Construction and evaluation of a primary core collection of apricot germplasm in China

Wang, Yuzhu; Zhang, Junhuan; Sun, Hui; Ning, Ning; Li, Yang

doi:10.1016/j.scienta.2011.01.025

Cited by 40 publications

(32 citation statements)

References 25 publications

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“…The expected heterozygosity (0.713) revealed by the SSR markers was also higher than the apricot accessions ( P. armeniaca ) in the Maghreb region (0.593), but similar to the core collection apricot germplasm in China (0.731) [27,28]. As the same wild apricot resource, Siberia apricot has a slightly weaker genetic diversity index than wild apricot in the Ili Valley ( PPB = 91.3% vs. 94.84%) but a larger population size and distribution area.…”

Section: Resultsmentioning

confidence: 81%

Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China

Zhong

Miao

et al. 2013

IJMS

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The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program) analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG) 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY.

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Section: Resultsmentioning

confidence: 81%

Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China

Zhong

Miao

et al. 2013

IJMS

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“…Arabidopsis thaliania [29], Oryza sativa [30], Triticum aestivum [31] and Zea mays [32], and perennial species, e.g. Annona cherimola [33], Malus domestica [34], Prunus armeniaca [35] and Vitis vinifera [36], using different eco-geographical, agro-morphological, biochemical or molecular data. Despite the many approaches used to design core collections that optimize the genetic distance between accessions and/or the allelic diversity [37]–[44], most of core collections have been constructed based on the so-called maximizing method (M-method) [37] through the M strat program [40] by optimizing the number of alleles/trait classes for germplasm conservation purposes, whereas core sizes depend on the number of accessions and the diversity available in the base collections.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2013

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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.

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“…In this conservation context, the use of molecular markers to achieve the representativeness definition of a core collection is important because population persistence and resilience to environmental changes are usually positively correlated with genetic diversity. Methodologically, efforts to create germplasm core collections commonly use statistical and clustering methods (Holbrook et al 1993;Li et al 2004;Laghetti et al 2008;Wang et al 2011;Zhang et al 2011;Belaj et al 2012;Mei et al 2012;Rao et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability

Schlottfeldt

Walter

Carvalho

et al. 2015

Tree Genetics & Genomes

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Germplasm collections play a significant role among strategies for conservation of diversity. It is common to select a core collection to represent the genetic diversity of a germplasm collection, in order to minimize the cost of conservation, while ensuring the maximization of genetic variation. We aimed to solve two main problems: (1) to select a set of individuals, from an in situ data set, that is genetically complementary to an existing germplasm collection, and (2) to define a core collection for a germplasm collection. We proposed a new multi-objective optimization (MOO) approach based on principles of systematic conservation planning (SCP) incorporating heterozygosity information; therefore, optimization takes genotypic diversity and variability patterns into account as well. As a case study, we used Dipteryx alata microsatellite loci information from two sources, an ex situ germplasm collection located at the Agronomy School of the Federal University of Goiás (UFG-AS), and an in situ data set composed of 642 sampled individual trees. We were able to identify within a population of several individuals, the exact accessions/samples that should be chosen in order to preserve the species diversity. We found that material from nine in situ individual trees are enough to complement the UFG-AS germplasm collection as it is, and that it is possible to define a core collection of 20 individual trees representing all studied genetic diversity. Moreover, we defined a method (a protocol) to deal with large amounts of accessions in the context of MOO. The proposed approach can be used to help constructing collections with maximal allelic richness and can also be extended to the in situ conservation. As far as we know, this is the first time that principles of SCP and the MOO approach are applied to the problem of complementing a germplasm collection and of finding a core collection for a germplasm collection.

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Construction and evaluation of a primary core collection of apricot germplasm in China

Cited by 40 publications

References 25 publications

Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China

Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China

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

Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability

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