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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #294157
Title: Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Author
item MASCHER, MARTIN - Leibniz Institute Of Plant Genetics And Crop Plant Research
item MUEHLBAUER, GARY - University Of Minnesota
item ROKHSAR, DANIEL - Department Of Energy Joint Genome
item CHAPMAN, JARROD - Department Of Energy Joint Genome
item SCHMUTZ, JEREMY - University Of Minnesota
item BARRY, KERRIE - Department Of Energy Joint Genome
item MUNOZ-AMATRIAIN, MARIA - University Of Minnesota
item CLOSE, TIMOTHY - University Of California
item Wise, Roger
item SCHULMAN, ALAN - University Of Helsinki
item HIMMELBACH, AXEL - Leibniz Institute Of Plant Genetics And Crop Plant Research
item MAYER, KLAUS - Helmholtz Centre
item SCHOLZ, UWE - Leibniz Institute Of Plant Genetics And Crop Plant Research
item Poland, Jesse
item STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item WAUGH, ROBBIE - The James Hutton Institute

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2013
Publication Date: 9/6/2013
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.