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Triticum monococcum (Einkorn wheat) Transcriptome Assembly and Light Regulated Gene Expression Analyses.

Source: Department of Botany and Plant Pathology News

Common bread wheat with a genome that is ~5 times the size of the human genome is a hexaploid, with three times more number of chromosomes compared to ancestral diploid genomes. This means that the bread wheat combines three different genomes and can make studying the genetic makeup of modern wheat difficult. Therefore, "studying ancestral genomes such as the wheat A, B and D genomes individually provide a baseline reference and new opportunities to investigate the genetic contribution of each of these genomes that lead to the development of bread wheat”. “It also gives us an opportunity to identify novel and beneficial stress tolerant genes in the wild ancestral genomes, that can be introduced into common bread wheat for improving varieties” added Jaiswal.

"Einkorn wheat Triticum monococcum is one of the earliest domesticated crops. However, it was abandoned for cultivation before the Bronze Age and has infrequently been used in wheat breeding. Little is known about the genetic variation in adaptively important biological traits in T. monococcum" (Source:Jing et al 2007[1]). The wild and cultivated germplasms are classified as separate subspecies of T. monococcum. The Einkorn wheat is a diploid (one-third the size of bread wheat) and is a close relative of T. urartu, the A-genome donor to the hexaploid bread wheat that is made up of A, B and D genomes.

By using a domesticated and wild variety, researchers can pinpoint the gain and loss of genetic diversity based on both human selection for cultivation and adaptation in wild natural populations of ancestral wheat. The study found that compared to the domesticated spring wheat DV92, the wild winter relative G3116 preserves a higher number of genes and genetic variation that may have contributed to adaptation and building resistance to stresses like temperature, water deficit, photoperiod, salinity and diseases in wild populations. SNP diresity in DV92 and G3116 T. monococcum (Source: PLoS ONE)These datasets may prove handy for researchers studying the ecology, adaptation, evolution and genetic variation in wheat and related species.

The assembled and annotated transcriptome from the two sub-species reported in the publication also provide experimental evidences/proofs that are often sought by the genome annotation projects (in this case a wheat and barley genome) for improving the gene annotations derived by their computational methods. The transcriptome also contributes to the study of the genetic components regulating photomorphogenesis in wheat and related species.

The authors published the study "De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum" in the May issue of PLoS ONE.

Data sets generated from the project and those reported in the publication are available under Creative Commons CC0 1.0 open access license from the ScholarsArchive at OSU (URI: http://hdl.handle.net/1957/47475).

Additional OSU authors include Samuel Fox, Mamatha Hanumappa, Sushma Naithani, Justin Preece, Justin Elser and Abigail Sage with the OSU Department of Botany and Plant Pathology; Matthew Geniza (co-first author with Sam Fox on the publication) of the OSU Molecular and Cellular Biology (MCB) Graduate Program; Chris Sullivan of the OSU Center for Genome Research and Biocomputing (CGRB); and Vijay K. Tiwari and Jeffrey M. Leonard of OSU Department of Crop and Soil Science (CSS).

Funding for the work was provided by OSU with in-kind support from the collaborators on the research team, which include colleagues Cathy Gresham (Mississippi State University), Fiona McCarthy (University of Arizona), Gerard Lazo (USDA-ARS) and Arnaud Kerhornou, Dan Bolser and Paul Kersey (European Bioinformatics Institute in UK).

Publication citation:

Fox, SE, Geniza M, Hanumappa M, Naithani S, Sullivan CM, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P; (2014) De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS ONE 9(5): e96855. doi:10.1371/journal.pone.0096855

Links and References:

Publication: http://dx.plos.org/10.1371/journal.pone.0096855

Data acces: ScholarsArchive at OSU (URI: http://hdl.handle.net/1957/47475).

Jaiswal lab’s wheat project: http://jaiswallab.cgrb.oregonstate.edu/genomics/wheat

[1] Jing H-C, Kornyukhin D, Kanyuka K, Orford S, Zlatska A, et al. (2007) Identification of variation in adaptively important traits and genome-wide analysis of trait–marker associations in Triticum monococcum. J Exp Bot 58: 3749–3764 doi:10.1093/jxb/erm225.