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Maximization of minority classes in core collections designed for association studies

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Abstract

Core collections are nowadays widely employed in diverse studies on plant genetics. The more extensively used method to build core collections (maximization strategy) is based on the selection, from a global collection, of those accessions which maximize the number of different alleles and phenotypic classes (classes’ richness). However, different core collections should be created for different types of studies, and though several years ago most of core collections were developed to make the characterization and use of germplasm collections easier with a smaller sample size, for either conservation or breeding purposes, today, they are widely employed for association studies that are broadly applied in plant genetic improvement. Following the M strategy, some alleles or phenotypic classes often appear in a very low frequency, which may reduce the power of the analysis, avoiding the detection of real associations (false negatives). In this work, we propose and evaluate a new way to build core collections using the maximization strategy in several sequential steps, to maximize the frequency of minority classes, thus increasing the statistical power of the association study.

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Acknowledgments

This study was made possible with the funding from the GrapeGen project (joint venture between Genome Canada and Genoma España) and the AGL2010-15694 (MINECO) and AGL2014-59171-R (MINECO, FEDER). A.M. Vargas was funded by a predoctoral fellowship from Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario. Thanks to Rafael Torres-Pérez for helping with the structure analysis and to Joaquín Borrego, Carmen Fajardo, Carlos González Guillén, Mª Dolores Vélez, Silvia Hernáiz, Paz Fernández, Nuria Rodríguez Jiménez, and Concepción López Rivas for their technical assistance in the grapevine morphological descriptions.

Data archiving statement

The phenotypic dataset for 1000 rice accessions was downloaded from http://www.genebank.go.kr/eng/PowerCore/ (Kim et al. 2007), and it is included in the supplementary material. The grapevine dataset is also included in the supplementary material, with a list of the accessions used. Additional information about the accessions of IMIDRA grapevine collection (ESP080) can be found in the website http://www.madrid.org/coleccionvidencin/.

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Authors and Affiliations

  1. Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA). Finca “El Encín”, Ctra. A2, Km 38.200, Alcalá de Henares, Madrid, 28800, Spain

    Alba María Vargas & María Teresa de Andrés

  2. Instituto de Ciencias de la Vid y del Vino—ICVV, CSIC, Universidad de La Rioja, Gobierno de La Rioja, Carretera de Burgos Km. 6, Finca La Grajera, Logroño, 26071, Spain

    Javier Ibáñez

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  1. Alba María Vargas
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  2. María Teresa de Andrés
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  3. Javier Ibáñez
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Corresponding author

Correspondence to Javier Ibáñez.

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The authors declare that they have no conflict of interests.

Research involving human participants and/or animals

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Communicated by D. Grattapaglia

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

Global data and core collections obtained for rice (Kim et al. 2007). (XLSX 624 kb)

Online Resource 2

Global data and core collections obtained for grapevine (XLSX 364 kb)

Online Resource 3

Simulation of SNP bi-allelic data correlated with class 9 of the trait “Time of Budburst”. (XLSX 28 kb)

Online Resource 4

Frequency thresholds used for the selection of accessions for the kernel file in the Method 3. (XLSX 10 kb)

Online Resource 5

Population stratification in the different collections using the software Structure and the Evanno correction (ΔK). a) ΔK for each collection; b) Structure plot of estimates of membership coefficient (Q) for the run with the highest LnP(D) in each collection. Each accession is represented by a single vertical line, which represents Q coefficients, proportionally in different colors for the different populations. (PPTX 162 kb)

Online Resource 6

Population assignment of each accession in the different core collections considering a membership coefficient threshold of 0.8. (XLSX 22 kb)

Online Resource 7

Distribution of accessions belonging to each population in the different collections. (XLSX 9 kb)

Online Resource 8

Simulated genotypic data for association analysis with “Time of Budburst”. (XLSX 26 kb)

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Vargas, A.M., de Andrés, M.T. & Ibáñez, J. Maximization of minority classes in core collections designed for association studies. Tree Genetics & Genomes 12, 28 (2016). https://doi.org/10.1007/s11295-016-0988-9

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