Abstract
The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.
Highlights
The diverse and ecologically dominant grass family provides most human and domestic animal nutrition
Each bacterial artificial chromosome (BAC) clone from both libraries was end sequenced, yielding 58,894 BAC-end sequences (BES) and a total of 41 Mb of genome sequence (Table 1)
The compact and well characterised genome of Brachypodium distachyon, the first pooid grass to be sequenced [7], provides an important foundation for analysing and assembling the genome sequences of other pooid grasses, such as wheat and barley, which are characterised by their large size and complexity
Summary
The diverse and ecologically dominant grass family provides most human and domestic animal nutrition. Members of the Ehrhartoideae (rice), Panicoideae (maize, sorghum) and Pooideae (wheat, barley) grass subfamilies are the main grain crops worldwide and have been extensively improved by selective breeding to enhance productivity and end user qualities. Past yield increases have been achieved by the application of nitrogenous fertilisers, and it is widely accepted that the energy and environmental costs of this and current agronomic practices are no longer sustainable. Major efforts to develop new generations of grass crops with higher potential yields from reduced inputs, nitrogenous fertilizers and water, are underway. Strategies for creating new crops include the use of genomic resources for marker-assisted breeding [1] to incorporate a far wider range of genetic variation into elite breeding lines, and genetic engineering to create crops with enhanced agronomic properties. The complete genome sequence of crop plants is an essential foundation for efficient breeding and gene discovery
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