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Title:   Author  item
                                            BAJGAIN, PRABIN - University Of Minnesotaitem
                                            Rouse, Matthew

                                                         - *Matt*item
                                            TSILO, TOI - University Of The Free Stateitem
                                            MACHARIA, GODWIN - Kenya Agricultural And Livestock Research Organizationitem
                                            BHAVANI, SRIDHAR - International Maize & Wheat Improvement Center (CIMMYT)item
                                            Jin, Yueitem
                                            ANDERSON, JAMES - University Of Minnesota
  Submitted to: PLOS ONE
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 6/1/2015
                                    Publication  Date: 5/17/2016
                                    Citation: Bajgain, P., Rouse, M.N., Tsilo, T.J., Macharia, G.K., Bhavani, S., Jin, Y., Anderson, J. 2016. Nested association mapping of stem rust resistance in wheat using genotyping by sequencing. PLoS One. 11(5):e0155760.Interpretive Summary: Wheat stem rust is a fungal disease of wheat that decreases yield. A strain of the wheat stem rust fungus known as Ug99 emerged in Uganda in 1999 and threatens global wheat production, because it is able to infect nearly all wheat varieties. In order to find identify quantitative trait loci (QTL) associated with resistance to Ug99, ten genetic populations of bread wheat were assessed for field reaction to stem rust in Kenya, South Africa, and Minnesota. The recombinant inbred lines in each population were genotyped by sequencing to identify single nucleotide polymorphsims (SNPs). Since the ten populations shared a common susceptible parent line, the marker-trait associations were analyzed using nested association mapping (NAM). The NAM identified QTL on 11 chromosomes associated with stem rust resistance. This study was important because of the resistance identified and also the demonstrated success of utilizing genotyping by sequencing in combination with NAM for marker-trait association studies. The SNPs found to be associated with stem rust resistance will need to be validated before use in wheat breeding to select for resistance to Ug99. The resistance-liniked markers identified, once validated, can be utlized in wheat breeding for Ug99 resistant wheat varieties. Ug99 resistant wheat cultivars will protect United States wheat production from yield loss if a Ug99 epidemic were to occur in the United States.
                                Technical Abstract: Nested association mapping is an approach to map trait loci in which families within populations are interconnected by a common parent. By implementing joint-linkage association analysis, this approach is able to map causative loci with higher power and resolution compared to biparental linkage mapping. The recently developed genotyping by sequencing (GBS) method is a relatively fast, efficient and cost-effective means of genotyping a large number of individuals. Additionally, the GBS method allows for discovery of de novo markers that are specific to the individuals or populations under study. We combined the nested association mapping approach with GBS 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 at four environments in Kenya, South Africa, and St. Paul, Minnesota, USA. We identified 27 minor effect QTL (explained phenotypic variance range of 0.6% – 5%) on 11 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Validation of markers that are significantly associated with each QTL is necessary to generate diagnostic markers for marker assisted resistance breeding. 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.


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