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The Moore Lab

Understanding the make-up of the Ph1 complex and its role in chromosome pairing

Cereal comparative genomics

Rice as a model for cereal and grass genomics

In the early 1990s, we demonstrated that gene order was conserved between rice and wheat despite their genomes differing greatly in size (Moore et al, 1993; Kurata et al, 1994).  Other cereal genomes were examined, and conservation of gene order (synteny) was found at the genetic and physical level (Moore et al, 1995; Dunford et al, 1995; Foote et al, 1997; Griffiths et al, 2006).  The rice genome is one of the smallest among the cereals and grasses, and in 1995, we demonstrated that rice could be a model for cereals based on this ‘synteny’ because its genome can be divided into groups of genes - a series of genomic building blocks - from which the other larger cereal genomes can be constructed. This analysis exploited mapping data provided by Professor Mike Gale, FRS as well as from groups in France, US and Japan.  Comparison of the order of blocks within the different cereal chromosomes revealed that each cereal genome can be derived from the cleavage of a single structure, a hypothetical ‘ancestral’ genome, from which the genomes of present day cereals and grasses have evolved.

‘Lego block’ model of cereal genome organization (view larger image)

A) The12 chromosomes of the rice genome are dissected into linkage blocks.
B-F) The rice blocks are rearranged to construct the genomes of five economically important grass species. 
G) A hypothetical ancestral chromosome is reconstructed on the basis of the rice blocks.

Comparative mapping of cereal genomes

With Professor Mike Gale FRS, we then developed a circularised consensus map of the genomes of six major grasses (Moore et al, 1995), in which the chromosomes of the six grass species are aligned such that any radius passes through homoeologous (orthologous) genes.  This allows us to exploit the small genome of rice and the extensive resources now available for this model genome, to isolate genes in other cereals by map-based cloning in rice, then by homology in the target species.  The “crop circles” diagram shows at a glance the chromosomal region in which a target gene is likely to map.

Crop circles’: Alignment of the genomes of six major grass crop species. A radius taken through a particular gene (eg Ss1 in maize) can be used to predict the position of the orthologous genes in other cereal species.

Brachypodium as a model for temperate cereals

Comparative mapping has provided a strategy to clone genes for important traits from the wheat genome, including the Ph1 locus. During our molecular characterisation of this locus, the rice genome was exploited to provide markers within the wheat Ph1 region, but additional markers were obtained from a closer relative of wheat, the temperate grass Brachypodium sylvaticum, which we proposed as a potential model for temperate cereals.  Like rice, Brachypodium possesses a small genome and the gene order is highly conserved with that of the wheat genome (Foote et al., 2004; Griffiths et al., 2006).   Markers generated from the rice and Brachypodium comparative mapping played an important part in defining the region containing the Ph1 locus.  More recently, the sequence for Brachypodium distachyon has been published by  The International Brachypodium Initiative, allowing Brachypodium to act as a powerful functional genomics resource for the grasses.


Dunford, R, Kurata N, Laurie D, Money T, Minobe Y, Moore G (1995) Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucleic Acids Res. 23: 2724-2728.

Foote T, Roberts M, Kurata N, Sasaki T, Moore G (1997) Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat.  Genetics 147: 801-807.

Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M, Reader S, Colas I, Moore G (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439: 749-752.  Figure legends to accompany supplementary information  (Cell Research Highlight- Leading edge- Cell (2006) 124: 869)

Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Nature Biotech.  12: 276-278.

Moore G, Gale MD, Kurata N, Flavell R.(1993) Molecular analysis of small grain cereal genomes. Nature Biotech. 11: 584-589.

Moore G, Devos K, Wang Z, Gale M (1995) Cereal genome evolution: Grasses, line up and form a circle. Curr. Biol.  5: 737-739


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