title: Genome wide association mapping of stripe rust resistance in Afghan wheat landraces.
abstract: Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R2≈0.16 at 0cM) due to germplasm peerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across all environments representing five QTL. The extensively short LD blocks required us to repeat the analysis with less diverse subset of 220 landraces in which R2decayed below 0.2 at 0.3cM. The subset GWAS resulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detected in the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical origin of this germplasm through time have permitted for selecting novel resistance loci.
authors.affiliation: Kihara Institute for Biological Research, Yokohama City University, Yokohama, 2440813, Japan; Present address: Department of Genome Science, School of Biological Science, Central University of Kerala, Kasaragod, 671314, Kerala, India. Electronic address: manicks@yokohama-cu.ac.jp.
authors.forename: Alagu
authors.initials: A
authors.lastname: Manickavelu
authors.affiliation: AgriBio, Centre for Agribioscience, DEDJTR, 5 Ring Road, Bundoora, Vic. 3083, Australia; Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic. 3083, Australia.
authors.forename: Reem
authors.initials: R
authors.lastname: Joukhadar
authors.affiliation: AgriBio, Centre for Agribioscience, DEDJTR, 5 Ring Road, Bundoora, Vic. 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Vic. 3083, Australia; The International Center for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria.
authors.forename: Abdulqader
authors.initials: A
authors.lastname: Jighly
authors.affiliation: CIMMYT, Apdo. Postal 6-641, 06600, Mexico.
authors.forename: Caixia
authors.initials: C
authors.lastname: Lan
authors.affiliation: Campo Experimental Valle de México, INIFAP, Chapingo, Estado de México, Mexico.
authors.forename: Julio
authors.initials: J
authors.lastname: Huerta-Espino
authors.affiliation: Kihara Institute for Biological Research, Yokohama City University, Yokohama, 2440813, Japan; Ministry of Agriculture, Irrigation and Livestock, Afghanistan.
authors.forename: Ahmad Shah
authors.initials: AS
authors.lastname: Stanikzai
authors.affiliation: Diversity Arrays Technology Pvt. Ltd., Australia.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.affiliation: CIMMYT, Apdo. Postal 6-641, 06600, Mexico.
authors.forename: Ravi P
authors.initials: RP
authors.lastname: Singh
authors.affiliation: Kihara Institute for Biological Research, Yokohama City University, Yokohama, 2440813, Japan.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Ban
mesh_terms: D060467:Disease Resistance / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics*; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics* / Q000382:microbiology
keywords: Afghan wheat landraces; GWAS; Genotyping-by-sequencing; Stripe rust