Nested association mapping of stem rust resistance in wheat using genotyping by sequencing

Prabin Bajgain, Matthew N. Rouse, Toi J. Tsilo, Godwin K. Macharia, Sridhar Bhavani, Yue Jin, James A. Anderson

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87 Scopus citations


We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1%- 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar markertrait association studies in other plant species.This is an open access article, free of all copiright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Original languageEnglish (US)
Article numbere0155760
JournalPloS one
Issue number5
StatePublished - May 2016

Bibliographical note

Funding Information:
We thank University of Minnesota Genomics Center, Minnesota Supercomputing Institute, the Microbial & Plant Genomics Institute, Kenya Agricultural and Livestock Research Organization, Ethiopia Institute of Agricultural Research, Agricultural Research Council of South Africa, USDA-ARS Cereal Disease Laboratory personnel, and Anderson Wheat Lab for their help and support during various phases of the project. Funding for this work was provided by the United States Department of Agriculture, Agriculture and Food Research Initiative and 2011-68002-30029 (Triticeae Coordinated Agricultural Project), and the Borlaug Global Rust Initiative Durable Rust Resistance in Wheat Project (administered by Cornell University with a grant from the Bill & Melinda Gates Foundation), and the UK Department for International Development.


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