Unlocking Triticeae genomics to sustainably feed the future

Abstract

The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.

Keywords: Barley; Brachypodium; Crop improvement; Next-generation sequencing; Triticeae; Wheat.

Fig. 1

An overview of the publicly available sequence data in grasses. (A) The growth of sequence data in GenBank (number of entries) and the sequence read archive (number of bases). (B) Number of NGS runs of the four staple crops in Poaceae submitted to the sequence read archive (September 8, 2013).

Fig. 2

A phylogenetic tree of grass species based on the ndhF gene: YP 008239279 (T. urartu), YP 008239142 (T. monococcum), YP 008474350 (A. tauschii), AGP51333 (T. aestivum), YP 008474440 (A. speltoides), AGP50802 (H. vulgare subsp. vulgare), AGP50881 (H. vulgare subsp. spontaneum), YP 008239219 (Secale cereale), ABH02660 (Bromus suksdorfii), AAA64204 (Avena sativa), ABH02669 (Deschampsia cespitosa subsp. cespitosa), AAA64698 (Poa pratensis), YP 001531329 (Lolium perenne), ABH02677 (Festuca rubra), YP 002000532 (B. distachyon), YP 004733625 (Phyllostachys edulis), YP 654249 (Oryza sativa Indica group), NP 039441 (O. sativa Japonica group), YP 899454 (Sorghum bicolor), NP 043084 (Zea mays), YP 004841996 (Panicum virgatum), AAA64841 (Setaria viridis), AAM22087 (S. italica) and NP 051106 (A. thaliana). The phylogenetic tree was constructed with the aligned NdhF protein sequences by MEGA [version 5.2; http://www.megasoftware.net/ (Tamura et al. 2011)] using the Neighbor–Joining method with the following parameters: Poisson model, complete deletion and bootstrap method. The bootstrap values from 1,000 replicates are given at each node. The NdhF protein sequences were aligned by ClustalW implemented in MEGA.

Fig. 3

Comparative mapping of Triticeae cDNAs to the Brachypodium genome. A data set of full-length cDNAs of barley (GenBank accession Nos. AK353559–AK377172 deposited by NIAS, and available in TriFLDB) and wheat retrieved from TriFLDB, shotgun genome analysis of wheat by Roche 454 sequencing (downloaded from MIPS), cDNAs of T. urartu and A. taucschii (downloaded from Ensembl Plants) and barley cDNAs annotated on the cv. Morex genome (downloaded from MIPS and from Ensembl Plants) were used to the comparative mapping analysis. Cross-species mapping using cDNA data sets for querying the Brachypodium Bd21 genome was performed by sim4 with default parameter settings, followed by a BLASTN search, with e-value cut-offs of <1e-20. (A) An overview of the mapping results represented by a circular image. (B) Numbers of queries of wheat full-length cDNAs [Wheat FLcDNA (TriFLDB) and those of barley (Barley FLcDNA (TriFLDB + NIAS)], cDNAs annotated in the draft sequences of T. urartu [T. urartu cDNA (Ensembl Plants)] and of A. tauschii [Ae. tauschii cDNA (Ensembl Plants)], gene models annotated in the barley Morex genome of MIPS [Barley cDNA (MIPS)] and those of Ensembl Plants [Barley cDNA (Ensembl Plants)] and wheat cDNAs from the shotgun genome analysis [Wheat cDNA (UK454)], respectively, mapped to the genic or intergenic regions of the Brachypodium genome, or not mapped, are represented. (C) An example screen shot of a genome browser for mapped cDNAs to the Brachypodium genome aligned with annotated genes of Brachypodium. The mapping results were implemented in the Gbrowse interface of the RBFLDB web site and are available from http://brachy.bmep.riken.jp/ver.1/tools.pl?t=gbrowse&sp=Bdi.