
the order of markers, contained on the same YAC and
thus separated by 1 mb in rice, was indeed maintained in barley. In a similar comparative study of a
region of barley chromosome 7H with rice chromosome 6, Kilian et al. [37] also concluded that a very
high degree of synteny exists at the sub-cM level. Foote
et al. [24] have similarly shown extensive colinearity
between a small region of wheat chromosome 5 and
rice chromosome 9. The similarity in gene content and
order are adequate to allow Andris Kleinhof’s group
to continue their search for the barley rust resistance
gene, Rpg1, in rice and Graham Moore’s group to
continue towards the wheat gene controlling homoeologous chromosome pairing, Ph1, from rice.
These studies have, however, also shown disruption of simple relationships, and small deviations from
strict colinearity are likely to be common. Kilian’s
study has revealed a duplicated segment of their target
region proximal to the site of the Rpg1 gene in barley.
Foote et al. have shown that part of their target region
is duplicated on rice chromosome 9, and that duplications and, possibly, triplications may disrupt synteny at
the microlevel in wheat. The same study also revealed
that close by the target region the syntenic relationship
wheat 5 – rice 9 was disrupted by a short segment with
homoeology to rice chromosome 11 intercalated into
the larger R9 region in wheat and barley. In a detailed
study of the Sh2 – a1 region in maize, sorghum and
rice, Chen et al. [8] demonstrated a direct duplication of a1 at the homoeolocus in sorghum. The Sh2
– a1 region, however, exhibited extensive colinearity, but spanned 140 kb in maize, and only 19 kb in
rice and sorghum. Sequence homology between Sh2
and a1 in maize, sorghum and rice amounted to at
least 80%. Most of the intergenic regions, however, were populated with species-specific repetitive elements and failed to cross-hybridize across species [8].
This result serves to remind us that the comparative
story that is emerging relates only to genes. Intergenic
regions are likely to have accumulated species-specific
sequences which prohibits prediction of physical distances between homoeologous genes in related species.
Based on the current comparative data, it is clear
that gene content and gene orders are highly conserved
between species within the grass family, and that the
amount and organisation of repetitive sequences has
diverged considerably. Rearrangements, both at the
map and megabase level have taken place, but 60
million years of evolution has left large chromosome
regions apparently untouched.
Conclusions
The stage is now set to exploit the synteny between
grass genomes in many ways. Moreover, more species
will be added. The comparative maps of pearl mil-
12
Figure 6. Putative orthologous genes across the Triticeae, maize and rice.
let, Pennisetum glaucum, finger millet, Eleusine coracana and rye grass, Lolium perenne, will soon be
available, the latter from work currently being completed at the Institute of Grassland and Environmental
Research, Aberystwyth and the former two projects are
from work at the John Innes Centre. In the immediate
future we can expect successes in cross-genome mapbased cloning, but in the longer term we can expect an
increased level of understanding from a coalescing of
information about genes and traits as key agronomic
genes in different species become linked on the comparative map.
Figure 6 shows a few such genes which have
already been demonstrated to show synteny across the
three major cereals. If we assume that a cereal genome
carries about 25 000 genes, as has been predicted in
Arabidopsis, then we should be able to align homoeoal-
leles across the grass genomes on 25 000 radii on the
circles. We can expect the mapping to continue apace,
but integration and applications will be hampered without advances in bioinformatics. The amount of data
in individual species genome projects is overwhelming. The total data for all grass programmes is vast
and requires a new approach to bioinformatics that is
compatible with the species-specific databases, such
as GrainGenes, MaizeDB, RiceGenes, MilletGenes,
which already serve the community.
This conservation of genome organisation has since
been observed in other groups of species, for example
over various legume crops and the brassicas, including
Arabidopsis which is a member of the Cruciferae. Possibly the next ten years may reveal that conservation
of colinearity is maintained across the monocots and
dicots, and maybe even further.
13
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