Development of microsatellite markers for the neotropical tree species <i>Dipteryx alata</i> (Fabaceae)

Soares, Thannya Nascimento; Melo, Dayane; Resende, Lucileide Vilela; Vianello, R. P.; Chaves, Lázaro José; Collevatti, Rosane Garcia; Telles, Mariana Pires de Campos

doi:10.3732/ajb.1100377

Cited by 32 publications

(30 citation statements)

References 7 publications

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“…This problem is similar to the one stated in Schlottfeldt-Santos et al (2012), but instead of treating populations as a unit, here we solved the problem at individual level.…”

Section: Experiments 1: Complementing the Ufg-as Germplasm Collectionmentioning

confidence: 99%

“…4). Sample sizes within local populations ranged from 12 to 32 (see Diniz-Filho et al (2012a) and Soares et al (2012) for sampling methodological details).…”

Section: Datamentioning

confidence: 99%

“…The D. alata samples were genotyped for nine microsatellite loci (Bm164, DaE06, DaE12, DaE20, DaE34, DaE41, DaE63, DaE67, DaE46) (Soares et al 2012;DinizFilho et al 2012b) finding a total of 55 distinct alleles. All 55 alleles are represented among the in situ sampled trees.…”

Section: Datamentioning

confidence: 99%

“…In a previous work, our group solved a problem that looked for the smallest set of local populations of D. alata that might be preserved in order to represent the genetic diversity of this species to its in situ conservation (Schlottfeldt-Santos et al 2012;Schlottfeldt et al 2014). That study was pioneer in the use of information about allele frequency, heterozygosity, and Hardy-Weinberg equilibrium as objectives for simultaneous optimization.…”

Section: Introductionmentioning

confidence: 99%

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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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“…This problem is similar to the one stated in Schlottfeldt-Santos et al (2012), but instead of treating populations as a unit, here we solved the problem at individual level.…”

Section: Experiments 1: Complementing the Ufg-as Germplasm Collectionmentioning

confidence: 99%

“…4). Sample sizes within local populations ranged from 12 to 32 (see Diniz-Filho et al (2012a) and Soares et al (2012) for sampling methodological details).…”

Section: Datamentioning

confidence: 99%

Section: Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…We used data from D. alata (a Fabaceae tree species widely distributed and endemic to Brazilian Cerrado) consisting of 55 alleles from 9 microsatellite loci (Table 2) coding for a total of 642 individual trees sampled in 25 local populations distributed throughout species' geographical range ( Figure 1), with sample sizes within the local populations ranging from 12-32 (Tables 3 and 4) Soares et al, 2012).…”

Section: Datamentioning

confidence: 99%

Multi-objective optimization in systematic conservation planning and the representation of genetic variability among populations

Schlottfeldt¹,

Walter²,

Carvalho³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Biodiversity crises have led scientists to develop strategies for achieving conservation goals. The underlying principle of these strategies lies in systematic conservation planning (SCP), in which there are at least 2 conflicting objectives, making it a good candidate for multi-objective optimization. Although SCP is typically applied at the species level (or hierarchically higher), it can be used at lower hierarchical levels, such as using alleles as basic units for analysis, for conservation genetics. Here, we propose a method of SCP using a multiobjective approach. We used non-dominated sorting genetic algorithm II in order to identify the smallest set of local populations of Dipteryx alata (baru) (a Brazilian Cerrado species) for conservation, representing the known genetic diversity and using allele frequency information associated with heterozygosity and Hardy-Weinberg equilibrium. We worked in 3 variations for the problem. First, we reproduced a previous experiment, but using a multi-objective approach. We found that the smallest set of populations needed to represent all alleles under study was 7, corroborating the results of the previous study, but with more distinct solutions. In the 2nd and 3rd variations, we performed simultaneous optimization of 4 and 5 objectives, respectively. We found similar but refined results for 7 populations, and a larger portfolio considering intraspecific diversity and persistence with populations ranging from 8-22. This is the first study to apply multi-objective algorithms to an SCP problem using alleles at the population level as basic units for analysis.

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Patterns of genetic variability in central and peripheral populations of Dipteryx alata (Fabaceae) in the Brazilian Cerrado

Soares

Diniz‐Filho²,

Nabout

et al. 2014

Plant Syst Evol

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Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)

Cited by 32 publications

References 7 publications

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

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

Multi-objective optimization in systematic conservation planning and the representation of genetic variability among populations

Patterns of genetic variability in central and peripheral populations of Dipteryx alata (Fabaceae) in the Brazilian Cerrado

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