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.

Association mapping for kernel phytosterol content in almond

“…Phytosterol content in plants is a complex trait known to be controlled by both major and minor genetic factors (Amar et al, 2008 ). As far as we know, this is the first time that the phytosterol content is genetically studied in almond, and also it represents the second AM analysis in this nut crop (Font i Forcada et al, 2015 ). However, there have so far been few studies on genotypic effects and QTL mapping phytosterols in other species.…”

Using Living Germplasm Collections to Characterize, Improve, and Conserve Woody Perennials

“…Although historical phenotype data are valuable, they may be incomplete or include qualitative, imprecise data that are less useful for GWAS studies. Thus, the continued collection of new and diverse phenotype data is beneficial for GWAS, as indicated by recent studies including work examining a Chinese peach collection , French apricot collection (Mariette et al, 2016), and Spanish almond collection (Forcada et al, 2015), among others.…”

Application of Genomic Technologies to the Breeding of Trees

“…AM has been successfully applied in mapping genes involved in several traits in different plant species (maize, sunflower, lettuce, potato, tomato, wheat, etc. ), but only a few studies have been carried out in fruit tree crops, such as peach (Font i Forcada et al, 2013; Micheletti et al, 2015), apple (Cevik et al, 2010), pear (Oraguzie et al, 2010), almond (Font i Forcada et al, 2015a,b), and apricot (Mariette et al, 2016). In almond, these studies have been able to detect the genomic regions where candidate genes involved in the accumulation of important compounds for fruit quality such as tocopherol and phytosterol are located, using the peach reference genome.…”