PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets

Kim, Kyu‐Won; Chung, Hun‐Ki; Cho, Gyu-Taek; Ma, Kyung‐Ho; Chandrabalan, Dorothy; Gwag, Jae‐Gyun; Kim, Tae‐San; Cho, Eun-Gi; Park, Yong‐Jin

doi:10.1093/bioinformatics/btm313

Cited by 274 publications

(359 citation statements)

References 24 publications

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“…Genebanks, which served as the major means of genetic resource conservation, encounter problems such as superfluous conservation of crop varieties and the increasing cost of maintenance. Nowadays, core sets represent a more efficient approach to preserving genetic diversity and minimizing sample collection (Brown, 1989;Frankel, 1984;Kim et al, 2007). A core set of Amaranthus has been developed from a total of 634 accessions and its relatives conserved using a heuristic approach (Khaing et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Comparison of Genetic Diversity among Amaranth Accessions from South and Southeast Asia using SSR Markers

Wang¹,

Park²

2013

Korean Journal of Medicinal Crop Science

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: This study was conducted to assess the genetic diversity and population structure of 70 amaranth accessions collected from South and Southeast Asia using 14 simple sequence repeat (SSR) markers. In total, 67 alleles were detected, with an average of 4.79 per locus. Rare alleles comprised a large portion (46.3%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. The mean major allele frequency (MAF), genetic diversity (GD) and polymorphic information content (PIC) of the 14 SSR loci were 0.77, 0.36, and 0.34, respectively. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbor-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. All 70 accessions showed a clear relationship to each cluster without any admixtures. We observed a relatively low extent of genetic exchange within or among amaranth species from South and Southeast Asia. The genetic diversity results could be used to identify amaranth germplasms and so facilitate their use for crop improvement.

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Section: Introductionmentioning

confidence: 99%

Comparison of Genetic Diversity among Amaranth Accessions from South and Southeast Asia using SSR Markers

Wang¹,

Park²

2013

Korean Journal of Medicinal Crop Science

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“…The efficiency evaluation of a sampling strategy involved validating the representativeness of the obtained core collection (Hu et al 2000;Li et al 2004;Wang et al 2007;Oliveira et al 2010). The representativeness of the original genetic diversity in the core collections was validated using the difference of means and a multivariate variation measure of traits in the core subsets and the entire collection (Li et al 2004(Li et al , 2005Franco et al 2005;Kim et al 2007; Figure 1. A schematic of the sampling strategies used for constructing core collections from the Polish orchardgrass germplasm collection Oliveira et al 2010).…”

Section: Methodsmentioning

confidence: 99%

“…A schematic of the sampling strategies used for constructing core collections from the Polish orchardgrass germplasm collection Oliveira et al 2010). The respective differences of the mean and variation measured in the simulated core collections and the entire collection can be described using the following two statistical parameters based on the predicted genotypic values of the quantitative traits in accessions: (a) the difference between the means in a core collection and the entire collection, relative to those in the entire collection across all traits (Kim et al 2007 The use of both statistical parameters (MD% and d -D%) to compare the efficiency of sampling strategies permits the identification of core collections without losing genetic diversity and without too many duplicates. The means of MD% and d -D% parameters were calculated for 10 000 simulated samples using each sampling strategy.…”

Section: Methodsmentioning

confidence: 99%

“…Several sampling strategies have been introduced to form a core collection. These strategies include simple random and stratified random and nonrandom sampling (Brown 1989a, b;Charmet & Balfourier 1995;Grenier et al 2000;Li et al 2002;Upadhyaya et al 2003Upadhyaya et al , 2007Upadhyaya et al , 2009Xu et al 2006) as well as more sophisticated sampling methods (Marita et al 2000;Van Raamsdonk & Wijnker 2000;Chandra et al 2002;Jansen & van Hintum 2007;Kim et al 2007).…”

Section: Comparing the Efficiency Of Sampling Strategies To Establishmentioning

confidence: 99%

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Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

Studnicki¹,

Mądry²,

Schmidt³

2013

CZECH J GENET PLANT

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Studnicki M., Mądry W., Schmidt J. (2013): Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.). Czech J. Genet. Plant Breed., 49: 36-47.Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d -D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d -D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.Keywords: core collection; genetic diversity; germplasm collection; orchardgrass; phenotypic variation; representativeness; sampling strategies Plant germplasm collections facilitate the conservation of the genetic diversity available in the genetic resources of a crop species before that diversity is lost as a result of landrace replacement by high-yielding cultivars under high input cropping and farming systems (Yan et al. 2007).Czech J. Genet. Plant Breed., 49, 2013 (1): 36-47 37 Currently, many germplasm collections are so large as to interfere with achieving the main goals for which the collections have been established, i.e., the collection, maintenance, evaluation and utilis...

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“…The M strategy with random and advanced selection with heuristic search, as proposed by Kim et al (2007), was carried out using the PowerCore v1.0 software. The M strategy with random and heuristic searches selects the most diverse accessions to represent the entire set of alleles from the SNPs in the entire collection.…”

Section: Construction Of the Core Collectionmentioning

confidence: 99%

Development of a cassava core collection based on single nucleotide polymorphism markers

et al. 2014

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ABSTRACT. Single nucleotide polymorphism (SNP) markers were used in the largest cassava (Manihot esculenta Crantz) germplasm collection from Brazil to develop core collections based on the maximization strategy. Subsets with 61, 64, 84, 128, 256, and 384 cassava accessions were selected and named PoHEU, MST64, PoRAN, MST128, MST256, and MST384, respectively. All the 798 alleles identified by 402 SNP markers in the entire collection were captured in all core collections. Only small alterations in the diversity parameters were observed for the different core collections compared with the complete collection. Because of the optimal adjustment of the validation parameters representative of the complete collection, the absence of genotypes with high genetic similarity and the maximization of the genetic distances between accessions of the PoHEU core collection, which contained 4.7% of the accessions of the complete collection, maximized the genetic conservation of this important cassava collection. Furthermore, the development of this core collection will allow concentrated efforts toward future characterization and agronomic evaluation of accessions to maximize the diversity and genetic gains in

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PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets

Abstract: PowerCore software uses the .NET Framework Version 1.1 environment which is freely available for the MS Windows platform. The files can be downloaded from http://genebank.rda.go.kr/powercore/. The distribution of the package includes executable programs, sample data and a user manual.

Cited by 274 publications

References 24 publications

Comparison of Genetic Diversity among Amaranth Accessions from South and Southeast Asia using SSR Markers

Comparison of Genetic Diversity among Amaranth Accessions from South and Southeast Asia using SSR Markers

Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

Development of a cassava core collection based on single nucleotide polymorphism markers

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