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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 Title: Development of high-density genetic maps for barley and wheat using a novel two enzyme genotyping-by-sequencing approach

Authors
item Poland, Jesse
item Brown, Patrick -
item Sorrells, Mark -
item Jannink, Jean-Luc

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 24, 2012
Publication Date: February 28, 2012
Repository URL: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032253#pone-0032253-g005
Citation: Poland, J.A., Brown, P.J., Sorrells, M.E., Jannink, J. 2012. Development of high-density genetic maps for barley and wheat using a novel two enzyme genotyping-by-sequencing approach. PLoS One. 7(2): e32253.

Interpretive Summary: The barley and wheat genomes are large and complex, a feature that has greatly hindered the development of molecular markers useful for marker-assisted selection in plant breeding programs. Further, new statistical approaches such as genomic selection can make predictions of expected performance for yield and other complex traits by using information from dense genome-wide molecular markers. In this study we have utilized next-generation sequencing capacity to generate tens of thousands of molecular markers in barley and wheat in an approach termed “Genotyping-by-sequencing”. These markers were developed at a relatively low per sample cost and represent a considerable advance in the tools available for wheat and barley breeding and genetics. Advancements in sequencing technology will continue to decrease the per sample costs for this approach while providing more and more marker data points, making the genotyping-by-sequencing method the molecular marker platform of choice in the future.

Technical Abstract: Advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. Genotyping-by-sequencing (GBS) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. GBS uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. Here we present a GBS approach for species that currently lack a reference genome sequence. We developed a novel two-enzyme GBS protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified SNPs and tags. We were able to map over 56,000 SNPs and 289,000 tags onto the Oregon Wolfe Barley reference map, and over 35,000 SNPs and 309,000 tags on the Synthetic W9784 x Opata85 (SynOpDH) wheat reference map. To further evaluate GBS in wheat, we also constructed a de novo genetic map using only SNP markers from the GBS data. The GBS approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. Development of the sequenced reference genome(s) will in turn increase the utility of GBS data enabling physical mapping of genes and haplotype imputation of missing data. Finally, the low per-sample costs of GBS have broad application in genomics-assisted plant breeding programs.

Last Modified: 12/27/2014
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