Construction of Core Collections Suitable for Association Mapping to Optimize Use of Mediterranean Olive (Olea europaea L.) Genetic Resources

Abstract

Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

Selection of Core Collection from <i>Jesso-Balam</i> Rice (<i>Oryza sativa</i> L.) Accessions Using Quantitative, Qualitative and Molecular Characters-A Review

“…It is convenient to study and utilize germplasm resources (Zhang et al, 2010), characterization could be more efficient (El Bakkali et al, 2013) and facilitate the study of its genetic diversity (Mario Paredes et al, 2010).It is considered as a helpful mean to better evaluate and use of plant germplasm and Mini core approach is an effective methodology to enrich and enhance crop improvement programmes (Upadhyaya et al, 2010). Recent studies showed that backcrossing twice using modern varieties as receptor and mini core collection as doner, most of the undesirable traits could be improved remarkably (Yan et al, 2012) which need to be utilized for bringing back the allele diversity into rice fields.…”

Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection

“…Similarly, Belaj et al (2012) found most likely genetic structure as K = 2 and clustered 361 olive genotypes from 19 countries into two gene pools. On the other hand, El Bakkali et al (2013) found K = 3 as the most likely number of gene pools and assigned 502 genotypes to three gene pools according to their geographical origins (Western, central and eastern Mediterranean).…”

“…Although there is no report on the association mapping of agronomic traits in olives, studies on the development of olive core collections suitable for association mapping have been recently reported by several groups (Belaj et al, 2012;El Bakkali et al, 2013). In other horticultural crops, peaches and nectarines, significant associations between agronomic traits and SSR makers were determined in a recent study by Forcada et al (2013).…”

“…Olive has very long juvenile period which restricts breeding programs in olive (El Bakkali et al, 2013). Some cross-breeding efforts in olive during the last decades have been initiated to develop new cultivars and segregating populations for evaluation of the genetic basis of agronomic characters (Fabbri et al, 2009).…”

“…Some cross-breeding efforts in olive during the last decades have been initiated to develop new cultivars and segregating populations for evaluation of the genetic basis of agronomic characters (Fabbri et al, 2009). In addition, some recent studies have reported on the construction of olive core collections and their utilization in association mapping (Belaj et al, 2012;Díez et al, 2012;El Bakkali et al, 2013). It has been demonstrated that it is possible to identify DNA markers linked to traits of interest in fruit crops by association mapping (Forcada et al, 2013).…”