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Molecular marker data and genomic relatedness matrix of 89 lettuce varieties

lettuce_markers.Rd

Molecular marker data and genomic relatedness matrix of 89 lettuce varieties

Usage

lettuce_markers

lettuce_GRM

Format

lettuce_markers

A data frame with 89 rows and 301 columns:

  • gen genotype identifier

  • 300 genetic markers scored as -1, 0, 1 (see Details)

lettuce_GRM

A matrix array with 89 rows and 89 columns where each row/column represents a genotype

Source

https://figshare.com/articles/dataset/Lettuce_trial_phenotypic_and_marker_data_/8299493

Details

The varieties were genotyped with a total of 300 markers (i.e. 95 single nucleotide polymorphisms and 205 amplified fragment length polymorphism markers, see Hayes et al. (2014) for more details of marker matrix. The biallelic marker \(M_iw\) for the ith genotype and the \(w\)th marker with alleles \(A_1\) (i.e. the reference allele) and \(A_2\) was coded as:

  • 1 for \(A_1\) \(A_1\),

  • -1 for \(A_2\) \(A_2\)

  • 0 for \(A_1\) \(A_2\) and \(A_2\) \(A_1\)

References

Hadasch, S., Simko, I., Hayes, R.J., Ogutu, J.O. and Piepho, H.-P. (2016), Comparing the Predictive Abilities of Phenotypic and Marker-Assisted Selection Methods in a Biparental Lettuce Population. The Plant Genome, 9: plantgenome2015.03.0014. doi:10.3835/plantgenome2015.03.0014

Hayes, R. J., Galeano, C. H., Luo, Y., Antonise, R., & Simko, I. (2014). Inheritance of Decay of Fresh-cut Lettuce in a Recombinant Inbred Line Population from ‘Salinas 88’ × ‘La Brillante’. Journal of the American Society for Horticultural Science, 139(4), 388–398. doi:10.21273/JASHS.139.4.388