Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures

Thachuk, Chris; Crossa, J.; Franco, Jorge; Dreisigacker, Susanne; Warburton, Marilyn L.; Davenport, Guy

doi:10.1186/1471-2105-10-243

Cited by 143 publications

(146 citation statements)

References 30 publications

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“…Because different strategies result in different core collections (Thachuk et al 2009, Wang et al 2007), we used four different methods. As the M strategy is based on maximizing the number of alleles, it can automatically generate a sampling ratio on the basis of the genetic diversity of the species; this strategy has been widely used in recent years (Belaj et al 2012, Liu et al 2015, Zhang et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction

et al. 2017

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Diversity analysis of rapeseed accessions preserved in the Japanese Genebank can provide valuable information for breeding programs. In this study, 582 accessions were genotyped with 30 SSR markers covering all 19 rapeseed chromosomes. These markers amplified 311 alleles (10.37 alleles per marker; range, 3–39). The genetic diversity of Japanese accessions was lower than that of overseas accessions. Analysis of molecular variance indicated significant genetic differentiation between Japanese and overseas accessions. Small but significant differences were found among geographical groups in Japan, and genetic differentiation tended to increase with geographical distance. STRUCTURE analysis indicated the presence of two main genetic clusters in the NARO rapeseed collection. With the membership probabilities threshold, 227 accessions mostly originating from overseas were assigned to one subgroup, and 276 accessions mostly originating from Japan were assigned to the other subgroup. The remaining 79 accessions are assigned to admixed group. The core collection constructed comprises 96 accessions of diverse origin. It represents the whole collection well and thus it may be useful for rapeseed genetic research and breeding programs. The core collection improves the efficiency of management, evaluation, and utilization of genetic resources.

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Section: Discussionmentioning

confidence: 99%

Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction

et al. 2017

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“…As a result, the genebank users obtain a focused selection of the germplasm with more useful diversity of the trait of interest than core collections. Likewise, algorithms such as Core Hunter assist defining core subsets based on user preference but having enough genetic diversity and appropriate average genetic distance among accessions (Thachuk et al 2009). Core Hunter can also find small core subsets that still keep all unique alleles found in the reference germplasm collection.…”

Section: Genebank Sampling and Core Subsetsmentioning

confidence: 99%

Plant Genetic Resources for Food and Agriculture

Ríos

2015

Plant Breeding in the Omics Era

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“…M-Strat (Gouesnard et al 2001), Genetic distance sampling (Jansen and Van Hintum 2007), Power Core (Kim et al 2007) and Core Hunter (Thachuk et al 2009). Similarly core has been developed using several kinds of data ranging from genealogical data in the Czech spring wheat (Stehno et al 2006), agronomic data in groundnut (Upadhyaya 2003;Upadhyaya et al 2003) and molecular data or integration of data in bread wheat (Balfourier et al 2007) and in rice (Borba et al 2009;Yan et al 2007).…”

Section: Core Set Developmentmentioning

confidence: 99%

Development of Core Set of Wheat (Triticum spp.) Germplasm Conserved in the National Genebank in India

Dutta

Phogat

Kumar

et al. 2015

Advances in Wheat Genetics: From Genome to Field

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Plant genetic resources, the source of genetic diversity provides a broad genetic foundation for plant breeding and genetic research, however, large germplasm resources are difficult to preserve, evaluate and use. Construction of core and mini core collections is an efficient method for managing genetic resources and undertaking intensive surveys of natural variation, including the phenotyping of complex traits and genotyping of DNA polymorphisms allowing more efficient utilization of genetic resources. A mega characterization and evaluation programme of the entire cultivated gene pool of wheat conserved in the National Genebank, India was undertaken. Wheat accessions with limited seed quantity, were multiplied in the off-season nursery at IARI Regional Station, Wellington during rainy season 2011 and the entire set of 22,469 wheat accessions were characterized and evaluated at CCS HAU, Hisar, Haryana during winter season 2011-12 for 34 characters including 22 highly heritable qualitative, and 12 quantitative parameters. The core sets were developed using PowerCore Software with stepwise approach and grouping method and validated using Shannon-Diversity Index and summary statistics. Based on Shannon-Diversity index, PowerCore with stepwise approach was found better than PowerCore with grouping. The core set included 2,208 accessions comprising 1,770 T. aestivum, 386 T. durum, and 52 T. dicoccum accessions as a representative of the total diversity recorded in the wheat germplasm. The core set developed will be further validated at different agro-climatic conditions and will be utilized for development of mini core set to enhance the utilization by wheat researchers and development of climate resilient improved varieties.

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Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures

Cited by 143 publications

References 30 publications

Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction

Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction

Plant Genetic Resources for Food and Agriculture

Development of Core Set of Wheat (Triticum spp.) Germplasm Conserved in the National Genebank in India

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