|RIFE, TREVOR - Kansas State University
Submitted to: The Plant Genome
Publication Type: Review Article
Publication Acceptance Date: 8/31/2012
Publication Date: 11/1/2012
Citation: Poland, J.A., Rife, T. 2012. Genotyping-by-sequencing for plant breeding and genetics. The Plant Genome. 5(3):92-102.
Interpretive Summary: New DNA sequencing technologies are providing tools to understand not only the human genome but also the genomes of important crop plants. Here we describe how “next-generation sequencing” can be used for plant breeding and genetics research for inexpensive and rapid characterization of various populations of interest. This approach termed “genotyping-by-sequencing” takes advantage of next-generation sequencing capacity and can produce tens to hundreds of thousands of low-cost molecular markers. High-density markers can then be used to connect observed phenotypes (i.e. grain yield) with underlying genetic determinants. Better understanding of the genomes of crop species will lead to improved methods for prediction of important agronomic traits, increasing the rate of gain in breeding programs.
Technical Abstract: Rapid advances in post-Sanger sequencing technology have brought the $1000 human genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotyping-by-sequencing (GBS) has been developed as rapid and robust approach for reduced representation sequencing of multiplexed samples that combines marker discovery and genotyping. The flexibility and low-cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. Here we address some of the new research opportunities that are becoming more feasible with GBS. Further, we highlight areas where GBS will become more powerful with the continued increase of sequencing output, development of reference genomes, and improved bioinformatics. The ultimate goal of plant biology scientists is to understand the connection between the material of inheritance (DNA) and the observable characteristics (phenotype) and make informed predictions of the expected phenotype resulting from a given DNA compliment. Furthering our understanding of the connection between heritable genetic factors and the resulting phenotypes will enable genomics-assisted breeding to exist on the scale needed to increase global food supplies in the face of decreasing arable land and climate change.