title: Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping.
abstract: To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.
authors.affiliation: Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America.
authors.forename: Carolina
authors.initials: C
authors.lastname: Font i Forcada
authors.affiliation: Washington State University, Irrigated Agriculture Research and Extension Center, 24106 N Bunn Road, Prosser, WA 99350, United States of America.
authors.forename: Nnadozie
authors.initials: N
authors.lastname: Oraguzie
authors.affiliation: Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Reyes-Chin-Wo
authors.affiliation: Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Espiau
authors.affiliation: Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Socias i Company
authors.affiliation: Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America; Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain.
authors.forename: Angel
authors.initials: A
authors.lastname: Fernández i Martí
mesh_terms: D056726:Genetic Association Studies / Q000379:methods*; D014644:Genetic Variation; D018745:Genome, Plant; D016014:Linear Models; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010802:Phylogeny; D000068181:Prunus dulcis / Q000235:genetics*; D040641:Quantitative Trait Loci