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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC ENHANCEMENT FOR RESISTANCE TO BIOTIC AND ABIOTIC STRESSES IN HARD WINTER WHEAT

Location: Hard Winter Wheat Genetics Research Unit

Title: Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Authors
item Mascher, Martin -
item Muehlbauer, Gary -
item Rokhsar, Daniel -
item Chapman, Jarrod -
item Schmutz, Jeremy -
item Barry, Kerrie -
item Munoz-Amatriain, Maria -
item Close, Timothy -
item Wise, Roger
item Schulman, Alan -
item Himmelbach, Axel -
item Mayer, Klaus -
item Scholz, Uwe -
item Poland, Jesse
item Stein, Nils -
item Waugh, Robbie -

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 29, 2013
Publication Date: September 6, 2013
Citation: Mascher, M., Muehlbauer, G.J., Rokhsar, D.S., Chapman, J., Schmutz, J., Barry, K., Munoz-Amatriain, M., Close, T.J., Wise, R.P., Schulman, A.H., Himmelbach, A., Mayer, K.F., Scholz, U., Poland, J.A., Stein, N., Waugh, R. 2013. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant Journal. doi: 10.1111/tpj.12319.

Interpretive Summary: Next generation sequencing (NGS) is a powerful approach to understanding plant and animal genomes. Large amounts of sequence data can be easily generated at continually decreasing costs. However, to be fully leveraged for genetic studies and genomic-assisted breeding, this sequence information needs to be put in the ordered context of chromosomes representative of an organism’s genome. This has typically been a long, expensive and arduous process necessitating the development of integrated physical maps along the length of individual chromosomes. In the present study, barley populations consisting of many individuals derived from two parents were used to order sequence information on the chromosomes using genetic linkage information. The resulting order of genomic sequence was as good or better than the current draft reference genome of barley, which was put together through a large international consortium over many years. The demonstrated population sequencing approach (PopSeq) is a rapid and inexpensive method to develop a working ordered assembly for complex genomes.

Technical Abstract: Next-generation, whole genome shotgun (WGS) assemblies of complex genomes are highly enabling, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows the de novo production of a genetically anchored, linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1-Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to different genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources and will enable the rapid and cost efficient establishment of powerful genomic information for many species.

Last Modified: 4/20/2014
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