title: Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing.
abstract: 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 marker-trait association studies in other plant species.
authors.affiliation: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN 47907, United States of America.|Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, United States of America.
authors.forename: Prabin
authors.identifier: 0000-0002-3093-5582
authors.initials: P
authors.lastname: Bajgain
authors.affiliation: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN 55108, United States of America.|Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States of America.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Rouse
authors.affiliation: Agricultural Research Council - Small Grain Institute, Bethlehem, 9700, Free State, South Africa.
authors.forename: Toi J
authors.initials: TJ
authors.lastname: Tsilo
authors.affiliation: Kenya Agricultural and Livestock Research Organization (KALRO), Njoro, Kenya.
authors.forename: Godwin K
authors.initials: GK
authors.lastname: Macharia
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, Nairobi, Kenya.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Bhavani
authors.affiliation: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN 55108, United States of America.
authors.forename: Yue
authors.initials: Y
authors.lastname: Jin
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, United States of America.
authors.forename: James A
authors.initials: JA
authors.lastname: Anderson
mesh_terms: D001487:Basidiomycota / Q000502:physiology*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018744:DNA, Plant; D017343:Genes, Plant; D060005:Genotyping Techniques; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D018547:Plant Stems / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics* / Q000382:microbiology*
chemical_list: D018744:DNA, Plant