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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 #318917
Title: Application of population sequencing (POPSEQ) for ordering and inputting genotyping-by-sequencing markers in hexaploid wheat

Author
item Edae, Erena
item Bowden, Robert
item POLAND, JESSE - Kansas State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2015
Publication Date: 10/29/2015
Publication URL: http://handle.nal.usda.gov/10113/5491328
Citation: Edae, E.A., Bowden, R.L., Poland, J.A. 2015. Application of population sequencing (POPSEQ) for ordering and inputting genotyping-by-sequencing markers in hexaploid wheat. G3, Genes/Genomes/Genetics. 5(12):2547- 2553. doi:10.1534/g3.115.020362.

Interpretive Summary: Genotyping-by-sequencing (GBS) is a method that provides a large number of genetic markers at a very low cost per marker in wheat. One challenge for application of GBS markers to plant gene mapping and breeding is to correctly order the markers along each chromosome. POPSEQ is a new method to genetically anchor and order plant genome assemblies based on low-coverage sequencing of the DNA of progeny from a cross between two parents. We tested the utility of POPSEQ by comparing it to conventional linkage mapping of a new recombinant population derived from a cross of a synthetic wheat line called W7984 and a bread wheat line called Opata M85. The results showed strong agreement between the independent new linkage map and the POPSEQ mapping approach. A second challenge for application of GBS data is the large number of missing data points for many markers. Following ordering by POPSEQ, we were able to impute missing data points very accurately. The POPSEQ-based ordering method enables the application of GBS markers to gene mapping and breeding in wheat without the need for creating new linkage maps for each study.

Technical Abstract: The advancement of next-generation sequencing technologies in conjunction with new bioinformatics tools enabled fine-tuning of sequence-based high resolution mapping strategies for complex genomes. Although genotyping-by-sequencing (GBS) provides a large number of markers, its application for association mapping and genomics-assisted breeding is limited by a large proportion of missing data per marker. For species with a reference genomic sequence, markers can be ordered on the physical map. However, in the absence of reference marker order, the use and imputation of GBS markers is challenging. Here, we demonstrate how the population sequencing (POPSEQ) approach can be used to provide marker context for GBS in wheat. The utility of a POPSEQ-based genetic map as a reference map to create genetically ordered markers on a chromosome for hexaploid wheat was validated by constructing an independent de novo linkage map of GBS markers from a Synthetic W7984 x Opata M85 recombinant inbred line (SynOpRIL) population. The results indicated that there is strong agreement between the independent de novo linkage map and the POPSEQ mapping approach in mapping and ordering GBS markers for hexaploid wheat. Following ordering, a large number of GBS markers were imputed, thus providing a high-quality reference map that can be used for QTL mapping for different traits. The POPSEQ-based reference map and whole genome sequence assemblies are valuable resources that can be used to order GBS markers and enable the application of highly accurate imputation methods to leverage the application GBS markers in wheat.